Contacts of the helix formed by residues 67 - 89 (chain A) in PDB entry 3QOW
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 SER 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A TRP* 3.5 2.2 - - - -
64A ASP* 2.8 26.0 + - - +
66A LYS* 1.3 77.9 - - - +
68A PHE* 1.3 59.0 + - - +
69A GLU* 3.6 9.4 + - - +
70A SER* 3.4 24.0 + - - -
71A MET* 2.9 26.9 + - - +
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Residues in contact with PHE 68 (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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5A LEU* 3.7 37.7 - - + -
6A GLU 3.7 27.1 - - - -
7A LEU* 4.3 7.2 - - + -
22A TRP* 3.3 57.4 - + + +
67A SER* 1.3 68.4 + - - +
69A GLU* 1.3 65.4 + - + +
71A MET* 2.9 2.1 + - - +
72A GLN* 2.7 68.6 + - + +
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A SER* 3.4 9.5 + - - +
68A PHE* 1.3 85.1 - - + +
70A SER* 1.3 52.3 + - - +
72A GLN* 3.5 8.7 + - - +
73A ARG* 2.8 36.8 + - - +
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Residues in contact with SER 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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62A ASP 3.7 9.0 + - - -
63A TYR* 3.9 3.9 - - - -
64A ASP* 3.0 36.1 + - - +
67A SER* 3.3 20.3 + - - -
68A PHE 3.1 0.2 - - - -
69A GLU* 1.3 80.5 - - - +
71A MET* 1.3 57.6 + - - +
73A ARG* 3.4 10.9 - - - +
74A LEU* 3.1 26.3 + - - +
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Residues in contact with MET 71 (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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7A LEU* 3.7 18.4 - - + -
22A TRP* 3.9 16.8 - - + -
24A LEU* 4.2 5.8 - - + -
34A ALA* 3.7 34.8 - - + +
37A ILE* 4.0 20.0 - - + -
38A ILE* 4.1 16.4 - - + -
63A TYR* 4.9 4.5 - - - -
64A ASP 3.8 8.3 - - - +
65A THR* 3.8 22.2 - - - +
67A SER 2.9 20.1 + - - +
68A PHE 2.9 2.9 + - - +
70A SER* 1.3 75.9 - - - +
72A GLN* 1.3 59.0 + - - +
74A LEU* 3.3 11.0 + - + +
75A CYS* 3.0 33.4 + - - -
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Residues in contact with GLN 72 (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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6A GLU 4.8 4.8 + - - -
7A LEU* 3.5 19.3 - - + +
68A PHE* 2.7 50.3 + - + +
69A GLU* 3.7 8.7 - - - +
71A MET* 1.3 72.0 - - - +
73A ARG* 1.3 57.4 + - - +
75A CYS* 3.4 2.6 + - - +
76A ASP* 3.0 51.1 + - - +
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Residues in contact with ARG 73 (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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69A GLU 2.8 22.6 + - - +
70A SER* 3.4 11.4 - - - +
71A MET 3.2 0.2 - - - -
72A GLN* 1.3 74.8 - - - +
74A LEU* 1.3 60.8 + - - +
76A ASP* 3.3 11.0 + - + +
77A LYS* 3.1 58.3 + - - +
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Residues in contact with LEU 74 (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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37A ILE* 4.7 2.2 - - + -
38A ILE* 3.6 35.2 - - + -
41A ILE* 4.0 21.5 - - + -
55A MET* 4.5 18.7 - - + +
61A ILE* 6.1 3.1 - - + +
63A TYR* 4.8 14.4 - - + -
70A SER 3.1 16.4 + - - +
71A MET* 3.3 16.1 + - + +
73A ARG* 1.3 73.4 - - - +
75A CYS* 1.3 64.5 + - - +
77A LYS* 3.3 13.0 + - + +
78A TYR* 3.2 20.8 + - - +
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Residues in contact with CYS 75 (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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7A LEU* 3.9 27.4 - - + -
8A ARG 3.8 16.6 - - - +
9A LEU* 3.8 25.6 - - + -
37A ILE* 4.1 19.1 - - - -
41A ILE* 4.9 0.9 - - - -
71A MET 3.0 21.9 + - - +
72A GLN* 3.7 7.2 - - + +
74A LEU* 1.3 76.9 - - - +
76A ASP* 1.3 53.1 + - - +
78A TYR* 3.4 3.9 + - - +
79A ASN* 2.8 42.4 + - - +
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Residues in contact with ASP 76 (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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72A GLN* 3.0 40.7 + - - +
73A ARG* 3.3 11.9 - - - +
75A CYS* 1.3 75.2 - - - +
77A LYS* 1.3 60.0 + - - +
79A ASN* 3.2 8.5 + - - +
80A ARG* 2.8 53.7 + - + +
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Residues in contact with LYS 77 (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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55A MET* 3.9 17.8 - - + +
58A TYR* 3.9 27.7 + - - +
60A LEU 5.9 0.9 - - - +
61A ILE* 5.1 14.1 - - + -
73A ARG* 3.1 55.2 + - - +
74A LEU* 3.3 11.0 + - + +
76A ASP* 1.3 76.1 - - - +
78A TYR* 1.3 57.6 + - - +
80A ARG* 4.0 33.5 + - - +
81A ALA* 3.1 27.2 + - - +
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Residues in contact with TYR 78 (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 LEU* 3.8 21.5 - - + -
10A LYS 2.7 33.2 + - - -
12A PRO* 3.8 1.7 - - - +
40A THR* 6.1 0.2 - - + -
41A ILE* 3.8 39.3 - - + -
44A VAL* 3.6 18.7 - - + +
51A LEU* 3.8 20.2 - - + -
