Contacts of the helix formed by residues 28 - 48 (chain B) in PDB entry 4CGS
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 ARG 28 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ASN* 2.8 12.0 + - - +
27B LEU* 1.3 92.9 - - + +
29B PRO* 1.3 66.0 - - - +
30B LEU 3.3 3.3 + - - -
31B GLU* 3.4 19.6 + - - +
32B ALA* 2.9 23.0 + - - +
163B ARG* 3.3 31.8 + - - +
166B GLU* 2.6 55.2 + - - +
167B LEU* 4.0 17.7 - - + +
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Residues in contact with PRO 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 4.6 3.6 - - + -
23B TRP* 3.5 41.3 - - + +
24B MET* 4.6 5.6 - - - +
26B ASN 3.4 9.9 - - - +
27B LEU 3.2 12.8 - - - +
28B ARG* 1.3 83.3 - - - +
30B LEU* 1.3 58.1 + - - +
32B ALA* 4.2 0.4 - - + -
33B ARG* 2.8 30.7 + - - +
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.7 26.8 - - + +
4B HIS* 3.6 47.6 - - + +
14B TRP* 3.9 15.5 - - + -
28B ARG 3.3 0.8 - - - -
29B PRO* 1.3 82.5 - - - +
31B GLU* 1.3 79.7 + - - +
33B ARG* 3.2 1.7 + - - +
34B ILE* 3.0 39.5 + - + +
160B LEU* 6.1 1.1 - - + -
163B ARG* 6.3 0.4 - - - -
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Residues in contact with GLU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ARG* 3.4 25.3 + - + +
30B LEU* 1.3 95.2 - - - +
32B ALA* 1.3 65.7 + - - +
34B ILE* 3.3 7.7 + - - +
35B VAL* 3.0 27.0 + - - +
160B LEU* 4.4 8.6 - - + +
163B ARG* 3.6 53.7 - - + +
164B MET* 3.9 13.2 - - + +
167B LEU* 3.9 20.6 - - + -
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Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ARG* 5.5 1.1 - - - +
23B TRP* 3.6 13.1 - - + +
26B ASN* 3.6 32.3 - - + +
28B ARG 2.9 18.1 + - - +
29B PRO 3.8 3.8 - - - +
31B GLU* 1.3 76.6 - - - +
33B ARG* 1.3 58.3 + - - +
35B VAL* 3.4 3.4 + - - +
36B GLU* 2.9 30.0 + - - +
167B LEU* 4.0 11.3 - - + +
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Residues in contact with ARG 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B ALA 6.0 0.2 - - - +
1B MET* 3.3 41.7 - - - +
14B TRP* 2.9 62.6 + - + +
15B ALA* 4.8 0.2 - - - +
17B SER* 2.9 19.9 + - - +
18B GLU* 3.5 23.4 + - - +
23B TRP* 3.4 47.3 - - + +
29B PRO 2.8 19.4 + - - +
30B LEU* 3.2 6.0 + - - +
32B ALA* 1.3 72.9 - - - +
34B ILE* 1.3 65.4 + - - +
36B GLU* 3.3 2.4 + - - +
37B CYS* 2.9 24.2 + - - -
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Residues in contact with ILE 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B HIS 4.3 2.9 - - - +
6B PRO* 3.9 29.4 - - + -
9B ILE* 4.7 2.2 - - + +
14B TRP* 3.9 23.1 - - + -
30B LEU* 3.0 33.3 + - + +
31B GLU* 3.7 7.2 - - - +
33B ARG* 1.3 76.0 - - - +
35B VAL* 1.3 58.2 + - - +
37B CYS* 3.2 4.9 + - - +
38B ILE* 2.8 41.0 + - + +
151B ILE* 4.4 5.2 - - + -
160B LEU* 3.6 27.6 - - + -
164B MET* 3.9 24.0 - - + -
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Residues in contact with VAL 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLU 3.0 17.1 + - - +
32B ALA* 3.4 4.2 + - - +
34B ILE* 1.3 73.8 - - - +
36B GLU* 1.3 59.0 + - - +
