Contacts of the helix formed by residues 414 - 446 (chain B) in PDB entry 4XK8
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 414 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A TRP* 6.1 3.1 - - + -
410B ARG* 2.9 27.9 + - + -
411B MET* 3.7 24.6 + - - +
413B GLU* 1.3 77.4 - - + +
415B LYS* 1.3 63.2 + - - +
416B GLU* 3.2 4.7 - - - -
417B ALA* 3.1 27.2 + - + +
418B ILE* 3.3 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A SER* 6.1 0.2 - - - -
411B MET 3.6 9.5 + - - +
412B LEU* 3.5 30.3 + - + +
413B GLU 3.3 1.4 + - - +
414B HIS* 1.3 76.1 - - - +
416B GLU* 1.3 82.1 + - + +
418B ILE* 3.2 9.8 + - + +
419B ILE* 2.9 48.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A GLU* 5.0 1.8 - - + +
706A SER* 3.9 24.0 - - - +
709A TRP* 3.5 50.0 + - + -
413B GLU 3.6 13.9 - - - +
414B HIS* 4.2 1.2 - - - -
415B LYS* 1.3 99.7 + - + +
417B ALA* 1.3 50.5 + - - +
420B SER* 2.6 40.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A TRP* 3.6 26.2 - - + -
414B HIS* 3.1 28.3 + - + +
416B GLU* 1.3 77.7 - - - +
418B ILE* 1.3 66.3 + - - +
420B SER* 3.0 5.7 + - - -
421B HIS* 2.8 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B MET* 3.7 46.0 - - + +
414B HIS* 3.4 33.2 - - + +
415B LYS* 3.2 8.5 + - + +
417B ALA* 1.3 77.5 - - - +
419B ILE* 1.3 61.1 + - + +
421B HIS* 3.8 3.0 - - - +
422B LEU* 3.0 45.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703A LEU* 3.8 24.6 - - + +
706A SER* 3.5 29.4 - - - +
415B LYS* 2.9 36.6 + - + +
418B ILE* 1.3 79.1 - - + +
420B SER* 1.3 57.2 + - - +
422B LEU* 3.4 11.1 + - + +
423B SER* 2.9 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A SER* 3.9 13.9 - - - -
707A ILE* 4.5 5.6 - - - -
709A TRP* 4.1 1.7 - - - -
710A ALA* 3.8 29.6 - - - +
416B GLU 2.6 23.2 + - - -
417B ALA* 3.0 16.5 + - - -
419B ILE* 1.3 77.7 - - - +
421B HIS* 1.3 62.1 + - - +
423B SER* 3.3 9.5 - - - -
424B TRP* 2.9 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A TRP* 5.3 5.6 - + - -
710A ALA* 6.1 1.8 - - + -
417B ALA* 2.8 37.7 + - + +
418B ILE* 3.9 3.6 - - - +
420B SER* 1.3 83.6 + - - +
422B LEU* 1.3 64.6 + - - +
424B TRP* 3.2 18.7 + + + +
425B ALA* 2.9 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B ILE* 3.0 34.3 + - + +
419B ILE* 3.6 9.9 - - + +
421B HIS* 1.3 74.1 - - - +
423B SER* 1.3 56.5 + - - +
425B ALA* 3.3 8.4 + - + +
426B SER* 3.0 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703A LEU* 4.6 17.5 - - - +
707A ILE* 3.8 22.9 - - - +
419B ILE 2.9 15.2 + - - -
420B SER* 3.3 14.1 - - - -
422B LEU* 1.3 77.5 - - - +
424B TRP* 1.3 57.0 + - - +
426B SER* 3.9 5.0 - - - -
427B LEU* 2.9 42.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 424 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B SER 2.9 14.4 + - - +
421B HIS* 3.2 21.9 + + + +
423B SER* 1.3 73.9 - - - +
425B ALA* 1.3 87.7 + - + +
427B LEU* 3.3 10.0 + - + +
428B PHE* 2.9 58.3 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 425 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B HIS 2.9 13.6 + - - +
