Contacts of the helix formed by residues 51 - 76 (chain A) in PDB entry 2IB0
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 VAL 51 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A SER* 3.7 23.3 - - - +
48A PRO* 3.0 21.5 + - + +
50A GLY* 1.3 82.6 - - - +
52A ASN* 1.3 60.3 + - - +
53A PHE* 3.3 3.8 - - - +
54A LEU* 3.2 12.2 + - + +
55A VAL* 3.0 24.3 + - + +
144A TRP* 3.9 17.9 - - + -
147A VAL* 3.8 38.8 - - + -
151A TRP* 4.5 7.9 - - + -
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Residues in contact with ASN 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A SER* 4.8 11.4 + - - +
47A SER* 4.7 6.6 - - - +
48A PRO 3.1 19.2 - - - +
49A PRO* 3.1 33.2 + - - +
50A GLY 3.6 0.4 - - - -
51A VAL* 1.3 76.1 - - - +
53A PHE* 1.3 60.6 + - - +
55A VAL* 4.2 12.5 - - + +
56A ALA* 3.0 29.3 + - - +
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Residues in contact with PHE 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PRO 5.0 0.4 + - - -
50A GLY 5.4 3.1 + - - +
51A VAL* 5.1 1.3 - - - -
52A ASN* 1.3 75.2 - - - +
54A LEU* 1.3 56.5 + - - +
56A ALA* 3.9 4.5 - - + +
57A ASP* 3.1 37.5 + - - +
143A ARG* 5.6 1.1 - - - +
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A VAL* 3.2 17.2 + - + +
53A PHE* 1.3 77.1 - - - +
55A VAL* 1.3 60.4 + - - +
57A ASP* 3.3 6.0 + - - +
58A ALA* 2.8 31.5 + - - +
140A MET* 3.4 28.5 - - + -
143A ARG* 3.4 44.8 - - + +
144A TRP* 3.6 33.9 - - + -
147A VAL* 3.6 31.0 - - + -
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Residues in contact with VAL 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TYR* 4.2 10.1 - - + +
43A VAL* 4.0 11.9 - - + -
44A SER* 3.7 34.3 - - - +
47A SER* 4.5 2.2 - - - +
51A VAL* 3.0 26.3 + - + +
52A ASN* 3.9 11.0 - - + +
53A PHE 3.5 0.2 - - - -
54A LEU* 1.3 75.9 - - - +
56A ALA* 1.3 64.9 + - - +
58A ALA* 3.2 4.1 + - - +
59A LEU* 2.9 40.3 + - + +
144A TRP* 3.7 25.4 - - + -
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASN 3.0 20.0 + - - +
53A PHE* 3.9 6.5 - - + +
55A VAL* 1.3 78.7 - - - +
57A ASP* 1.3 62.9 + - - +
59A LEU* 3.4 6.7 + - - +
60A LYS* 3.0 26.4 + - - +
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Residues in contact with ASP 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PHE* 3.1 25.8 + - - +
54A LEU* 3.4 7.2 - - - +
56A ALA* 1.3 77.6 - - - +
58A ALA* 1.3 62.1 + - - +
60A LYS* 3.5 16.6 + - - +
61A GLN* 3.1 25.1 + - - +
140A MET* 5.2 2.2 - - - -
143A ARG* 3.6 32.5 + - - +
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Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TYR* 3.4 39.0 - - + +
54A LEU 2.8 19.5 + - - +
55A VAL 3.7 3.4 - - - +
57A ASP* 1.3 73.5 - - - +
59A LEU* 1.3 58.2 + - - +
61A GLN* 3.4 4.0 + - - +
62A HIS* 2.8 39.3 + - + -
107A GLU* 4.4 0.2 - - - +
140A MET* 3.9 20.8 - - + -
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Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 3.7 26.0 - - + +
40A TYR* 3.7 33.9 - - + +
41A GLY* 4.8 2.9 - - - +
44A SER* 5.3 2.9 - - - -
55A VAL* 2.9 34.6 + - + +
56A ALA* 3.8 6.1 - - - +
58A ALA* 1.3 76.6 - - - +
60A LYS* 1.3 57.0 + - - +
62A HIS* 3.8 4.1 - - - +
63A ARG* 2.9 72.3 + - - +
