Contacts of the helix formed by residues 426 - 447 (chain F) in PDB entry 7KHC
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 LYS 426 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425F TYR* 1.3 77.0 - - - +
427F PHE* 1.3 66.1 + - - +
428F SER* 3.2 32.8 - - - +
429F THR* 2.9 45.6 - - + +
430F TYR 3.1 4.5 + - - -
31Y T 2.8 42.9 + - - +
32Y A 5.4 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 427 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383F ASN* 4.7 25.6 - - - -
386F LEU* 6.3 2.2 - - + -
412F LEU* 5.6 1.1 - - + -
415F ALA* 6.1 0.9 - - + -
416F VAL* 4.9 14.6 - - + -
419F PHE* 3.4 57.9 - + + -
421F TYR* 5.8 2.5 - - + -
425F TYR 3.1 4.6 + - - -
426F LYS* 1.3 78.5 - - - +
428F SER* 1.3 81.5 + - - +
430F TYR* 3.0 6.7 + + - +
431F ALA* 2.9 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 428 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386F LEU* 6.0 4.7 - - - -
426F LYS* 3.2 26.4 - - - +
427F PHE* 1.3 89.4 - - - +
429F THR* 1.3 67.8 + - - +
431F ALA* 3.2 6.1 + - - +
432F THR* 2.9 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 429 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425F TYR* 3.4 18.2 + - + -
426F LYS* 2.9 43.0 - - + +
428F SER* 1.3 82.7 + - - +
430F TYR* 1.3 61.7 + - - +
432F THR* 2.8 9.7 + - - -
433F TRP* 2.8 36.5 + - - +
31Y T 4.5 0.7 - - - -
32Y A 2.3 48.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 430 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415F ALA* 3.6 7.6 - - + -
418F LYS* 3.0 41.3 + - - +
419F PHE* 3.3 40.6 - + + -
420F GLU* 4.6 10.3 + - + +
423F ARG* 5.8 5.4 - - - -
425F TYR* 3.2 40.6 - + + -
426F LYS 3.6 1.8 - - - +
427F PHE* 3.0 13.9 + + - +
429F THR* 1.3 81.3 - - - +
431F ALA* 1.3 65.2 + - - +
433F TRP* 3.2 4.9 - - + +
434F TRP* 3.0 62.1 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 431 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386F LEU* 4.8 11.0 - - + -
412F LEU* 4.1 22.7 - - + -
415F ALA* 3.9 14.4 - - + +
427F PHE* 2.9 25.7 + - + +
428F SER* 3.5 11.4 - - - +
430F TYR* 1.3 76.9 - - - +
432F THR* 1.3 64.5 + - - +
434F TRP* 3.0 6.9 + - - +
435F ILE* 2.8 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 432 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386F LEU* 4.7 14.1 - - + -
390F ILE* 3.6 25.8 - - + -
428F SER* 2.9 24.5 + - - +
429F THR* 2.8 25.5 + - - -
431F ALA* 1.3 72.2 - - - +
433F TRP* 1.3 63.4 + - - +
435F ILE* 3.1 10.7 + - - +
436F ARG* 2.9 43.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 433 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425F TYR* 4.4 10.1 - + + +
429F THR* 2.8 25.2 + - - +
430F TYR* 3.2 9.4 - - + +
432F THR* 1.3 75.8 + - - +
434F TRP* 1.3 106.9 + + + +
436F ARG* 3.2 11.3 + - - +
437F GLN* 2.8 55.8 + - + +
46X C 5.7 8.1 - + - -
32Y A 5.5 1.6 - - + -
33Y T 3.7 39.6 + - + +
34Y A 5.8 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 434 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411F GLY* 3.7 12.3 - - - +
414F LYS* 5.1 13.7 - - + -
415F ALA* 3.3 32.5 - - + +
418F LYS* 4.0 36.3 - - + +
430F TYR* 3.0 51.5 + + - -
431F ALA 3.0 6.9 + - - +
433F TRP* 1.3 110.0 - + + +
435F ILE* 1.3 65.4 + - - +
437F GLN* 3.2 15.4 + - + +
438F ALA* 2.9 24.9 + - - +
45X C 5.7 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 435 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386F LEU* 4.4 14.8 - - + -
387F VAL* 4.3 19.1 - - + -
390F ILE* 3.7 42.8 - - + -
408F GLY* 4.1 18.8 - - - +
411F GLY* 4.6 6.5 - - - -
412F LEU* 4.3 14.6 - - + +
431F ALA 2.8 19.4 + - - +
432F THR* 3.1 11.9 + - - +
434F TRP* 1.3 77.4 - - - +
436F ARG* 1.3 65.3 + - - +
438F ALA* 3.1 2.8 + - - +
439F ILE* 2.9 45.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 436 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390F ILE* 4.7 20.6 - - + +
394F TYR* 4.1 21.0 + - + +
432F THR* 2.9 33.2 + - - +
433F TRP* 3.6 9.6 - - - +
435F ILE* 1.3 75.7 - - - +
437F GLN* 1.3 66.3 + - - +
438F ALA 2.8 1.7 + - - -
439F ILE* 3.0 3.3 + - - +
440F THR* 2.8 29.5 + - + +
