Contacts of the helix formed by residues 32 - 43 (chain B) in PDB entry 3C5C
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 32 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLY 3.3 0.8 - - - -
31B ALA* 1.3 79.0 - - - +
33B LYS* 1.3 60.3 + - - +
34B SER 3.4 2.2 - - - -
35B ALA* 3.7 0.7 - - - +
36B LEU* 2.9 37.9 + - - +
97B VAL* 4.7 0.4 - - - -
134B ASN* 3.5 10.1 - - - -
201B GDP 3.0 33.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ILE* 3.7 27.4 - - + +
26B LEU* 3.4 33.2 - - - +
27B GLY* 3.1 12.8 + - - +
28B ARG 2.9 23.0 + - - -
29B ARG* 3.7 4.6 - - - +
31B ALA* 3.8 2.2 - - + -
32B GLY* 1.3 76.6 - - - +
34B SER* 1.3 60.7 + - - +
36B LEU* 3.4 3.8 + - - +
37B THR* 3.0 26.9 + - - -
74B ASP* 3.3 12.8 - - - +
75B THR* 3.1 29.2 - - - +
76B ALA* 4.7 5.0 - - - +
77B ASP 5.2 1.5 + - - +
97B VAL* 4.1 13.9 - - + +
201B GDP 2.6 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LYS* 1.3 73.3 - - - +
35B ALA* 1.3 59.8 + - - +
37B THR* 3.2 2.2 + - - -
38B VAL* 2.8 37.1 + - - +
49B TYR* 3.6 33.2 - - - -
53B LEU 4.6 1.4 + - - -
74B ASP* 2.4 28.3 + - - -
201B GDP 2.9 14.0 + - - -
202B MG 2.1 29.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLY 3.4 1.8 + - - +
34B SER* 1.3 72.9 - - - +
36B LEU* 1.3 57.2 + - - +
38B VAL* 3.8 3.5 - - - +
39B LYS* 2.9 31.5 + - - +
44B ARG 4.8 1.0 - - - +
45B PHE* 4.0 12.1 - - + -
46B ILE 4.2 14.3 + - - +
49B TYR* 5.5 0.6 - - - +
165B ALA* 3.6 11.2 - - + +
201B GDP 2.8 52.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ILE* 5.8 2.0 - - + -
32B GLY 2.9 20.5 + - - +
33B LYS 3.7 3.8 - - - +
35B ALA* 1.3 77.0 - - - +
37B THR* 1.3 52.5 + - - +
39B LYS* 3.3 3.3 + - - +
40B PHE* 2.8 35.3 + - - +
95B LEU* 6.0 0.4 - - + -
97B VAL* 3.8 35.0 - - + -
132B LEU* 4.2 9.6 - - + -
134B ASN* 3.5 26.7 - - - +
163B VAL* 3.9 20.2 - - + -
165B ALA* 3.8 18.6 - - + +
172B VAL* 3.6 22.6 - - + +
175B VAL* 6.0 1.1 - - + -
176B PHE* 4.2 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ILE* 4.0 8.1 - - - +
33B LYS 3.0 19.9 + - - -
34B SER* 3.6 7.9 - - - -
36B LEU* 1.3 74.9 - - - +
38B VAL* 1.3 59.1 - - + +
40B PHE* 3.3 3.9 + - + +
41B LEU* 2.9 53.1 + - + +
57B TYR* 4.0 21.8 - - + -
72B VAL* 3.9 27.2 - - + +
74B ASP* 3.8 14.1 - - + +
176B PHE* 4.0 9.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B SER* 2.8 21.1 + - - +
35B ALA* 4.0 4.0 - - - +
37B THR* 1.3 77.3 - - + +
39B LYS* 1.3 58.0 + - - +
41B LEU* 4.4 5.6 - - + +
42B THR* 2.6 60.6 + - + +
44B ARG 3.7 8.7 - - - +
46B ILE* 3.7 27.1 - - + +
49B TYR* 3.8 39.0 - - + +
57B TYR* 5.8 3.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ALA 2.9 19.6 + - - +
36B LEU* 3.5 7.6 - - - +
38B VAL* 1.3 76.5 - - - +
40B PHE* 1.3 57.9 + - - +
43B LYS* 2.8 51.7 + - - -
44B ARG 3.3 22.3 + - - +
45B PHE* 4.4 6.0 - - - +
165B ALA* 2.9 30.1 + - - +
166B CYS* 3.8 5.7 - - - +
167B LEU 2.6 29.0 + - - -
169B PHE* 3.3 25.9 - - - +
172B VAL* 4.0 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU 2.8 20.5 + - - +
37B THR* 3.3 4.2 + - + +
39B LYS* 1.3 74.2 - - - +
41B LEU* 1.3 80.8 + - + +
59B SER* 4.6 0.7 - - - -
61B GLU* 3.6 36.4 - - + +
70B LEU* 3.5 31.0 - - + -
72B VAL* 4.6 1.6 - - + -
169B PHE* 3.3 22.7 - + - -
172B VAL* 4.0 4.8 - - + +
173B GLN* 4.0 20.2 - - + -
176B PHE* 3.4 52.5 - + + -
177B HIS* 4.2 16.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B THR* 2.9 32.6 + - + +
38B VAL* 4.9 3.4 - - + -
40B PHE* 1.3 91.8 - - + +
42B THR* 1.3 71.3 + - + +
43B LYS* 5.4 4.9 + - - -
57B TYR* 3.6 47.6 - - + +
58B SER 4.8 3.8 - - - +
59B SER* 4.0 26.2 - - - +
61B GLU* 6.0 0.4 - - - -
72B VAL* 5.3 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B VAL* 2.6 35.8 + - + +
41B LEU* 1.3 88.4 - - + +
43B LYS* 1.3 71.9 + - - +
44B ARG* 3.0 35.6 + - - +
46B ILE* 5.2 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LYS* 2.8 33.0 + - - -
41B LEU 5.4 4.2 + - - -
42B THR* 1.3 82.2 + - - +
44B ARG* 1.3 82.2 + - - +
169B PHE* 3.8 47.0 - - + +
----------------------------------------------------------
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