Contacts of the helix formed by residues 28 - 48 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ASN* 2.8 11.9 + - - +
27A LEU* 1.3 85.0 + - + +
29A PRO* 1.3 66.1 - - - +
30A LEU 3.4 2.5 - - - -
31A GLU* 3.4 29.5 + - - +
32A ALA* 2.9 22.9 + - - +
163A ARG 4.7 0.4 - - - -
166A GLU* 3.1 48.1 + - - +
167A LEU* 4.0 9.9 - - + +
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Residues in contact with PRO 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.7 2.7 - - + -
23A TRP* 3.6 39.9 - - + +
24A MET* 4.8 4.7 - - - +
26A ASN 3.4 9.4 - - - +
27A LEU 3.4 8.3 - - - +
28A ARG* 1.3 89.6 - - - +
30A LEU* 1.3 59.2 + - + +
31A GLU* 5.0 0.4 - - - +
32A ALA* 3.8 0.3 - - - +
33A ARG* 2.8 31.4 + - - +
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.9 19.9 - - + +
4A HIS* 3.5 48.2 - - + +
14A TRP* 3.8 16.4 - - + -
28A ARG 3.4 0.6 - - - -
29A PRO* 1.3 81.4 - - - +
31A GLU* 1.3 71.3 + - + +
33A ARG* 3.2 1.6 + - - +
34A ILE* 2.9 42.2 + - + +
160A LEU* 5.4 5.2 - - + -
163A ARG* 3.9 25.1 - - - +
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Residues in contact with GLU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG* 3.4 34.2 - - + +
29A PRO* 5.0 0.3 - - - +
30A LEU* 1.3 77.7 + - + +
32A ALA* 1.3 63.5 + - - +
34A ILE* 3.3 6.7 + - - +
35A VAL* 3.0 27.5 + - - +
160A LEU* 5.3 3.1 - - + -
163A ARG* 2.8 74.8 + - + +
164A MET* 3.9 12.4 - - + +
166A GLU* 5.4 0.5 - - - +
167A LEU* 3.9 20.9 - - + -
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Residues in contact with ALA 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TRP* 3.6 13.4 - - + +
26A ASN* 3.6 33.2 - - + +
28A ARG 2.9 18.5 + - - +
29A PRO 3.8 3.1 - - - +
31A GLU* 1.3 77.0 - - - +
33A ARG* 1.3 55.3 + - - +
35A VAL* 3.4 3.2 + - - +
36A GLU* 2.9 30.1 + - - +
167A LEU* 3.9 10.2 - - + +
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Residues in contact with ARG 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0A ALA 5.9 0.4 - - - +
1A MET* 3.2 41.5 - - - +
2A ASP* 4.6 2.2 + - - -
14A TRP* 3.0 64.5 + - + +
15A ALA* 4.8 0.2 - - - +
17A SER* 2.9 19.2 + - - +
18A GLU* 3.6 22.6 + - - +
23A TRP* 3.4 49.5 - - + +
29A PRO 2.8 18.1 + - - +
30A LEU* 3.5 5.6 - - - +
32A ALA* 1.3 73.1 - - - +
34A ILE* 1.4 60.6 + - - +
36A GLU* 3.2 2.0 + - - +
37A CYS* 2.9 30.4 + - - -
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Residues in contact with ILE 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A HIS 4.3 3.1 - - - +
6A PRO* 3.8 39.0 - - + -
9A ILE* 5.0 1.3 - - + -
14A TRP* 4.0 10.8 - - + -
30A LEU* 2.9 38.2 + - + +
31A GLU* 3.7 4.9 - - - +
33A ARG* 1.4 76.4 - - - +
35A VAL* 1.3 58.2 + - - +
37A CYS* 3.2 8.1 + - - +
38A ILE* 2.9 36.9 + - + +
151A ILE* 4.2 7.4 - - + -
160A LEU* 3.5 28.9 - - + -
164A MET* 3.7 21.8 - - + -
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Residues in contact with VAL 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLU 3.0 20.0 + - - +
32A ALA* 3.9 4.0 - - - +
34A ILE* 1.3 74.6 - - - +
36A GLU* 1.3 58.9 + - - +
38A ILE* 3.2 9.1 + - - +
