Contacts of the helix formed by residues 63 - 87 (chain A) in PDB entry 1COJ
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 GLU 63 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A PHE* 3.4 54.2 - - + +
52A ALA* 4.4 0.9 - - - -
53A ASP 5.2 0.7 - - - +
56A LYS* 5.4 8.3 - - - +
61A TYR* 2.6 35.3 + - - +
62A SER* 1.3 72.9 - - - +
64A TYR* 1.3 64.8 + - - +
66A GLU* 3.4 4.7 + - - +
67A LEU* 3.1 29.8 + - - +
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Residues in contact with TYR 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 4.2 8.1 - - + -
52A ALA* 4.4 13.1 - - + +
53A ASP 4.2 18.1 + - - +
54A ARG* 3.8 51.3 - - + +
57A ALA* 4.1 23.8 - - + -
62A SER* 3.1 5.1 - - - +
63A GLU* 1.3 79.4 - - - +
65A ARG* 1.3 65.8 + - - +
67A LEU* 3.4 3.3 + - - +
68A LYS* 3.1 63.8 + - + +
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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
----------------------------------------------------------
58A ASN 3.6 11.4 - - - +
59A GLN* 3.5 35.2 + - - +
60A ASN 5.0 2.4 + - - -
61A TYR 4.6 1.3 - - - +
62A SER* 3.1 22.4 + - - +
64A TYR* 1.3 84.0 - - + +
66A GLU* 1.3 78.8 + - - +
68A LYS* 3.1 7.2 + - - +
69A VAL* 2.9 50.6 + - + +
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ASN 4.8 0.5 - - - +
61A TYR* 3.5 39.0 - - + +
62A SER 3.1 21.5 + - - +
63A GLU* 4.0 4.7 - - - +
65A ARG* 1.3 103.5 + - - +
67A LEU* 1.3 62.5 + - + +
69A VAL* 3.3 8.7 + - - +
70A GLU* 3.1 31.9 + - + +
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE* 3.6 33.4 - - + +
45A LYS* 3.9 29.4 - - + -
46A LEU* 3.7 17.9 - - + -
51A PHE* 3.7 26.0 - - + -
52A ALA* 3.8 25.6 - - + -
63A GLU* 3.1 22.4 + - - +
64A TYR 3.7 1.1 - - - +
66A GLU* 1.3 75.6 - - + +
68A LYS* 1.3 58.8 + - - +
70A GLU* 3.5 2.7 + - - +
71A GLU* 2.9 29.3 + - - +
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Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 4.0 16.6 - - + +
64A TYR* 3.1 52.0 + - + +
65A ARG* 3.1 9.5 + - - +
67A LEU* 1.3 73.5 - - - +
69A VAL* 1.3 67.6 + - + +
71A GLU* 2.9 42.2 + - - +
72A THR* 3.5 13.5 + - - +
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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
----------------------------------------------------------
65A ARG* 2.9 52.6 + - + +
66A GLU* 3.6 12.8 - - - +
68A LYS* 1.3 76.4 - - + +
70A GLU* 1.3 75.8 + - + +
72A THR* 2.7 28.0 + - - +
73A PHE 3.6 2.1 + - - -
149A ASN* 3.8 8.0 - - - +
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Residues in contact with GLU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE* 3.7 17.3 - - + -
66A GLU* 3.1 18.5 + - + +
67A LEU* 4.3 0.7 - - - +
69A VAL* 1.3 85.7 - - + +
71A GLU* 1.3 64.4 + - - +
72A THR 3.2 0.2 - - - -
73A PHE* 3.2 21.7 + - - +
74A ASN* 2.9 34.8 + - - +
149A ASN* 5.1 0.3 - - - +
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Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 4.2 14.1 + - + -
42A ILE* 4.0 14.1 - - + -
43A GLN* 2.8 32.1 + - - +
46A LEU* 3.8 11.7 - - - +
67A LEU 2.9 19.4 + - - +
68A LYS* 2.9 41.5 + - - +
69A VAL 3.2 0.4 - - - -
70A GLU* 1.3 76.2 - - - +
72A THR* 1.3 61.1 + - + +
74A ASN* 5.1 0.9 - - - -
75A TYR* 2.9 35.9 + - + +
