Contacts of the helix formed by residues 428 - 443 (chain A) in PDB entry 3RS9
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 GLY 428 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A LEU* 3.7 22.7 - - - +
426A LYS 3.2 0.2 + - - -
427A GLY* 1.3 73.2 - - - -
429A SER* 1.3 62.4 + - - +
430A GLY 3.3 2.2 - - - -
431A ASP* 3.2 22.8 + - - +
432A VAL* 3.3 17.3 + - - +
474A ALA* 3.7 8.1 - - - +
494A BA3 3.3 9.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A GLY 4.3 2.9 + - - -
424A LEU* 2.9 44.1 + - - +
426A LYS* 3.1 8.9 + - - +
427A GLY 3.5 0.9 + - - -
428A GLY* 1.3 76.3 - - - +
430A GLY* 1.3 62.9 + - - +
432A VAL* 3.3 4.3 + - - +
433A LEU 3.2 8.8 + - - -
458A HIS* 2.8 27.8 + - - -
474A ALA* 4.3 5.6 + - - +
477A LEU* 4.6 9.3 - - - +
494A BA3 3.2 16.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ASP* 3.7 5.7 - - - +
402A LYS* 3.9 14.8 + - - -
429A SER* 1.3 77.9 - - - +
431A ASP* 1.3 66.2 + - - +
433A LEU* 3.3 6.2 + - - +
434A THR* 3.1 26.0 + - - -
492A MG 4.3 0.4 - - - -
494A BA3 3.0 32.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ALA* 3.4 29.7 - - - +
250A LEU* 4.0 15.1 - - + +
251A SER* 2.9 34.6 + - - +
316A PRO* 3.5 15.6 - - - +
317A GLY 5.3 0.2 + - - -
342A ASP* 4.2 7.6 - - - +
343A ALA* 5.1 3.3 - - - +
428A GLY* 3.2 21.6 + - - +
430A GLY* 1.3 79.7 - - - +
432A VAL* 1.3 63.1 + - - +
434A THR* 3.4 1.3 + - - -
435A GLY 3.4 6.8 + - - -
494A BA3 3.6 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A LEU* 3.8 22.2 - - + +
254A GLY* 3.9 2.2 - - - -
428A GLY 3.3 13.6 + - - +
429A SER 3.5 7.6 - - - +
430A GLY 3.2 0.2 - - - -
431A ASP* 1.3 77.4 - - - +
433A LEU* 1.3 63.4 + - - +
435A GLY* 3.2 4.5 + - - -
436A MET* 3.0 26.0 + - + +
458A HIS* 4.3 0.4 - - + -
474A ALA* 4.1 19.3 - - + +
477A LEU* 4.2 17.0 - - + -
478A LEU* 3.9 21.8 - - + -
481A ILE* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A THR* 5.2 3.6 - - - -
400A VAL* 4.6 2.9 - - + -
402A LYS* 3.7 32.8 - - + +
429A SER 3.2 4.4 + - - +
430A GLY* 3.3 7.6 + - - +
432A VAL* 1.3 78.4 - - - +
434A THR* 1.3 64.2 + - - +
436A MET* 3.1 5.2 + - - +
437A ILE* 2.9 35.4 + - + +
454A SER* 3.6 39.7 - - - +
455A VAL* 3.9 20.4 - - + +
458A HIS* 3.7 28.0 - - + +
494A BA3 3.8 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A SER* 4.4 4.5 - - - +
313A ALA* 3.8 23.1 - - + -
314A ILE 5.3 0.2 - - - +
316A PRO* 4.4 11.0 - - + -
340A VAL* 3.9 20.3 - - + +
342A ASP* 2.6 42.4 + - + +
364A THR* 3.8 6.1 + - - -
402A LYS* 5.2 0.2 + - - -
430A GLY 3.1 6.8 + - - -
431A ASP 3.6 9.6 - - - -
433A LEU* 1.3 78.4 - - - +
435A GLY* 1.3 60.3 + - - +
437A ILE* 3.4 5.6 + - - +
438A ALA* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ILE* 4.8 2.9 - - - -
251A SER* 3.2 28.9 - - - +
255A SER* 2.8 28.4 + - - -
313A ALA* 5.7 0.2 - - - -
431A ASP 3.4 4.2 + - - -
432A VAL 3.2 6.0 + - - -
434A THR* 1.3 76.1 - - - +
436A MET* 1.3 65.8 + - - +
438A ALA* 3.4 2.5 + - - -
439A GLY 2.9 13.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A GLY 3.8 12.9 - - - +
258A VAL* 3.8 28.4 - - + +