39A LYS* 2.9 27.6 + - + +
101A VAL* 4.2 28.2 - - + +
103A PRO* 4.5 12.3 - - + -
124A LEU* 4.7 6.7 - - + -
164A MET* 3.9 19.1 - - + -
167A LEU* 3.6 23.3 - - + -
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Residues in contact with GLU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A SER* 2.6 24.7 + - - -
22A GLU* 3.5 11.1 - - - +
23A TRP* 3.0 40.3 + - + +
32A ALA 2.9 16.2 + - - +
33A ARG* 3.7 6.1 - - - +
35A VAL* 1.3 76.9 - - - +
37A CYS* 1.3 58.3 + - - +
39A LYS* 3.3 10.9 + - + +
40A TYR* 3.0 23.7 + - - +
62A MET* 3.5 18.9 - - + +
63A TRP* 2.8 23.6 + - + +
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Residues in contact with CYS 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE* 3.9 16.2 - - + -
13A ILE* 3.9 21.8 - - + +
14A TRP* 3.8 20.2 - - - -
17A SER* 3.7 32.3 - - - -
33A ARG 2.9 20.5 + - - +
34A ILE* 3.6 4.9 - - - +
36A GLU* 1.3 75.6 - - - +
38A ILE* 1.3 59.0 + - - +
40A TYR* 3.8 1.2 - - - +
41A THR* 2.8 34.3 + - - -
63A TRP* 4.3 6.7 - - - -
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Residues in contact with ILE 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 4.2 0.4 - - + -
34A ILE* 2.9 26.6 + - + +
35A VAL* 3.4 11.9 - - - +
37A CYS* 1.3 76.4 - - - +
39A LYS* 1.4 55.9 + - - +
41A THR* 3.3 2.6 + - - -
42A VAL* 2.9 29.0 + - + +
101A VAL* 4.2 16.8 - - + -
124A LEU* 3.6 24.5 - - + -
147A PHE* 3.8 13.9 - - + -
148A LEU* 3.6 30.1 - - + -
151A ILE* 3.7 39.5 - - + -
164A MET* 4.5 5.2 - - + -
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Residues in contact with LYS 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A VAL* 2.9 13.8 + - + +
36A GLU* 3.4 12.6 - - + +
38A ILE* 1.4 76.3 - - - +
40A TYR* 1.3 61.3 + - - +
42A VAL* 3.3 6.5 + - - +
43A CYS* 3.1 21.5 + - - -
62A MET* 3.8 20.1 - - + +
87A ASP* 3.6 28.9 + - - -
99A VAL* 3.3 37.6 + - + +
100A LYS* 5.6 0.4 - - - -
101A VAL* 3.9 17.0 - - + +
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Residues in contact with TYR 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ILE* 3.9 18.6 - - + -
16A LEU* 3.9 1.5 - - + +
36A GLU 3.0 15.2 + - - +
37A CYS 3.8 2.7 - - - +
38A ILE 3.3 0.2 - - - -
39A LYS* 1.3 76.9 - - - +
41A THR* 1.3 56.6 + - - +
43A CYS* 3.1 6.6 + - + +
44A CME 2.9 50.7 + - - -
60A VAL* 4.0 12.6 - - + -
62A MET* 3.5 42.4 - - + -
63A TRP* 3.4 46.4 - + + -
1168A GOL 2.8 25.6 + - - -
81B ALA 2.7 29.8 + - - -
83B PRO* 3.8 3.8 - - - +
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Residues in contact with THR 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A SER 5.7 0.4 - - - +
9A ILE* 4.3 6.3 - - - +
10A SER 5.6 0.3 + - - -
13A ILE* 3.4 27.0 - - + +
37A CYS 2.8 22.9 + - - -
40A TYR* 1.3 77.8 - - - +
42A VAL* 1.3 54.6 + - - +
44A CME 3.1 8.9 + - + +
45A HIS* 2.9 45.9 + - + +
147A PHE* 3.6 36.2 - - + -
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Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ILE* 2.9 19.8 + - + +
39A LYS* 3.5 9.2 - - - +
40A TYR 3.2 0.2 - - - -
41A THR* 1.3 75.3 - - - +
43A CYS* 1.3 63.5 + - - +