38B ILE* 3.1 9.4 + - - +
39B LYS* 2.9 27.7 + - + +
101B VAL* 4.3 16.4 - - + +
124B LEU* 4.8 4.3 - - + -
164B MET* 3.7 21.8 - - + -
167B LEU* 3.6 21.8 - - + -
168B TYR* 3.5 27.6 - - + +
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Residues in contact with GLU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B SER* 2.6 24.6 + - - -
22B GLU* 3.5 11.1 - - - +
23B TRP* 3.0 40.5 + - + +
32B ALA 2.9 16.4 + - - +
33B ARG* 3.7 5.8 - - - +
34B ILE 3.3 0.2 - - - -
35B VAL* 1.3 76.1 - - - +
37B CYS* 1.3 57.5 + - - +
39B LYS* 3.3 10.5 + - + +
40B TYR* 3.0 24.1 + - - +
62B MET* 3.5 19.0 - - + +
63B TRP* 2.8 22.5 + - + +
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Residues in contact with CYS 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 3.9 22.2 - - + -
13B ILE* 4.0 16.3 - - + +
14B TRP* 3.8 20.6 - - - -
17B SER* 3.7 31.9 - - - -
33B ARG 2.9 21.0 + - - +
34B ILE* 3.6 5.4 - - - +
36B GLU* 1.3 72.3 - - - +
38B ILE* 1.3 65.9 + - - +
40B TYR* 3.8 1.2 - - - +
41B THR* 2.8 31.3 + - - -
63B TRP* 4.2 7.0 - - - -
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Residues in contact with ILE 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 4.2 2.2 - - + -
34B ILE* 2.8 19.7 + - + +
35B VAL* 3.1 9.6 + - - +
37B CYS* 1.3 76.6 - - - +
39B LYS* 1.3 61.9 + - - +
41B THR 3.3 1.0 + - - -
42B VAL* 2.9 27.7 + - - +
101B VAL* 4.2 17.0 - - + -
124B LEU* 3.8 22.4 - - + -
147B PHE* 3.7 14.8 - - + -
148B LEU* 3.7 29.4 - - + -
151B ILE* 3.9 38.4 - - + -
164B MET* 3.9 17.0 - - + -
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Residues in contact with LYS 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B VAL* 2.9 17.0 + - + +
36B GLU* 3.5 11.9 - - + +
38B ILE* 1.3 71.9 - - - +
40B TYR* 1.3 63.5 + - - +
42B VAL* 3.2 6.7 + - - +
43B CYS* 3.0 21.5 + - - -
62B MET* 3.8 21.2 - - + +
87B ASP* 3.5 29.4 + - - -
99B VAL* 3.4 36.3 + - + +
100B LYS* 5.7 0.4 - - - -
101B VAL* 4.0 18.4 - - + +
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Residues in contact with TYR 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ILE* 3.9 20.6 - - + -
16B LEU* 3.8 16.1 - - + +
36B GLU 3.0 15.5 + - - +
37B CYS* 3.8 2.9 - - - +
39B LYS* 1.3 76.6 - - - +
41B THR* 1.3 62.9 + - - +
43B CYS* 3.1 6.8 + - + +
44B CME 3.0 55.3 + - - -
60B VAL* 4.1 16.6 - - + +
62B MET* 3.6 46.5 + - + -
63B TRP* 3.4 45.1 - + + -
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Residues in contact with THR 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B SER 5.6 0.7 - - - +
9B ILE* 4.3 5.8 - - - +
10B SER 5.6 0.5 + - - -
13B ILE* 3.4 26.5 - - + +
37B CYS 2.8 22.3 + - - -
38B ILE 3.3 0.2 + - - -
40B TYR* 1.3 75.8 - - - +
42B VAL* 1.3 57.3 + - - +
44B CME 3.1 9.5 + - + +
45B HIS* 2.9 47.5 + - + +
147B PHE* 3.5 35.8 - - + -
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Residues in contact with VAL 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ILE* 2.9 21.6 + - + +
39B LYS* 3.2 9.4 + - - +
41B THR* 1.3 72.6 - - - +
43B CYS* 1.3 67.3 + - - +