33Y T 5.4 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 437 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433F TRP* 2.8 60.6 + - + +
434F TRP* 3.2 17.7 + - + +
436F ARG* 1.3 73.1 - - - +
438F ALA* 1.3 56.5 + - - +
440F THR* 4.0 8.5 - - - +
441F ARG* 3.0 51.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 438 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407F GLU* 4.0 18.9 - - - +
410F ILE* 5.8 1.8 - - + -
411F GLY* 3.9 20.4 - - - +
434F TRP 2.9 15.4 + - - +
435F ILE 3.6 3.1 - - - +
437F GLN* 1.3 78.5 - - - +
439F ILE* 1.3 60.5 + - - +
441F ARG* 3.3 4.2 + - - +
442F SER* 2.9 30.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 439 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387F VAL 5.5 0.7 - - - +
390F ILE* 5.0 1.1 - - + -
391F ALA* 4.7 20.2 - - + +
394F TYR* 3.3 37.7 - - + -
404F LEU* 4.0 15.0 - - + +
407F GLU* 4.3 2.7 - - + -
408F GLY* 3.8 28.0 - - - +
435F ILE* 2.9 40.0 + - + +
436F ARG* 4.0 2.0 - - - +
438F ALA* 1.3 75.7 - - - +
440F THR* 1.3 60.6 + - - +
442F SER* 2.6 23.9 + - - -
443F ILE* 2.6 29.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 440 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394F TYR* 3.8 27.1 - - - +
436F ARG* 2.8 27.6 + - + +
437F GLN* 4.0 12.1 - - - +
439F ILE* 1.3 74.6 - - - +
441F ARG* 1.3 66.5 + - + +
443F ILE* 3.8 3.1 - - - +
444F ALA* 2.9 32.8 + - - +
458F GLU* 5.4 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 441 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437F GLN* 3.0 42.5 + - - +
438F ALA* 3.3 5.6 + - - +
439F ILE 3.2 0.4 - - - -
440F THR* 1.3 86.3 - - + +
442F SER* 1.3 56.3 + - - +
444F ALA* 3.6 4.8 - - - +
445F ASP* 2.5 47.1 + - - +
454F VAL* 5.1 15.0 - - - +
44X C 3.5 39.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 442 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399F LEU* 5.5 1.8 - - - +
404F LEU* 5.4 0.5 - - - +
407F GLU* 3.6 28.0 - - - +
438F ALA 2.9 13.8 + - - -
439F ILE* 2.6 20.8 + - - -
441F ARG* 1.3 76.0 - - - +
443F ILE* 1.3 71.9 + - - +
445F ASP* 3.0 10.2 + - - -
446F GLN* 2.9 50.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 443 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394F TYR* 4.1 12.3 - - + -
397F ARG* 3.4 35.0 - - + +
399F LEU* 3.9 13.5 - - + -
404F LEU* 3.5 26.5 - - + -
439F ILE* 2.6 48.9 + - + +
440F THR* 4.0 4.5 - - - +
442F SER* 1.3 87.6 + - - +
444F ALA* 1.3 64.4 + - - +
447F ALA* 2.7 39.4 + - + +
457F ILE* 5.2 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 444 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440F THR* 2.9 21.0 + - - +
441F ARG* 3.6 5.6 - - - +
443F ILE* 1.3 79.4 - - - +
445F ASP* 1.3 61.1 + - - +
447F ALA* 4.5 1.4 + - - +
448F ARG* 5.1 3.8 + - - +
451F ARG* 4.9 0.7 - - - +
452F ILE* 4.3 10.7 + - - +
454F VAL* 3.7 29.4 - - + -
457F ILE* 3.5 34.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 445 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441F ARG* 2.5 40.6 + - - +
442F SER* 3.0 13.9 - - - +
444F ALA* 1.3 81.2 - - + +
446F GLN* 1.3 91.8 + - - +
447F ALA 3.4 1.4 + - - -
448F ARG* 4.2 4.7 + - - +
451F ARG* 3.3 46.8 - - - +
452F ILE 5.6 0.4 - - - -
454F VAL* 5.9 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 446 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D PRO* 5.4 6.3 - - + -
270D ARG* 4.6 8.8 + - - +
274D ASN* 3.1 45.1 + - - +
278D ARG* 4.2 9.6 + - - +
398F GLY 5.3 0.3 - - - +
399F LEU* 4.4 21.6 - - + +
403F ASP* 5.7 0.6 - - - +
407F GLU* 3.8 17.2 + - - +
442F SER* 2.9 36.3 + - - +
445F ASP* 1.3 88.3 + - - +
447F ALA* 1.3 65.5 + - - +
448F ARG 4.1 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 447 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D ARG* 5.0 6.8 + - - -
397F ARG* 3.5 24.0 - - + +
398F GLY* 4.4 7.4 - - - +
399F LEU* 3.6 15.3 - - + -
442F SER 3.9 0.2 + - - -
443F ILE* 2.7 28.5 + - + +
445F ASP 3.4 1.0 - - - -
446F GLN* 1.3 79.4 - - - +
448F ARG* 1.3 73.7 + - + +
449F THR* 3.6 1.2 + - - -
503F GLU* 5.3 1.6 - - - +
----------------------------------------------------------
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