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Residues in contact with LYS 60 (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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56A ALA 3.0 17.4 + - - +
57A ASP* 4.0 14.7 + - - +
58A ALA 3.4 0.2 - - - -
59A LEU* 1.3 74.4 - - - +
61A GLN* 1.3 61.2 + - - +
63A ARG* 4.1 7.4 - - - +
64A HIS* 3.0 37.0 + - + +
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Residues in contact with GLN 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ASP 3.1 18.0 + - - +
58A ALA 3.6 3.4 - - - +
60A LYS* 1.3 80.2 - - - +
62A HIS* 1.3 64.7 + - - +
64A HIS* 3.9 3.9 - - - +
65A ARG* 3.0 56.8 + - - +
107A GLU* 4.8 0.3 - - - +
136A GLU* 3.7 32.0 + - - +
140A MET* 3.4 32.3 - - - +
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Residues in contact with HIS 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLU* 2.6 28.4 + - - +
36A THR* 3.6 19.6 - - + +
37A ILE* 3.6 20.2 - - + +
40A TYR* 3.6 16.1 - + - -
58A ALA* 2.8 38.3 + - - +
59A LEU* 4.0 2.5 - - - +
61A GLN* 1.3 77.6 + - - +
63A ARG* 1.3 61.1 + - - +
65A ARG* 3.4 22.1 + - - +
66A ARG* 2.9 31.4 + - - +
106A MET 6.0 0.2 - - - -
107A GLU* 2.7 36.6 + - - -
110A GLY* 6.4 2.0 - - - -
137A SER* 5.1 0.9 - - - -
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Residues in contact with ARG 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 4.1 26.2 - - + +
59A LEU* 2.9 58.9 + - + +
60A LYS* 4.1 5.8 - - - +
62A HIS* 1.3 72.2 - - - +
64A HIS* 1.3 58.1 + - - +
66A ARG* 3.5 29.2 - - - +
67A ASP* 3.0 37.7 + - - +
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Residues in contact with HIS 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LYS* 3.0 22.5 + - + +
61A GLN* 3.9 4.7 - - - +
63A ARG* 1.3 74.7 - - - +
65A ARG* 1.3 64.1 + - - +
67A ASP* 3.4 8.4 + - + +
68A ASP* 2.9 50.8 + - - +
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Residues in contact with ARG 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLU* 2.9 31.7 + - - +
61A GLN* 3.0 33.5 + - - +
62A HIS* 3.4 28.3 + - - +
64A HIS* 1.3 78.5 + - - +
66A ARG* 1.3 56.6 + - - +
68A ASP* 3.2 9.4 + - - +
69A VAL* 3.0 32.8 + - + +
114A TRP* 3.7 23.7 - - + +
129A PHE* 4.1 13.9 - - + -
133A ALA* 3.5 23.0 + - + +
136A GLU* 3.0 44.0 + - - +
137A SER* 3.6 13.9 + - - +
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Residues in contact with ARG 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 3.9 14.2 - - + +
33A GLU* 4.4 11.6 - - + +
34A HIS* 3.5 38.4 - - + +
37A ILE* 3.7 32.2 - - + +
62A HIS 2.9 20.5 + - - +
63A ARG* 3.5 31.6 + - - +
65A ARG* 1.3 73.7 - - - +
67A ASP* 1.3 85.9 + - - +
69A VAL* 3.3 5.4 + - - +
70A ILE* 3.0 35.8 + - + +
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Residues in contact with ASP 67 (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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63A ARG* 3.0 17.8 + - - +
64A HIS* 3.7 7.7 - - + +
66A ARG* 1.3 103.2 + - - +
68A ASP* 1.3 64.6 + - - +
70A ILE* 3.3 13.6 + - - +
71A VAL* 3.2 26.3 + - + +
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Residues in contact with ASP 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A HIS* 2.9 44.6 + - - +
65A ARG* 3.3 10.8 - - - +
67A ASP* 1.3 76.8 - - - +
69A VAL* 1.3 56.5 + - - +