45B HIS* 3.1 8.4 + - - +
46B ILE* 2.9 36.2 + - + +
99B VAL* 3.8 22.2 - - + -
101B VAL* 5.0 0.9 - - + -
120B VAL* 4.7 6.1 - - + -
122B VAL* 4.6 8.3 - - + -
144B VAL* 4.0 23.7 - - + +
147B PHE* 4.2 8.3 - - + -
148B LEU* 4.0 25.8 - - + -
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Residues in contact with CYS 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LYS 3.0 19.7 + - - -
40B TYR* 3.1 8.7 + - + +
42B VAL* 1.3 75.0 - - - +
44B CME 1.3 61.0 + - - +
46B ILE* 3.3 8.7 + - - +
47B SER* 2.9 27.4 + - - -
60B VAL* 4.4 14.8 - - + -
62B MET* 4.1 19.1 - - - -
87B ASP* 4.0 13.9 - - - -
88B LEU* 3.7 33.2 - - + +
99B VAL* 3.9 13.9 - - - -
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Residues in contact with CME 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLU* 4.4 17.4 + - - +
13B ILE* 3.9 30.1 - - + +
40B TYR* 3.0 53.3 + - - -
41B THR* 3.1 11.2 + - + +
43B CYS* 1.3 76.0 + - - +
45B HIS* 1.3 59.8 + - + +
47B SER* 3.3 6.9 + - - -
48B ASP* 2.8 43.0 + - + +
60B VAL* 5.3 8.7 - - - -
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Residues in contact with HIS 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B THR* 2.9 39.6 + - + +
42B VAL 3.1 6.0 + - - +
44B CME 1.3 74.2 + - + +
46B ILE* 1.3 65.9 + - - +
47B SER 3.3 0.3 + - - -
48B ASP* 3.9 7.8 + - - +
50B HIS* 4.2 10.0 + - - -
140B GLN* 4.6 3.1 - - - +
143B ASP* 3.7 38.5 - - + +
144B VAL* 3.9 18.8 - - + -
146B ASN* 6.1 2.2 - - - -
147B PHE* 3.6 33.4 - + + +
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Residues in contact with ILE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B VAL* 2.9 33.9 + - + +
43B CYS* 3.3 8.7 + - - +
45B HIS* 1.3 78.5 - - - +
47B SER* 1.3 58.4 + - - +
50B HIS* 3.3 10.6 - - - -
58B TYR* 3.4 32.5 - - + +
88B LEU* 4.0 12.1 - - + -
97B VAL* 5.0 1.1 - - + -
99B VAL* 4.1 19.3 - - + -
120B VAL* 4.3 21.1 - - + -
135B TYR* 5.1 2.5 - - + +
136B LEU* 4.0 13.5 - - + -
140B GLN* 2.8 34.5 + - - +
144B VAL* 4.0 14.8 - - + -
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Residues in contact with SER 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B CYS 2.9 16.1 + - - -
44B CME 3.3 10.0 + - - -
46B ILE* 1.3 79.3 - - - +
48B ASP* 1.3 65.6 + - - +
49B MET 3.2 0.9 + - - -
50B HIS* 3.1 20.4 + - - +
56B PRO* 5.7 2.9 - - - +
58B TYR* 3.7 35.3 + - - +
60B VAL* 3.6 15.3 - - - +
88B LEU* 4.0 4.5 - - - -
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Residues in contact with ASP 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B CME 2.8 30.0 + - + +
45B HIS* 3.9 5.7 + - - +
46B ILE 3.7 1.4 - - - -
47B SER* 1.3 71.3 - - - +
49B MET* 1.3 83.0 + - - +
50B HIS* 3.1 17.2 + - - -
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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
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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) + - + + + + + -
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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