432A VAL* 3.0 21.9 + - + +
433A LEU* 3.1 6.9 + - - +
435A GLY* 1.3 74.3 - - - +
437A ILE* 1.3 62.9 + - - +
439A GLY* 3.2 1.4 + - - -
440A PHE* 3.0 28.6 + - - -
454A SER* 3.3 20.9 - - - +
457A LEU* 3.8 14.8 - - + -
458A HIS* 3.7 46.0 - - - +
481A ILE* 3.8 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A VAL* 4.1 9.6 - - + -
362A VAL* 4.3 6.5 - - + -
364A THR* 3.8 28.0 - - + -
400A VAL* 4.5 7.6 - - + -
433A LEU* 2.9 35.5 + - + +
434A THR* 3.8 4.3 - - - +
436A MET* 1.3 76.0 - - - +
438A ALA* 1.3 62.9 + - - +
440A PHE 3.2 2.1 + - - -
441A ILE* 3.0 39.7 + - + +
450A ALA* 3.7 8.8 - - + +
451A SER* 3.9 30.5 - - - +
454A SER* 3.3 23.6 - - - -
455A VAL* 5.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A VAL* 3.8 25.4 - - + -
255A SER* 4.3 0.7 - - - +
311A VAL* 3.2 20.7 - - + +
313A ALA* 4.2 11.9 - - + -
340A VAL* 3.9 18.8 - - + +
434A THR 3.1 17.6 + - - +
435A GLY* 3.7 4.9 - - - +
437A ILE* 1.3 75.3 - - - +
439A GLY* 1.3 58.7 + - - +
441A ILE* 3.3 1.9 + - - +
442A ALA* 2.9 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A VAL* 4.0 8.9 - - - +
255A SER* 4.3 1.1 - - - -
258A VAL* 4.0 4.5 - - - -
260A THR* 3.0 22.3 + - - -
435A GLY 2.9 15.0 + - - -
436A MET 3.6 3.8 - - - -
437A ILE 3.1 0.2 - - - -
438A ALA* 1.3 73.8 - - - +
440A PHE* 1.3 63.6 + - - +
442A ALA* 3.2 4.3 + - - +
443A GLN* 3.0 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A LEU* 3.9 17.3 - - + -
221A PRO* 3.9 21.8 - - + -
258A VAL* 3.6 42.4 - - + -
436A MET* 3.0 16.5 + - + +
439A GLY* 1.3 73.7 - - - +
441A ILE* 1.3 65.6 + - - +
443A GLN* 3.2 16.8 + - - +
444A GLY 3.3 0.7 + - - -
445A LEU* 3.0 29.7 + - + +
450A ALA* 3.7 22.9 - - + -
453A VAL* 3.5 30.1 - - + -
454A SER* 3.2 24.9 - - - -
457A LEU* 3.8 15.5 - - + -
485A ILE* 5.0 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ASP* 5.2 1.9 - - + +
311A VAL* 4.2 17.5 - - + -
338A PRO* 4.2 22.9 - - + -
339A ALA 5.4 0.9 - - - +
340A VAL* 3.8 28.5 - - + -
362A VAL* 4.1 7.0 - - + -
437A ILE* 3.0 22.3 + - + +
438A ALA 3.6 6.3 - - - +
440A PHE* 1.3 76.3 - - - +
442A ALA* 1.3 64.2 + - - +
444A GLY* 2.9 15.8 + - - -
445A LEU 3.5 16.7 - - - +
447A PRO* 4.0 26.5 - - + -
450A ALA* 3.5 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A THR 5.3 0.9 - - - +
233A GLY* 3.5 16.6 + - - -
234A LYS 3.9 18.8 - - - +
235A VAL* 3.6 20.6 - - + -
260A THR* 4.0 6.7 - - + -
310A ASP* 4.2 16.8 - - + +
311A VAL* 3.9 6.0 - - + +
438A ALA 2.9 13.5 + - - +
439A GLY 3.2 9.4 + - - +
441A ILE* 1.3 77.6 - - - +
443A GLN* 1.3 59.8 + - - +
444A GLY* 3.2 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A PRO* 3.4 38.7 - - + +
223A ARG* 3.9 13.5 + - - -
231A THR 5.2 4.4 - - - +
232A TYR* 3.5 33.1 - - + +
258A VAL* 3.0 31.2 + - - +
259A GLY 3.8 9.0 - - - +
260A THR* 3.5 14.7 + - - +
439A GLY 3.0 22.6 + - - +
440A PHE* 3.7 10.5 - - - +
441A ILE 3.1 1.0 - - - -
442A ALA* 1.3 74.3 - - - +
444A GLY* 1.3 57.5 + - - +
445A LEU* 3.6 1.7 + - - +
----------------------------------------------------------
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