Contacts of the helix formed by residues 419 - 438 (chain B) in PDB entry 4EMX
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 SER 419 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B GLN 3.3 3.5 + - - -
418B VAL* 1.3 80.4 - - - +
420B THR* 1.3 63.1 + - - +
421B PRO* 3.9 11.4 - - - +
422B THR* 2.8 29.8 + - - -
423B LEU* 3.1 17.7 + - - +
469B VAL* 4.7 4.9 - - - +
534B LYS* 4.0 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B SER* 1.3 68.7 - - - +
421B PRO* 1.3 78.0 - - + +
423B LEU* 3.0 2.9 + - - +
424B VAL* 2.9 28.3 + - + +
527B THR* 3.9 26.9 - - + +
530B VAL* 3.5 29.0 - - + +
531B GLU* 2.5 30.5 + - - +
534B LYS* 2.7 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B SER* 3.7 11.4 - - - +
420B THR* 1.3 98.3 - - + +
422B THR* 1.3 60.4 + - - +
424B VAL* 3.4 6.1 + - + +
425B GLU* 3.1 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B VAL* 3.8 18.4 - - + -
419B SER* 2.8 23.1 + - - -
420B THR 3.3 0.6 - - - -
421B PRO* 1.3 75.6 - - - +
423B LEU* 1.3 56.4 + - - +
425B GLU* 4.7 4.7 - - - -
426B VAL* 3.0 34.8 + - + +
460B LEU* 3.8 19.7 - - + +
463B LEU* 3.9 38.6 + - + +
464B HIS* 5.1 1.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B LEU* 5.8 0.2 - - + -
411B TYR* 4.1 32.1 - - + +
412B THR* 3.5 28.7 - - + +
415B VAL* 4.2 12.3 - - + +
418B VAL* 3.7 38.1 - - + +
419B SER 3.1 10.1 + - - +
420B THR 3.0 7.4 + - - +
422B THR* 1.3 71.9 - - - +
424B VAL* 1.3 61.4 + - - +
426B VAL* 4.8 3.8 - - + -
427B SER* 2.9 38.8 + - - +
460B LEU* 5.6 4.7 - - + -
530B VAL* 4.0 21.3 - - + -
534B LYS* 4.1 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 424 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B LEU* 4.5 7.4 - - + +
420B THR* 2.9 17.0 + - + +
421B PRO* 3.8 4.9 - - + +
423B LEU* 1.3 74.9 - - - +
425B GLU* 1.3 57.3 + - - +
427B SER* 4.1 0.3 - - - -
428B ARG* 2.8 56.7 + - + +
523B ILE* 4.3 18.8 - - + +
526B GLN* 3.8 27.8 - - + +
527B THR* 3.8 17.0 - - - +
530B VAL* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 425 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B PRO 3.1 17.4 + - - +
422B THR* 4.1 5.4 - - - +
424B VAL* 1.3 77.2 - - - +
426B VAL* 1.3 64.8 + - + +
428B ARG* 3.7 7.8 - - - +
429B ASN* 3.2 35.2 + - - +
463B LEU* 5.1 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 426 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B TYR* 5.4 4.0 - - + -
422B THR* 3.0 25.4 + - + +
423B LEU* 4.1 5.2 - - + +
425B GLU* 1.3 75.6 - - + +
427B SER* 1.3 60.1 + - - +
429B ASN* 3.2 5.8 + - - +
430B LEU* 2.8 39.9 + - + +
456B VAL* 3.6 19.3 - - + +
457B LEU* 5.1 2.5 - - + -
459B GLN* 4.8 2.9 - - + -
460B LEU* 3.6 53.8 - - + +
463B LEU* 4.6 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B GLN* 4.2 7.1 - - - +
407B LEU* 3.8 7.8 + - - +
408B LEU* 3.3 44.2 + - - -
411B TYR* 3.9 13.9 - - - +
423B LEU* 2.9 27.5 + - - +
424B VAL 4.1 1.1 - - - -
426B VAL* 1.3 71.3 - - - +
428B ARG* 1.3 64.1 + - - +
430B LEU* 3.2 11.7 + - - +
431B GLY* 3.0 20.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B GLN* 2.8 42.3 + - - +
408B LEU* 5.8 1.3 - - + +
424B VAL* 2.8 39.3 + - + +
425B GLU* 3.7 7.4 - - - +
427B SER* 1.3 72.8 - - - +
429B ASN* 1.3 65.1 + - - +
431B GLY 3.3 0.9 + - - -
432B LYS* 3.2 23.4 + - - +
519B LYS* 3.1 38.5 + - - +
522B GLN* 3.2 26.7 + - - +
523B ILE* 3.3 33.1 - - - +