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Residues in contact with THR 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LYS* 3.7 12.8 - - - +
69A VAL* 2.7 19.5 + - - +
71A GLU* 1.3 78.6 - - + +
73A PHE* 1.3 63.7 + - - +
75A TYR* 4.7 2.7 - - - -
76A MET* 3.1 33.8 + - - +
149A ASN* 3.1 21.2 + - - +
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Residues in contact with PHE 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TYR* 3.9 17.7 - + - -
69A VAL 3.6 0.2 + - - -
70A GLU* 3.2 27.0 + - - +
72A THR* 1.3 83.0 + - - +
74A ASN* 1.3 72.6 + - - +
77A GLY* 3.0 22.3 + - - -
147A ALA* 4.7 3.8 - - + -
148A HIS* 3.5 40.6 - + + +
149A ASN* 3.4 34.1 - - - +
165A TYR* 3.8 15.3 - + - -
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Residues in contact with ASN 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TYR* 3.6 38.9 - - - +
38A LYS* 3.4 28.5 - - - +
39A TYR* 4.1 13.2 - - - +
42A ILE* 3.6 12.7 - - + +
70A GLU* 2.9 27.9 + - - +
71A GLU 4.3 0.9 - - - +
73A PHE* 1.3 87.0 - - - +
75A TYR* 1.3 60.7 + - - +
77A GLY* 3.1 2.1 + - - -
78A VAL* 2.9 33.4 + - - +
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Residues in contact with TYR 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A HIS* 5.6 3.5 + + - -
5A LEU* 4.0 24.9 - - + -
39A TYR* 3.5 38.2 - + + -
71A GLU* 2.9 22.1 + - + +
72A THR* 4.4 2.9 - - - +
74A ASN* 1.3 76.0 - - - +
76A MET* 1.3 75.6 + - + +
78A VAL* 3.2 5.8 + - + +
79A VAL* 3.0 49.1 + - + +
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Residues in contact with MET 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A THR* 3.1 25.1 + - - +
75A TYR* 1.3 101.2 - - + +
77A GLY* 1.3 60.8 + - - +
79A VAL* 4.2 17.3 - - + -
80A LEU* 2.9 50.7 + - + +
148A HIS* 3.3 30.1 - - + +
149A ASN* 4.8 3.1 - - + -
152A ASN* 3.9 17.9 - - - +
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Residues in contact with GLY 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TYR* 4.0 15.4 - - - -
73A PHE 3.0 17.2 + - - -
74A ASN 3.1 4.2 + - - -
76A MET* 1.3 77.6 - - - +
78A VAL* 1.3 61.2 + - - +
80A LEU* 5.1 0.2 - - - -
81A HIS* 2.6 29.9 + - - +
148A HIS* 3.9 22.6 - - - +
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Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 4.0 27.8 - - + -
32A TYR* 4.0 6.9 - - + -
35A TYR* 3.8 6.1 - - + +
36A VAL* 3.7 43.1 - - + +
39A TYR* 4.7 2.2 - - + -
74A ASN 2.9 20.0 + - - +
75A TYR* 3.4 8.5 - - - +
77A GLY* 1.3 75.2 - - - +
79A VAL* 1.3 68.8 + - + +
81A HIS* 3.2 4.3 + - - +
82A GLU* 3.0 49.0 + - - +
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Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TYR* 3.0 52.7 + - + +
76A MET* 4.1 14.6 - - + +
78A VAL* 1.3 78.8 - - + +
80A LEU* 1.3 70.0 + - + +
82A GLU* 3.2 11.2 + - - +
83A LEU* 3.0 40.8 + - + +
158A PRO* 6.1 0.7 - - + -
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A MET* 2.9 39.0 + - + +
79A VAL* 1.3 84.0 - - + +
81A HIS* 1.3 57.2 + - - +
83A LEU* 3.3 15.9 + - + +
84A TYR* 3.0 27.9 + - - +
128A TRP* 3.6 48.2 - - + +
130A ILE* 4.6 14.1 - - + -
145A LEU* 4.0 14.4 - - + -
148A HIS* 3.9 20.2 - - - +
152A ASN* 4.7 0.9 - - - +
158A PRO* 5.4 4.3 - - + -
161A VAL* 4.0 8.6 - - + +