55A MET* 3.8 9.5 - - - -
74A LEU 3.2 12.8 + - - +
75A CYS 3.6 5.2 - - - +
77A LYS* 1.3 75.4 - - - +
79A ASN* 1.3 82.6 + - - +
81A ALA* 3.2 3.3 + - - +
82A ILE* 2.8 56.8 + - + +
208A TRP* 3.5 15.0 - + - -
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Residues in contact with ASN 79 (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 ARG* 2.8 30.5 + - - +
9A LEU* 3.6 0.3 - - - -
10A LYS* 2.8 47.9 + - + +
75A CYS* 2.8 24.2 + - - +
76A ASP* 3.8 10.8 + - - +
78A TYR* 1.3 84.0 - - - +
80A ARG* 1.3 58.3 + - + +
82A ILE* 3.4 6.1 + - - +
83A ASP* 3.0 34.2 + - - +
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Residues in contact with ARG 80 (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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58A TYR 5.8 0.4 + - - -
76A ASP* 2.8 45.5 + - + +
77A LYS* 4.0 38.4 + - - +
79A ASN* 1.3 69.6 - - + +
81A ALA* 1.3 66.4 + - - +
83A ASP* 3.1 12.5 + - - +
84A SER* 3.1 22.3 + - - -
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Residues in contact with ALA 81 (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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51A LEU* 3.4 25.1 - - + -
54A ALA* 3.9 20.9 - - + -
55A MET* 4.3 6.5 - - - -
77A LYS 3.1 19.4 + - - +
78A TYR 3.6 1.3 - - - +
80A ARG* 1.3 76.6 - - - +
82A ILE* 1.3 56.0 + - - +
84A SER* 3.0 22.1 + - - -
85A ILE* 3.0 19.9 + - - +
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Residues in contact with ILE 82 (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 LYS* 4.0 16.6 - - + +
11A SER 3.9 7.4 - - - +
12A PRO* 4.1 16.8 - - + -
44A VAL* 4.3 1.6 - - + -
48A ILE* 5.2 3.6 - - + -
51A LEU* 3.9 16.8 - - + -
78A TYR* 2.8 65.1 + - + +
79A ASN* 3.5 9.6 - - - +
80A ARG 3.3 0.2 - - - -
81A ALA* 1.3 69.1 - - - +
83A ASP* 1.3 66.8 + - - +
85A ILE* 3.4 7.5 + - + +
86A HIS* 3.0 48.3 + - + +
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Residues in contact with ASP 83 (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 LYS* 2.7 35.8 + - - +
79A ASN 3.0 19.6 + - - +
80A ARG* 3.1 15.2 + - - +
82A ILE* 1.3 75.0 - - - +
84A SER* 1.3 65.5 + - - +
86A HIS* 3.1 12.0 + - - +
87A GLN* 3.1 25.4 + - - +
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Residues in contact with SER 84 (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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80A ARG 3.1 8.2 + - - -
81A ALA* 3.0 19.9 + - - -
83A ASP* 1.3 80.6 - - - +
85A ILE* 1.3 59.8 + - - +
87A GLN* 3.2 10.1 + - - +
88A LEU* 2.9 29.4 + - - +
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Residues in contact with ILE 85 (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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48A ILE* 4.2 11.4 - - + -
50A ASP* 3.8 24.2 - - + +
51A LEU* 3.5 35.9 - - + +
54A ALA* 4.9 4.7 - - + -
81A ALA 3.0 28.9 + - - +
82A ILE* 3.9 9.2 - - + +
84A SER* 1.3 80.5 + - - +
86A HIS* 1.3 64.7 + - + +
88A LEU* 3.2 14.5 + - + +
89A TRP* 3.0 63.2 + - + +
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Residues in contact with HIS 86 (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 LYS* 5.9 1.3 - - + +
11A SER 3.5 12.1 - - - -
12A PRO* 2.8 23.0 + - - +
13A VAL* 4.6 0.6 - - - -
14A GLY* 4.3 12.8 + - - -
82A ILE* 3.0 39.9 + - + +
83A ASP* 3.1 13.1 + - - +
85A ILE* 1.3 80.7 - - + +
87A GLN* 1.3 60.4 + - + +
89A TRP* 3.6 31.1 + + - +
90A LYS* 3.4 30.3 + - - +
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Residues in contact with GLN 87 (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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83A ASP 3.1 15.0 + - - +
84A SER* 3.2 12.3 + - - +
86A HIS* 1.3 73.2 - - - +
88A LEU* 1.3 58.2 + - - +
90A LYS* 2.8 58.3 + - - +
91A GLY 3.3 5.0 + - - -
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Residues in contact with LEU 88 (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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50A ASP* 4.0 33.4 - - + +
84A SER 2.9 12.3 + - - +
85A ILE* 3.2 20.0 - - + +
87A GLN* 1.3 76.2 - - - +
89A TRP* 1.3 57.9 + - + +
91A GLY* 3.1 20.1 + - - -
92A THR 4.0 0.2 + - - -
93A THR* 3.4 37.6 + - + +
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Residues in contact with TRP 89 (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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12A PRO 3.4 27.8 - - - -
13A VAL* 5.0 5.2 - - + -
48A ILE* 3.8 22.4 - - + +
50A ASP* 4.9 3.8 + - - -
85A ILE* 3.0 41.1 + - + +
86A HIS* 3.7 23.3 - + - +
87A GLN 3.2 0.4 - - - -
88A LEU* 1.3 77.0 - - + +
90A LYS* 1.3 59.6 + - - +
91A GLY 3.3 5.4 + - - +
93A THR* 3.8 23.7 - - + +
94A GLN 3.7 13.6 + - - -
95A PRO* 3.5 35.7 - - + +
96A MET* 3.4 34.1 - - + +
98A LEU* 6.3 1.6 - - + -
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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