526B GLN* 2.8 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B LYS* 5.1 6.9 + - - +
425B GLU* 3.2 23.6 + - - +
426B VAL* 3.2 5.6 + - - +
427B SER 3.2 0.4 - - - -
428B ARG* 1.3 79.4 - - - +
430B LEU* 1.3 66.1 + - - +
431B GLY 3.2 0.2 - - - -
432B LYS* 3.2 35.9 + - - +
452B TYR* 3.2 30.1 + - - +
456B VAL* 4.0 20.6 - - + +
459B GLN* 5.0 14.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B LEU* 3.6 17.4 - - + +
411B TYR* 3.8 46.4 - - + +
426B VAL* 2.8 24.8 + - + +
427B SER* 3.2 15.5 + - - +
429B ASN* 1.3 76.6 - - - +
431B GLY* 1.3 53.9 + - - +
433B VAL* 2.7 37.5 + - - +
452B TYR* 4.9 1.6 - - - -
453B LEU* 3.7 25.6 - - + -
456B VAL* 3.6 22.2 - - + -
457B LEU* 4.4 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE* 4.5 0.3 - - - -
400B GLU* 4.2 6.3 - - - +
403B PHE* 3.4 19.3 - - - -
404B GLN* 3.8 17.3 - - - -
407B LEU* 3.6 14.8 - - - +
427B SER 3.0 10.7 + - - -
428B ARG 3.3 5.4 + - - -
429B ASN 3.2 0.4 - - - -
430B LEU* 1.3 71.4 - - - +
432B LYS* 1.3 57.6 + - - +
433B VAL 3.0 9.4 + - - -
434B GLY* 3.1 12.6 + - - -
435B SER* 4.1 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ASP* 6.0 0.4 + - - -
190B LYS* 3.9 20.8 - - - +
400B GLU* 3.6 18.6 - - - +
404B GLN* 4.1 9.9 - - - +
428B ARG* 3.2 24.6 + - - +
429B ASN* 3.2 34.1 + - - +
430B LEU 3.2 0.8 - - - -
431B GLY* 1.3 75.1 - - - +
433B VAL* 1.3 56.7 + - - +
434B GLY 3.2 0.7 - - - -
435B SER* 3.6 11.3 + - - -
436B LYS* 3.2 27.5 + - - +
452B TYR* 4.0 13.3 - - + +
519B LYS* 5.6 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ASN* 6.4 0.4 - - + -
403B PHE* 4.1 14.8 - - + -
407B LEU* 5.2 0.7 - - + -
429B ASN 3.7 2.6 + - - -
430B LEU 2.7 24.8 + - - +
431B GLY 3.0 1.2 - - - -
432B LYS* 1.3 77.4 - - - +
434B GLY* 1.3 63.3 + - - +
436B LYS* 3.9 2.5 - - - -
437B CYS* 3.0 27.8 + - - +
438B CYS* 4.2 1.5 + - - -
449B ALA* 3.7 37.2 - - + +
452B TYR* 3.6 28.0 - - + -
453B LEU* 4.3 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE* 3.8 25.2 - - - -
403B PHE* 4.4 3.4 - - - -
431B GLY 3.1 4.4 + - - -
433B VAL* 1.3 82.9 - - - +
435B SER* 1.3 61.8 + - - +
438B CYS* 2.8 49.8 + - - +
439B LYS 4.3 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE* 3.5 18.2 - - - -
400B GLU* 3.0 38.1 + - - +
432B LYS* 3.6 8.6 + - - -
434B GLY* 1.3 73.8 - - - +
436B LYS* 1.3 59.5 + - - +
439B LYS* 3.0 30.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ALA* 5.1 11.9 - - - +
432B LYS 3.2 17.5 + - - +
433B VAL 4.0 1.8 - - - +
435B SER* 1.3 79.9 - - - +
437B CYS* 1.3 72.7 + - - +
439B LYS* 4.1 12.4 + - - +
440B HIS* 4.1 11.3 - - - -
448B CYS* 3.7 11.6 - - - -
452B TYR* 3.9 41.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B VAL* 3.0 21.8 + - - +
436B LYS* 1.3 86.7 - - - +
438B CYS* 1.3 67.2 + - - +
439B LYS 3.2 2.7 - - - -
440B HIS* 3.2 24.2 + - - +
445B ARG* 3.4 12.7 - - + +
448B CYS* 2.1 63.9 - - + -
449B ALA* 3.3 19.1 - - + +
452B TYR* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ASN 4.9 0.7 - - - -
392B CYS* 2.1 55.9 - - - -
395B PHE* 4.2 11.7 - - + -
396B GLU* 3.5 21.9 - - - +
403B PHE* 6.1 0.7 - - - -
433B VAL* 4.6 2.5 - - - -
434B GLY* 2.8 36.9 + - - +
437B CYS* 1.3 73.0 - - - +
439B LYS* 1.3 62.1 + - - +
440B HIS 3.2 2.2 + - - +
445B ARG* 3.3 19.4 + - - +
----------------------------------------------------------
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