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Residues in contact with HIS 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A HIS* 3.0 21.1 + + - -
31A HIS* 5.1 0.4 - - - +
32A TYR* 3.8 23.6 - - + -
35A TYR* 3.4 28.5 - + - -
77A GLY 2.6 25.4 + - - +
78A VAL 3.2 4.7 + - - +
80A LEU* 1.3 74.8 - - - +
82A GLU* 1.3 60.1 + - - +
84A TYR* 3.2 5.7 + + - +
85A PHE* 2.9 50.0 + + + -
128A TRP* 3.6 19.6 - + - -
148A HIS* 3.8 6.1 - + - -
163A ASP* 3.4 3.2 + - - -
167A HIS* 3.9 0.2 + - - -
213A FE 2.2 31.2 - - - -
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Residues in contact with GLU 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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6A GLU 4.6 4.0 - - - +
8A LYS* 3.6 37.1 + - - +
11A LEU* 3.8 19.9 - - + +
32A TYR* 2.8 32.7 + - + +
78A VAL* 3.0 36.3 + - - +
79A VAL* 3.6 11.5 - - - +
81A HIS* 1.3 75.7 - - - +
83A LEU* 1.3 59.4 + - + +
85A PHE* 5.1 2.0 - - - -
86A GLY* 3.0 26.9 + - - -
196A ARG* 4.6 0.3 + - - -
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL* 3.0 39.3 + - + +
80A LEU* 3.7 10.3 - - + +
82A GLU* 1.3 78.3 - - + +
84A TYR* 1.3 62.3 + - - +
87A MET* 3.2 13.7 + - - +
158A PRO* 3.9 37.0 - - + +
161A VAL* 4.1 15.3 - - + -
196A ARG* 2.8 48.6 + - - +
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Residues in contact with TYR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 4.8 5.7 - - - +
24A ILE* 5.7 3.6 - - + +
27A HIS* 3.7 27.0 + + - -
80A LEU 3.0 18.3 + - - +
81A HIS* 3.4 7.4 - + - +
83A LEU* 1.3 75.1 - - - +
85A PHE* 1.3 93.4 + + - +
87A MET* 3.3 19.4 + - - +
88A LEU* 3.5 23.4 - - + +
128A TRP* 4.1 6.5 - - + -
161A VAL* 3.4 24.4 - - + +
163A ASP* 3.7 21.3 - - + -
168A ALA* 4.4 3.6 + - - +
180A TYR* 2.7 38.4 + - - -
184A PHE* 3.6 24.0 - + - -
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Residues in contact with PHE 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.5 29.4 - - + +
13A PRO* 3.7 26.3 - - + +
24A ILE* 4.4 12.6 - - + -
27A HIS* 3.8 31.9 - + + -
28A PHE* 3.5 39.7 - + + -
32A TYR* 4.0 14.6 - + + -
81A HIS* 2.9 44.6 + + + +
82A GLU* 4.6 1.8 - - - +
84A TYR* 1.3 94.1 - + - +
86A GLY* 1.3 63.3 + - - +
87A MET 3.1 1.6 + - - -
88A LEU* 3.1 20.8 + - + +
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Residues in contact with GLY 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.0 21.0 - - - +
82A GLU 3.0 20.8 + - - -
83A LEU 4.3 0.7 - - - -
85A PHE* 1.3 77.0 - - - +
87A MET* 1.3 56.9 + - - +
88A LEU 3.4 2.5 + - - +
189A ASN* 5.0 2.4 + - - -
192A VAL* 3.6 19.3 - - - +
196A ARG* 4.3 7.4 - - - -
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Residues in contact with MET 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU 3.2 16.0 + - - +
84A TYR* 3.3 10.1 - - - +
85A PHE 3.1 0.2 - - - -
86A GLY* 1.3 77.4 - - - +
88A LEU* 1.3 59.6 + - + +
160A ILE* 3.9 16.2 - - + -
161A VAL 3.8 21.5 - - - +
184A PHE* 3.8 26.9 - - + -
187A ASN 3.6 1.4 - - - +
188A ILE* 3.6 22.6 - - + -
189A ASN* 2.9 29.8 + - - -
192A VAL* 4.2 10.3 - - + -
193A VAL* 3.8 24.2 - - + -
196A ARG* 3.5 28.3 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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