422B LEU* 3.6 13.5 - - + +
424B TRP* 1.3 95.4 - - + +
426B SER* 1.3 63.5 + - - +
428B PHE* 3.3 2.1 + - - +
429B LEU* 3.0 37.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 426 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B LEU* 3.0 21.3 + - - +
423B SER* 3.9 5.3 - - - -
425B ALA* 1.3 75.6 - - - +
427B LEU* 1.3 59.7 + - - +
429B LEU* 3.4 7.8 + - - +
430B GLY* 2.9 28.1 + - - -
525B LEU* 4.8 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707A ILE* 6.2 2.0 - - + -
423B SER* 2.9 30.1 + - - +
424B TRP* 3.5 8.5 - - + +
426B SER* 1.3 78.1 - - - +
428B PHE* 1.3 56.8 + - - +
430B GLY* 3.8 0.6 - - - -
431B PHE* 2.9 64.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B TRP* 2.9 49.6 + + + +
425B ALA* 3.6 4.3 - - - +
427B LEU* 1.3 74.4 - - - +
429B LEU* 1.3 81.1 + - + +
431B PHE* 4.7 3.1 - - - -
432B HIS* 2.9 73.0 + + + +
521B HIS* 6.4 0.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B ALA* 3.0 28.9 + - + +
426B SER* 3.9 4.3 - - - +
428B PHE* 1.3 91.2 - - + +
430B GLY* 1.3 57.5 + - - +
432B HIS* 5.2 1.1 - - - -
433B THR* 2.8 37.5 + - - +
521B HIS* 4.2 28.0 - - + +
524B ALA* 3.7 41.1 - - + +
525B LEU* 3.7 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B SER 2.9 16.6 + - - -
427B LEU* 3.8 0.7 - - - -
429B LEU* 1.3 73.6 - - - +
431B PHE* 1.3 65.5 + - - +
433B THR* 5.0 0.9 - - - -
434B LEU* 3.0 32.6 + - - +
525B LEU* 4.5 14.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B LEU* 2.9 52.5 + - + +
428B PHE* 3.7 4.7 - - - +
430B GLY* 1.3 73.7 - - - +
432B HIS* 1.3 71.0 + + + +
434B LEU* 4.3 3.2 - - + +
435B GLY* 2.9 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B PHE* 2.9 71.9 + + + +
429B LEU* 4.5 1.1 - - - +
431B PHE* 1.3 87.6 - + + +
433B THR* 1.3 61.1 + - - +
435B GLY* 4.7 0.9 - - - -
436B LEU* 2.9 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B LEU* 2.8 24.9 + - - +
430B GLY* 4.3 1.3 - - - -
432B HIS* 1.3 73.6 - - - +
434B LEU* 1.3 67.1 + - - +
436B LEU* 3.3 5.7 + - - +
437B TYR* 3.0 54.5 + - + -
518B LEU* 3.9 17.7 - - + +
521B HIS* 3.6 24.4 + - + +
522B ALA* 4.0 15.3 - - + +
525B LEU* 5.7 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A PHE* 3.6 44.2 - - + -
430B GLY 3.0 19.1 + - - +
431B PHE* 4.3 2.2 - - + +
433B THR* 1.3 77.8 - - - +
435B GLY* 1.3 57.8 + - - +
437B TYR* 3.7 7.4 - - + +
438B VAL* 2.9 54.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B PHE 2.9 21.9 + - - -
432B HIS* 3.9 1.6 - - - -
434B LEU* 1.3 78.1 - - - +
436B LEU* 1.3 60.2 + - - +
438B VAL* 3.5 4.2 + - - +
439B HIS* 2.9 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B HIS* 2.9 34.0 + - + +
433B THR* 3.9 3.8 - - - +
435B GLY* 1.3 75.0 - - - +
437B TYR* 1.3 66.5 + - - +
439B HIS* 3.3 6.7 - - + +
440B ASN* 3.0 31.1 + - - +
453B ILE* 3.7 40.6 - - + +
455B ILE* 4.1 19.1 - - + -
517B PHE* 4.8 4.0 - - + -
