Contacts of the helix formed by residues 88 - 106 (chain B) in PDB entry 2VE7
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 ASP 88 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B PRO* 2.9 27.7 + - + +
87B ASN* 1.3 81.1 + - - +
89B LYS* 1.3 68.0 + - - +
90B ALA* 3.0 21.3 + - - +
91B PHE* 3.1 19.0 + - + +
92B ILE* 3.1 14.4 + - - +
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Residues in contact with LYS 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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139A SER* 3.4 36.0 + - - +
140A TYR 4.2 5.1 + - - -
141A GLU* 3.2 43.2 + - - +
87B ASN 3.8 4.4 + - - +
88B ASP* 1.3 73.3 + - - +
90B ALA* 1.3 52.6 + - - +
92B ILE* 3.2 7.4 + - - +
93B GLN* 2.7 43.8 + - + +
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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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88B ASP* 3.0 14.9 + - - +
89B LYS* 1.3 78.1 - - - +
91B PHE* 1.3 57.2 + - - +
93B GLN* 3.3 7.8 + - - +
94B GLN* 2.7 30.2 + - - +
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Residues in contact with PHE 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ARG* 3.8 37.2 - - + -
85B PRO* 3.6 46.4 - - + +
86B LEU* 4.2 11.2 - - + -
88B ASP* 3.1 8.9 + - + +
90B ALA* 1.3 75.4 - - - +
92B ILE* 1.3 68.4 + - + +
94B GLN* 3.2 23.9 + - - +
95B CYS* 2.9 56.8 + - - -
183B ALA* 5.1 0.7 - - + -
74D MET* 6.3 1.6 - - - -
75D TYR* 3.5 25.4 - + - -
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Residues in contact with ILE 92 (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 LEU* 3.3 30.7 - - + +
87B ASN 5.5 0.2 - - - -
88B ASP 3.1 11.4 + - - +
89B LYS* 3.8 8.5 - - - +
91B PHE* 1.3 91.9 - - + +
93B GLN* 1.3 60.5 + - + +
95B CYS* 3.3 5.9 + - - +
96B ILE* 3.0 42.5 + - + +
178B TRP* 5.0 4.9 - - + -
179B PRO* 3.6 44.0 - - + +
182B VAL* 4.1 14.6 - - + -
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Residues in contact with GLN 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A SER* 5.2 4.3 + - - +
89B LYS* 2.7 24.4 + - + +
90B ALA* 3.6 8.3 - - - +
92B ILE* 1.3 76.4 - - + +
94B GLN* 1.3 63.7 + - - +
96B ILE* 3.4 9.4 + - - +
97B ARG* 3.0 29.2 + - - +
114B MET* 3.4 33.1 - - - +
118B GLN* 3.1 33.3 + - - +
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Residues in contact with GLN 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 2.7 21.3 + - - +
91B PHE* 3.4 29.1 - - - +
93B GLN* 1.3 73.2 - - - +
95B CYS* 1.3 61.9 + - - +
97B ARG* 3.3 10.5 + - + +
98B GLN* 3.0 45.1 + - + +
74D MET* 4.4 19.0 - - - +
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Residues in contact with CYS 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 PHE* 2.9 54.4 + - - -
92B ILE* 3.4 11.9 - - - +
93B GLN 3.3 0.2 - - - -
94B GLN* 1.3 76.8 - - - +
96B ILE* 1.3 62.3 + - - +
98B GLN* 3.1 6.9 + - - +
99B LEU* 3.0 19.4 + - - +
182B VAL* 3.9 22.4 - - + -
183B ALA* 4.5 15.3 - - - -
186B VAL* 3.5 27.3 - - + +
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Residues in contact with ILE 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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92B ILE* 3.0 27.9 + - + +
93B GLN* 3.5 27.4 - - - +
95B CYS* 1.3 73.5 - - - +
97B ARG* 1.3 52.8 + - - +
99B LEU* 3.1 5.2 + - - +
100B CYS* 2.7 33.1 + - - +
114B MET* 3.8 27.1 - - + +
117B LEU* 3.7 29.3 - - + +
118B GLN* 3.7 12.8 - - - +
178B TRP* 3.6 29.8 - - + +
182B VAL* 4.0 13.0 - - + -
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Residues in contact with ARG 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 GLN* 3.0 17.7 + - - +
94B GLN* 3.3 14.6 - - + +
96B ILE* 1.3 76.2 - - - +
98B GLN* 1.3 57.9 + - + +
100B CYS* 3.7 1.1 - - - +
101B GLU* 2.8 60.7 + - - +
114B MET* 3.5 46.6 - - - +
