Contacts of the helix formed by residues 81 - 102 (chain B) in PDB entry 2CVD
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 THR 81 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B GLY 3.4 0.4 - - - -
80B ASN* 1.3 81.9 - - + +
82B GLU* 1.3 59.9 + - - +
83B MET* 3.7 8.6 + - - +
84B GLU* 2.6 39.6 + - - +
85B GLN* 2.8 35.9 + - - +
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Residues in contact with GLU 82 (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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81B THR* 1.3 73.0 - - - +
83B MET* 1.3 58.6 + - - +
85B GLN* 3.2 18.4 + - - +
86B CYS 3.0 22.2 + - - -
70C TYR* 3.6 30.1 + - + +
73C LYS* 4.4 25.9 + - + +
74C ASN* 2.5 34.1 + - - -
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Residues in contact with MET 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B THR* 3.1 8.8 + - - +
82B GLU* 1.3 80.7 - - + +
84B GLU* 1.3 63.1 + - + +
86B CYS* 3.0 13.9 + - - +
87B HIS* 3.0 26.9 + - + +
56C VAL* 4.3 16.4 - - + +
59C LEU* 4.0 34.8 - - + -
61C LEU* 3.7 33.6 - - + +
70C TYR* 3.4 37.0 - - + +
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Residues in contact with GLU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLY* 4.4 0.7 - - - -
80B ASN* 3.7 22.4 + - - +
81B THR* 2.6 49.7 + - - +
83B MET* 1.3 75.7 - - + +
85B GLN* 1.3 57.6 + - - +
87B HIS* 3.1 17.0 + - + +
88B VAL* 2.9 32.8 + - - +
142B ILE* 3.8 15.8 - - + +
143B GLY* 3.5 25.6 + - - +
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Residues in contact with GLN 85 (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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78B ALA* 3.3 34.0 - - + +
79B GLY 3.1 20.3 + - - +
80B ASN 4.6 1.0 - - - -
81B THR* 2.8 23.8 + - - +
82B GLU* 3.4 15.3 - - - +
84B GLU* 1.3 76.9 - - - +
86B CYS* 1.3 56.9 + - - +
88B VAL* 3.4 3.0 + - - +
89B ASP* 3.0 34.4 + - - +
73C LYS* 2.6 40.2 + - - +
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Residues in contact with CYS 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLU 3.0 11.0 + - - +
83B MET 3.0 10.5 + - - +
85B GLN* 1.3 75.5 - - - +
87B HIS* 1.3 61.3 + - - +
89B ASP* 3.2 8.3 + - - +
90B ALA* 2.8 31.2 + - - +
61C LEU* 3.9 35.7 - - + -
62C HIS 4.8 2.2 - - - -
66C ALA* 3.6 30.7 - - - +
67C ILE* 4.0 4.5 - - - -
70C TYR* 3.9 17.7 - - + -
73C LYS* 5.2 0.6 - - - +
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Residues in contact with HIS 87 (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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83B MET* 3.0 26.2 + - + +
84B GLU* 3.1 22.9 + - + +
86B CYS* 1.3 76.0 - - - +
88B VAL* 1.3 62.8 + - - +
90B ALA* 3.2 5.3 + - - +
91B ILE* 3.0 29.5 + - - +
134B TYR* 4.0 14.3 + - - +
142B ILE* 3.7 20.0 - - + -
59C LEU* 5.8 5.8 - - + +
60C THR 3.9 13.4 + - - -
61C LEU* 3.4 30.2 - - + +
62C HIS* 5.6 6.2 - - - -
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Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ALA 3.5 17.5 - - - +
79B GLY* 4.4 0.4 - - - -
84B GLU 2.9 19.0 + - - +
85B GLN 3.6 7.2 - - - +
87B HIS* 1.3 77.2 - - - +
89B ASP* 1.3 64.3 + - - +
91B ILE* 3.3 2.3 + - - +
92B VAL* 3.1 27.4 + - + +
142B ILE* 4.0 17.3 - - + -
147B THR* 3.9 26.0 - - + +
148B TRP* 3.4 40.6 - - + +
149B ALA* 3.9 14.1 - - + +
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Residues in contact with ASP 89 (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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69B ARG* 2.9 37.3 + - - +