71A VAL* 3.4 10.0 + - - +
72A MET* 3.1 31.3 + - - +
129A PHE* 3.6 27.9 - - + -
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Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 3.7 26.7 - - + +
30A LEU* 3.7 33.0 - - + +
33A GLU* 5.5 0.9 - - + -
65A ARG 3.0 16.0 + - - +
66A ARG* 3.6 7.4 - - - +
68A ASP* 1.3 72.6 - - - +
70A ILE* 1.3 65.9 + - - +
72A MET* 3.3 7.3 + - - +
73A LEU* 3.0 27.8 + - + +
114A TRP* 3.5 32.8 - - + -
129A PHE* 3.8 11.2 - - + -
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Residues in contact with ILE 70 (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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30A LEU* 4.1 8.7 - - + -
34A HIS* 4.5 10.5 - - + +
66A ARG* 3.0 38.6 + - + +
67A ASP* 3.3 15.5 + - - +
69A VAL* 1.3 75.4 - - - +
71A VAL* 1.3 63.8 + - + +
73A LEU* 3.6 2.4 + - - +
74A SER* 3.1 29.3 + - - +
80A ALA* 4.1 28.1 - - + +
81A PRO 5.5 0.4 - - - +
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Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASP 3.2 13.6 + - - +
68A ASP* 3.5 11.4 - - - +
70A ILE* 1.3 79.0 - - + +
72A MET* 1.3 65.3 + - + +
74A SER* 3.1 9.8 + - - -
75A ALA* 3.0 22.6 + - + +
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Residues in contact with MET 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 4.0 23.8 - - + -
68A ASP 3.1 19.1 + - - +
69A VAL* 3.3 12.7 + - - +
71A VAL* 1.3 77.7 - - + +
73A LEU* 1.3 62.5 + - - +
75A ALA* 3.2 18.3 + - - +
76A ARG* 3.2 21.4 + - - +
117A VAL* 5.9 1.6 - - + -
126A ASP* 3.5 39.5 - - + +
129A PHE* 3.8 47.6 - - + -
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASN* 4.6 2.7 - - - +
26A LEU* 3.4 29.2 - - + -
27A CYS* 3.9 22.9 - - - +
30A LEU* 3.7 32.5 - - + -
69A VAL* 3.0 25.9 + - + +
70A ILE 4.0 3.4 - - - +
72A MET* 1.3 75.8 - - - +
74A SER* 1.3 60.0 + - - +
76A ARG* 3.1 19.8 + - - +
78A VAL* 2.8 47.2 + - + +
80A ALA* 4.0 14.6 - - + -
81A PRO* 4.1 7.6 - - + -
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Residues in contact with SER 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 3.1 18.3 + - - +
71A VAL* 3.1 12.8 + - - -
73A LEU* 1.3 71.9 - - - +
75A ALA* 1.3 65.3 + - - +
76A ARG 3.1 1.6 - - - -
77A GLY* 3.0 14.4 + - - +
78A VAL 3.5 9.7 + - - +
79A THR* 5.6 0.9 - - - -
80A ALA* 5.5 2.1 + - - +
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Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 3.0 14.9 + - + +
72A MET* 3.2 13.2 + - - +
74A SER* 1.3 75.3 - - - +
76A ARG* 1.3 58.9 + - + +
77A GLY 3.7 0.2 + - - -
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Residues in contact with ARG 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ASP* 2.8 50.2 + - - -
23A ASN* 2.9 32.7 + - - +
26A LEU* 3.9 29.3 - - - +
72A MET* 3.3 15.7 + - - +
73A LEU* 3.1 13.6 + - - +
74A SER 3.1 1.2 - - - -
75A ALA* 1.3 79.5 - - + +
77A GLY* 1.3 58.5 + - - +
78A VAL* 4.2 10.7 - - + +
117A VAL* 5.6 1.4 - - - +
121A ALA* 5.0 0.4 - - - +
126A ASP* 2.7 35.7 + - - +
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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
------------------------------------------------------------
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