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Residues in contact with GLN 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 GLN* 3.0 31.5 + - + +
95B CYS* 3.1 10.0 + - - +
97B ARG* 1.3 74.9 - - + +
99B LEU* 1.3 57.5 + - - +
101B GLU* 3.7 12.3 - - - +
102B PHE* 2.9 31.9 + - - +
186B VAL* 3.2 33.8 - - + +
189B ILE* 4.3 4.8 - - + +
190B ASP* 5.9 1.0 + - - -
74D MET* 3.2 35.2 - - - +
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Residues in contact with LEU 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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95B CYS 3.0 11.1 + - - +
96B ILE* 3.4 7.9 - - - +
98B GLN* 1.3 75.1 - - - +
100B CYS* 1.3 69.2 + - - +
102B PHE* 3.3 0.9 + - - +
103B LEU* 3.0 40.0 + - + +
117B LEU* 4.1 20.2 - - + -
128B ILE* 4.1 23.3 - - + -
132B LEU* 4.1 10.8 - - + -
178B TRP* 4.1 20.9 - - + -
182B VAL* 4.3 6.3 - - + -
185B LEU* 4.0 25.8 - - + -
186B VAL* 4.4 5.9 - - + +
189B ILE* 4.0 21.5 - - + -
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Residues in contact with CYS 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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96B ILE 2.7 19.6 + - - +
97B ARG 3.7 4.9 - - - +
99B LEU* 1.3 75.2 - - - +
101B GLU* 1.3 65.6 + - - +
103B LEU* 3.7 2.1 - - - +
104B THR* 3.1 27.5 + - - -
112B VAL* 4.1 12.7 - - - +
113B SER* 3.7 38.8 - - - -
114B MET* 3.9 15.0 - - - -
117B LEU* 3.7 12.1 - - + +
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Residues in contact with GLU 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 ARG* 2.8 52.5 + - - +
98B GLN* 3.7 10.2 - - - +
100B CYS* 1.3 72.2 - - - +
102B PHE* 1.3 62.8 + - - +
104B THR* 3.4 3.8 + - - -
105B GLU* 3.0 50.5 + - - +
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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 GLN 2.9 21.7 + - - +
99B LEU 3.8 1.3 - - - +
100B CYS 3.3 0.2 - - - -
101B GLU* 1.3 72.5 - - - +
103B LEU* 1.3 67.1 + - + +
105B GLU* 3.3 3.2 + - - -
106B ASN* 2.8 54.3 + - + +
131B PHE* 4.6 1.1 - + - -
132B LEU* 3.5 33.7 - - + -
135B PHE* 4.1 24.2 - + - -
189B ILE* 3.6 34.3 - - + -
192B ILE* 4.1 28.9 - - + -
193B LYS* 5.2 11.7 - - + -
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Residues in contact with LEU 103 (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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99B LEU* 3.0 39.4 + - + +
100B CYS 3.7 2.7 - - - +
102B PHE* 1.3 78.8 - - - +
104B THR* 1.3 61.6 + - - +
106B ASN* 3.3 5.2 + - - +
108B TYR* 3.1 46.6 + - + -
112B VAL* 4.1 28.0 - - + -
117B LEU* 4.7 2.5 - - + -
128B ILE* 3.9 31.9 - - + -
131B PHE* 3.5 30.7 - - + -
132B LEU* 4.2 15.3 - - + -
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Residues in contact with THR 104 (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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100B CYS* 3.1 22.0 + - - -
101B GLU* 3.8 5.6 - - - -
103B LEU* 1.3 77.0 - - - +
105B GLU* 1.3 66.0 + - + +
106B ASN 3.4 0.9 + - - -
107B GLY* 3.7 8.7 + - - -
108B TYR* 5.2 1.3 - - - +
112B VAL* 3.7 18.4 + - - +
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Residues in contact with GLU 105 (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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101B GLU* 3.0 44.5 + - - +
102B PHE* 4.0 3.5 - - - +
104B THR* 1.3 81.4 - - + +
106B ASN* 1.3 67.8 + - - +
107B GLY 3.5 1.1 - - - -
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Residues in contact with ASN 106 (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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102B PHE* 2.8 51.7 + - + +
103B LEU 3.3 0.6 + - - +
104B THR 3.2 0.6 - - - -
105B GLU* 1.3 87.2 + - - +
107B GLY* 1.3 61.4 + - - +
108B TYR 3.4 2.2 - - - -
131B PHE* 3.4 17.4 - - + -
135B PHE* 3.8 30.6 - - + -
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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