85B GLN* 3.0 20.1 + - - +
86B CYS* 3.5 9.3 - - - +
88B VAL* 1.3 78.3 - - - +
90B ALA* 1.3 58.6 + - - +
92B VAL* 3.4 5.3 + - - +
93B ASP* 2.9 33.0 + - - +
148B TRP* 3.8 10.0 + - - -
66C ALA* 3.7 16.1 - - + +
69C ARG* 3.0 31.9 + - - +
73C LYS* 5.0 4.9 + - - -
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Residues in contact with ALA 90 (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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86B CYS* 2.8 18.1 + - - +
87B HIS* 3.6 7.2 - - - +
89B ASP* 1.3 74.3 - - - +
91B ILE* 1.3 60.5 + - - +
93B ASP 3.3 0.3 + - - -
94B THR* 2.9 32.6 + - - -
62C HIS* 3.4 48.7 - - + +
63C GLN* 3.4 13.9 - - + +
66C ALA* 3.7 1.3 - - + +
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Residues in contact with ILE 91 (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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87B HIS 3.0 20.9 + - - +
88B VAL 3.9 3.4 - - - +
90B ALA* 1.3 71.9 - - - +
92B VAL* 1.3 66.6 + - - +
94B THR* 3.2 4.6 + - - -
95B LEU* 3.0 41.2 + - + +
131B LEU* 4.7 8.7 - - + -
134B TYR* 3.5 37.2 - - + +
141B LEU* 4.1 21.1 - - + -
142B ILE* 4.0 8.3 - - + -
149B ALA* 4.3 10.8 - - + -
48C PHE* 3.6 32.1 - - + -
62C HIS* 4.4 4.0 - - + +
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LEU* 3.6 37.7 - - + -
69B ARG* 5.3 1.6 - - - +
88B VAL 3.1 21.3 + - - +
89B ASP* 3.6 5.2 - - - +
91B ILE* 1.3 77.9 - - - +
93B ASP* 1.3 59.5 + - - +
95B LEU* 3.3 4.0 + - - +
96B ASP* 2.8 26.7 + - - +
148B TRP* 3.8 33.0 - - + -
149B ALA* 3.9 24.9 - - + -
152B TYR* 3.8 17.7 - - + -
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Residues in contact with ASP 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LEU* 4.0 16.8 - - - +
69B ARG* 4.9 8.2 + - - -
89B ASP* 2.9 19.3 + - - +
90B ALA 3.9 0.4 - - - +
92B VAL* 1.3 75.6 - - - +
94B THR* 1.3 62.1 + - - +
96B ASP* 4.3 3.5 - - - +
97B ASP* 2.8 37.7 + - - +
4002B MG 4.2 13.9 - - - -
63C GLN* 3.6 27.6 - - + +
65C LEU* 4.2 23.6 - - - +
66C ALA* 4.5 7.1 + - - +
69C ARG* 5.4 4.2 + - - -
93C ASP* 5.1 7.3 - - - +
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Residues in contact with THR 94 (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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90B ALA 2.9 19.3 + - - -
91B ILE* 3.2 8.5 + - - -
93B ASP* 1.3 77.1 - - - +
95B LEU* 1.3 64.1 + - - +
97B ASP* 3.5 4.9 + - - +
98B PHE* 3.4 18.2 + - - +
127B LEU* 3.9 19.6 - - + +
131B LEU* 5.2 3.4 - - + -
48C PHE* 3.9 31.6 - - + +
62C HIS* 3.3 17.5 + - - -
63C GLN* 3.2 16.7 + - - +
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Residues in contact with LEU 95 (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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91B ILE* 3.0 34.5 + - + +
92B VAL* 3.6 4.5 - - - +
94B THR* 1.3 77.5 - - - +
96B ASP* 1.3 62.4 + - - +
98B PHE* 3.2 8.0 + - - +
99B MET* 3.1 26.7 + - - +
127B LEU* 4.8 9.2 - - + -
128B MET* 5.9 0.2 - - + -
131B LEU* 3.8 33.2 - - + -
149B ALA 4.4 1.1 - - - +
152B TYR* 4.0 21.8 - - + +
153B TRP* 3.7 45.3 - - + +
156B CYS* 4.2 11.0 - - + -
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Residues in contact with ASP 96 (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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14B ARG* 2.9 25.4 + - - -