45A HIS* 3.1 8.6 + - - +
46A ILE* 2.9 35.8 + - + +
99A VAL* 3.8 22.4 - - + -
101A VAL* 5.0 1.1 - - + -
120A VAL* 4.8 5.2 - - + -
122A VAL* 4.7 8.1 - - + -
144A VAL* 4.1 23.8 - - + -
147A PHE* 4.2 8.3 - - + -
148A LEU* 4.0 26.0 - - + -
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Residues in contact with CYS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LYS 3.1 18.3 + - - -
40A TYR* 3.1 10.8 + - + +
42A VAL* 1.3 74.6 - - - +
44A CME 1.3 61.8 + - - +
46A ILE* 3.3 8.3 + - - +
47A SER* 2.8 27.5 + - - -
60A VAL* 4.4 14.6 - - + -
62A MET* 4.1 18.4 - - - -
87A ASP* 4.0 14.4 - - - -
88A LEU* 3.7 34.3 - - + +
99A VAL* 3.9 13.7 - - - -
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Residues in contact with CME 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A SER* 5.2 0.2 + - - -
12A GLU* 4.4 8.7 + - - +
13A ILE* 3.9 21.6 - - + +
40A TYR* 2.9 38.3 + - - -
41A THR* 3.1 12.8 + - + +
43A CYS* 1.3 78.5 + - - +
45A HIS* 1.3 58.2 + - + +
47A SER* 3.3 7.6 + - - -
48A ASP* 2.8 33.8 + - - +
60A VAL* 5.3 2.0 - - - -
80B PHE 4.2 4.0 + - - -
81B ALA* 3.4 31.9 - - - +
82B ARG 3.8 18.2 + - - +
83B PRO* 4.0 31.9 - - + -
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Residues in contact with HIS 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A THR* 2.9 40.3 + - + +
42A VAL* 3.1 4.5 + - - +
44A CME 1.3 74.5 + - + +
46A ILE* 1.3 65.9 + - - +
47A SER 3.4 0.3 + - - -
48A ASP* 3.8 20.1 + - - +
50A HIS* 4.2 8.5 + - - -
140A GLN* 4.7 2.9 - - - +
143A ASP* 3.8 36.4 - - + +
144A VAL* 3.9 19.3 - - + -
147A PHE* 3.5 34.3 - + + +
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Residues in contact with ILE 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 2.9 34.9 + - + +
43A CYS* 3.6 8.5 - - - +
45A HIS* 1.3 76.9 - - - +
47A SER* 1.3 57.9 + - - +
50A HIS* 3.2 11.3 - - - -
58A TYR* 3.5 32.1 - - + +
88A LEU* 4.1 11.7 - - + -
97A VAL* 5.0 1.6 - - + -
99A VAL* 4.1 20.0 - - + -
120A VAL* 4.2 20.6 - - + -
135A TYR* 5.2 2.5 - - + +
136A LEU* 4.1 13.7 - - + -
140A GLN* 2.9 34.5 + - - +
144A VAL* 4.0 14.4 - - + -
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Residues in contact with SER 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A CYS 2.8 20.7 + - - -
44A CME 3.3 12.6 + - - -
46A ILE* 1.3 78.9 - - - +
48A ASP* 1.3 63.7 + - - +
49A MET 3.1 4.0 + - - -
50A HIS* 3.1 17.4 + - - +
56A PRO* 5.7 3.3 - - - +
58A TYR* 3.7 35.0 + - - +
60A VAL* 3.6 13.3 - - - +
88A LEU* 4.1 4.5 - - - -
83B PRO* 5.2 4.6 - - - +
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Residues in contact with ASP 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A CME 2.8 22.4 + - - +
45A HIS* 4.0 19.4 + - - +
46A ILE 3.6 1.2 - - - -
47A SER* 1.3 68.9 + - - +
49A MET* 1.3 95.7 + - - +
50A HIS* 3.0 18.2 + - - -
143A ASP* 4.9 9.2 - - - +
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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
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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