Contacts of the helix formed by residues 435 - 447 (chain A) in PDB entry 2G9Y
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 GLN 435 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A TYR* 3.1 38.5 + - + +
85A THR 2.9 18.9 + - - +
86A HIS* 3.3 19.6 - - - +
87A TYR 5.4 0.2 - - - +
105A SER* 3.1 39.6 - - - +
108A ALA* 3.7 9.8 - - + +
109A TRP* 3.6 20.8 - - + -
114A LYS* 4.8 1.9 + - - +
369A ASP* 2.9 32.3 + - - +
434A ASP* 1.3 75.0 - - - +
436A THR* 1.3 62.2 + - - +
438A LEU* 3.2 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ALA* 3.8 26.9 - - + +
112A GLY 3.8 29.8 - - - +
113A VAL 4.1 5.2 - - - -
114A LYS* 4.0 17.9 - - + +
434A ASP* 2.7 27.0 + - - +
435A GLN* 1.3 74.5 - - - +
437A ASP* 1.3 67.3 + - - +
439A PHE* 3.1 13.4 + - - +
440A TYR* 3.2 17.5 - - - -
20B GLY* 5.6 0.2 - - - -
22B ALA* 3.7 19.9 - - + +
23B ARG* 3.7 6.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A ASN 5.5 0.9 - - - +
433A THR* 3.8 8.1 - - - -
434A ASP* 2.9 34.4 + - - +
436A THR* 1.3 79.6 + - - +
438A LEU* 1.3 49.4 + - - +
440A TYR* 3.0 10.0 + - - +
441A THR* 2.8 38.2 + - - +
23B ARG* 3.3 15.1 + - - +
24B ARG* 2.7 28.7 + - - +
25B LEU* 3.1 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 4.2 20.9 - - + -
49A ILE* 5.4 0.2 - - + -
84A TYR* 4.3 15.5 - - + +
109A TRP* 3.8 22.9 - - + -
365A ILE* 3.4 36.8 - - + -
367A THR* 4.4 6.1 - - + -
419A ILE* 4.2 21.1 - - + -
429A VAL* 5.2 2.5 - - + -
434A ASP 3.6 2.2 + - - +
435A GLN 3.2 12.7 + - - +
436A THR 3.1 0.6 - - - -
437A ASP* 1.3 80.0 - - - +
439A PHE* 1.3 61.1 + - - +
441A THR* 4.1 8.3 - - + -
442A MET* 3.0 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ALA 3.9 0.2 - - - +
109A TRP 3.1 21.5 + - - +
110A SER 3.4 29.4 - - - -
111A THR* 3.3 19.3 - - - -
112A GLY* 3.3 23.6 - - - +
130A PRO 4.5 2.5 - - - -
132A ILE* 4.0 12.5 - - + +
135A MET* 3.6 37.9 - - + -
435A GLN 4.0 0.6 + - - -
436A THR 3.1 11.6 + - - +
438A LEU* 1.3 78.4 - - - +
440A TYR* 1.3 86.3 + + - +
442A MET* 3.3 4.9 + - - +
443A LYS* 2.9 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A THR 4.8 0.7 + - - -
112A GLY* 3.7 18.6 + - - -
436A THR 3.2 19.5 - - - -
437A ASP* 3.0 8.1 + - - +
439A PHE* 1.3 101.4 - + - +
441A THR* 1.3 60.5 + - - +
443A LYS* 3.7 21.7 - - + +
444A ALA* 3.0 32.1 + - - +
19B PRO* 3.6 11.3 - - - +
20B GLY* 3.2 24.4 + - - -
23B ARG* 3.4 53.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A LEU* 4.6 12.6 - - + -
365A ILE* 4.9 9.9 - - + -
425A HIS* 4.3 9.7 - - + +
428A ASN* 3.5 47.0 + - + +
429A VAL* 5.2 4.4 - - + +
437A ASP 2.8 19.0 + - - -
438A LEU* 3.6 11.5 - - + +
439A PHE 3.3 0.2 - - - -
440A TYR* 1.3 77.9 - - - +
442A MET* 1.3 58.3 + - - +
444A ALA* 3.9 3.7 - - - +
445A ALA* 2.9 31.5 + - - +
25B LEU* 4.6 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE* 3.5 35.3 - - + +
47A LEU* 3.9 28.0 - - + -
109A TRP* 3.5 26.5 - - + +
132A ILE* 4.1 29.2 - - + -
318A PHE* 3.8 19.3 - - + -
363A LEU* 5.2 0.2 - - - -
365A ILE* 4.3 8.3 - - + -
438A LEU* 3.0 34.8 + - + +
439A PHE* 3.8 3.8 - - - +
441A THR* 1.3 74.7 - - - +
443A LYS* 1.3 64.8 + - - +
445A ALA 3.4 0.2 + - - -
446A LEU* 3.2 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE* 3.9 14.5 - - + +
135A MET* 3.8 25.9 - - + +
439A PHE* 2.9 31.4 + - + +
440A TYR* 3.7 23.1 - - + +
442A MET* 1.3 77.3 - - - +
444A ALA* 1.3 57.8 + - - +
446A LEU 3.5 0.3 + - - -
447A GLY 3.0 6.9 + - - -
448A LEU* 3.0 44.5 + - + +
449A LYS* 3.5 27.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A HIS* 4.8 8.8 + - + +
428A ASN* 6.0 2.5 - - - +
440A TYR 3.0 18.2 + - - +
441A THR* 3.9 4.7 - - - +
443A LYS* 1.3 77.3 - - - +
445A ALA* 1.3 66.1 + - - +
447A GLY* 2.9 15.6 + - - +
448A LEU 5.9 0.2 - - - -
28B ASP* 6.0 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PRO* 3.9 6.9 - - - +
42A ALA* 2.9 43.7 + - + +
45A ILE* 4.2 2.5 - - + -
363A LEU* 3.9 19.5 - - + -
425A HIS* 3.6 25.2 + - + -
441A THR 2.9 18.8 + - - +
442A MET 3.8 4.0 - - - +
443A LYS 3.4 0.2 - - - -
444A ALA* 1.3 77.0 - - - +
446A LEU* 1.3 59.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PRO* 6.1 1.6 - - - -
42A ALA 3.1 27.7 - - - +
43A LYS 3.7 18.2 - - - +
44A ASN* 4.2 3.1 - - - +
45A ILE* 3.6 33.4 - - + +
132A ILE* 4.9 3.1 - - + -
136A ALA* 5.2 1.6 - - + -
141A LEU* 4.1 21.0 - - + +
317A PHE 4.7 1.3 - - - +
318A PHE* 4.6 18.2 - - + -
442A MET 3.2 15.5 + - - +
445A ALA* 1.3 77.1 - - - +
447A GLY* 1.3 63.0 + - - +
448A LEU* 3.9 31.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A LYS 3.0 1.6 + - - -
444A ALA* 2.9 18.9 + - - -
445A ALA 3.2 0.6 + - - -
446A LEU* 1.3 80.5 - - - +
448A LEU* 1.3 63.8 + - - +
449A LYS 3.7 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