65B LEU* 3.6 24.5 - - + +
92B VAL 2.8 21.6 + - - +
93B ASP* 4.0 5.8 - - - +
95B LEU* 1.3 70.4 - - - +
97B ASP* 1.3 59.5 + - - +
99B MET* 4.4 2.5 - - - +
100B SER* 2.7 48.9 + - - -
152B TYR* 2.6 27.3 + - + -
2002B GSH 4.7 6.2 + - - +
2401B HQL 4.1 1.7 - - - -
4002B MG 4.0 12.1 - - - -
97C ASP* 5.1 1.2 - - - +
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Residues in contact with ASP 97 (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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93B ASP* 2.8 25.5 + - - +
94B THR* 3.6 5.8 - - - +
96B ASP* 1.3 72.6 - - - +
98B PHE* 1.3 63.2 + - - +
100B SER* 3.5 6.3 + - - -
101B CYS* 3.2 27.3 + - - -
4002B MG 4.1 14.4 - - - -
63C GLN* 3.1 15.1 + - - -
96C ASP* 5.0 2.3 - - - +
100C SER* 5.3 4.3 + - - -
2003C GSH 2.7 36.4 + - - +
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Residues in contact with PHE 98 (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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94B THR 3.4 4.9 + - - +
95B LEU 3.2 8.4 + - - +
96B ASP 3.2 0.4 - - - -
97B ASP* 1.3 77.5 - - - +
99B MET* 1.3 70.8 + - - +
101B CYS* 3.0 25.1 + - + +
102B PHE* 3.4 31.5 - + - -
119B LEU* 3.6 31.4 - - + -
123B ASN* 3.4 29.8 - - + -
124B ALA* 3.6 20.4 - - + -
127B LEU* 3.6 31.6 - - + -
160B LEU* 4.0 26.9 - - + -
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Residues in contact with MET 99 (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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14B ARG* 4.6 1.9 + - - -
95B LEU 3.1 17.2 + - - +
96B ASP* 3.9 5.6 - - - +
98B PHE* 1.3 78.8 - - - +
100B SER* 1.3 60.8 + - - +
101B CYS 3.2 1.2 + - - -
102B PHE* 3.4 8.5 + - - +
104B TRP* 5.1 0.7 + - - -
156B CYS* 3.6 42.4 - - - +
159B THR* 4.3 4.0 - - + -
160B LEU* 4.0 29.4 - - + -
2401B HQL 3.2 93.4 - - + -
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Residues in contact with SER 100 (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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14B ARG* 2.9 25.5 + - - +
96B ASP* 2.7 33.1 + - - -
97B ASP* 3.8 7.0 - - - -
99B MET* 1.3 73.6 - - - +
101B CYS* 1.3 63.0 + - - +
102B PHE 3.3 7.1 + - - +
2002B GSH 5.5 0.5 + - - -
97C ASP* 5.2 6.0 + - - -
100C SER* 6.3 2.7 - - - -
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Residues in contact with CYS 101 (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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97B ASP* 3.2 23.8 + - - -
98B PHE* 3.0 18.7 + - - +
100B SER* 1.3 76.5 - - - +
102B PHE* 1.3 63.7 + - - +
103B PRO* 3.2 9.9 - - - +
115B MET* 4.4 5.9 - - - +
119B LEU* 3.8 25.9 - - + +
123B ASN* 6.3 0.4 - - - -
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Residues in contact with PHE 102 (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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98B PHE* 3.4 45.5 - + - -
99B MET* 3.5 2.1 - - - +
100B SER 3.3 7.4 - - - +
101B CYS* 1.3 76.1 - - - +
103B PRO* 1.3 63.8 - - + +
104B TRP* 3.0 25.8 + - - +
116B PHE* 3.7 31.9 - + + -
119B LEU* 3.8 29.8 - - + -
120B LEU* 3.9 35.7 - - + -
160B LEU* 4.1 6.1 - - + -
163B PHE* 6.1 1.1 - + - -
2401B HQL 3.4 37.7 - + + -
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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
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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