518B LEU* 4.1 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B THR* 3.0 48.3 + - + +
434B LEU* 3.7 9.4 - - + +
436B LEU* 1.3 76.5 - - - +
438B VAL* 1.3 58.5 + - + +
440B ASN* 3.2 8.9 + - + +
441B ASP* 2.9 40.1 + - - +
515B GLY 4.5 1.2 + - - -
518B LEU* 3.3 33.3 - - + +
519B VAL* 3.3 31.0 + - - +
522B ALA* 4.9 5.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B LEU* 2.9 41.7 + - + +
435B GLY* 4.0 4.5 - - - +
437B TYR* 1.3 72.4 - - + +
439B HIS* 1.3 66.3 + - - +
441B ASP* 3.3 7.8 + - + +
442B VAL* 2.9 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B GLY 2.9 18.5 + - - +
436B LEU* 3.3 9.2 - - + +
438B VAL* 1.3 76.8 - - - +
440B ASN* 1.3 79.3 + - - +
442B VAL* 3.0 9.3 + - - +
443B MET* 2.9 46.7 + - + +
451B LYS 3.2 22.4 + - - -
453B ILE* 3.5 18.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B LEU 3.0 20.1 + - - +
437B TYR* 3.6 6.8 - - + +
439B HIS* 1.3 83.5 - - - +
441B ASP* 1.3 57.2 + - - +
443B MET* 3.2 2.4 + - - +
444B LEU* 2.9 34.9 + - - +
452B GLN* 3.4 25.5 + - - +
453B ILE* 2.9 43.8 + - - +
454B LEU* 3.8 11.5 - - - +
518B LEU* 4.0 19.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A TYR* 2.7 40.1 + - - +
677A LEU* 4.2 5.8 - - + -
680A LEU* 3.6 19.2 - - + +
437B TYR* 2.9 29.1 + - - +
438B VAL* 3.6 12.0 - - + +
439B HIS 3.2 0.2 - - - -
440B ASN* 1.3 76.5 - - - +
442B VAL* 1.3 58.1 + - - +
444B LEU* 3.3 2.4 + - - -
445B ALA* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A LEU* 4.2 22.9 - - + -
438B VAL* 2.9 30.4 + - + +
439B HIS* 3.4 8.5 - - - +
441B ASP* 1.3 75.5 - - - +
443B MET* 1.3 73.6 + - + +
445B ALA* 3.2 2.7 + - - +
446B PHE* 3.0 54.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A VAL* 5.0 9.6 - - + +
439B HIS* 2.9 49.1 + - + +
440B ASN 3.2 7.8 + - - +
442B VAL* 1.3 97.7 - - + +
444B LEU* 1.3 59.8 + - - +
446B PHE* 3.5 1.7 + - + -
447B GLY 3.3 2.9 + - - -
448B THR* 2.8 45.7 + - - +
451B LYS* 3.5 51.6 - - - +
452B GLN* 4.0 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A TYR* 3.5 27.2 - - + +
669A GLY* 3.5 10.2 + - - -
440B ASN 2.9 21.0 + - - +
441B ASP* 3.3 3.3 + - - +
443B MET* 1.3 76.3 - - - +
445B ALA* 1.3 63.4 + - - +
447B GLY* 3.3 11.1 + - - -
448B THR 4.9 0.9 - - - +
449B PRO* 3.9 21.3 - - + -
452B GLN* 3.4 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ILE* 3.8 2.4 - - - +
668A TYR* 3.7 17.5 - - + -
669A GLY* 2.9 21.5 + - - -
673A SER* 3.3 26.2 + - - +
677A LEU* 3.8 28.5 - - + -
441B ASP 2.9 16.8 + - - +
442B VAL 3.2 6.0 + - - +
444B LEU* 1.3 78.3 - - - +
446B PHE* 1.3 60.0 + - + +
447B GLY 3.1 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A VAL* 3.2 31.9 - - + -
128A GLY* 3.6 17.7 - - - +
129A GLN* 3.7 28.0 - - + -
131A ILE* 3.6 34.1 - - + +
132A LEU* 4.3 17.0 - - + -
673A SER* 4.3 5.6 - - - -
677A LEU* 4.5 17.3 - - + -
442B VAL* 3.0 38.1 + - + +
443B MET* 3.5 5.1 + - + +
445B ALA* 1.3 79.0 - - + +
447B GLY* 1.3 61.5 + - - +
448B THR* 3.3 16.3 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il