Contacts of the helix formed by residues 109 - 122 (chain B) in PDB entry 1VEW
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 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94B LEU* 4.0 30.5 - - + -
99B LYS* 4.4 12.1 - - + -
102B ILE* 4.1 11.4 - - + -
103B GLU* 4.3 23.0 + - + +
108B SER* 1.3 72.7 - - - +
110B ASP* 1.3 57.7 + - - +
112B PHE* 3.1 8.1 + - + +
113B LYS* 2.8 54.5 + - + +
194B TRP* 6.3 0.7 - - + -
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Residues in contact with ASP 110 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108B SER* 3.3 8.7 - - - +
109B VAL* 1.3 79.4 - - - +
111B ASN* 1.3 60.7 + - - +
113B LYS* 3.5 16.2 + - - +
114B ALA* 3.1 27.2 + - - +
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Residues in contact with ASN 111 (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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106B PHE* 3.2 28.7 + - + +
107B GLY* 3.9 5.5 - - - -
108B SER* 3.1 27.2 + - - +
109B VAL 3.3 0.2 - - - -
110B ASP* 1.3 75.4 - - - +
112B PHE* 1.3 65.6 - - - +
114B ALA* 3.4 6.4 + - - +
115B GLU* 3.1 29.7 + - + +
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Residues in contact with PHE 112 (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 LEU* 5.7 0.2 - - + -
102B ILE* 3.7 33.9 - - + -
106B PHE* 3.8 37.2 - + + +
108B SER 3.2 3.3 + - - +
109B VAL* 3.1 15.0 + - + +
111B ASN* 1.3 80.2 - - - +
113B LYS* 1.3 62.7 + - + +
115B GLU* 3.1 4.2 + - - +
116B PHE* 2.9 32.6 + + + +
131B LEU* 3.8 26.9 - - + -
140B VAL* 4.0 11.2 - - + -
164B MET* 3.8 24.2 - - + -
189B TRP* 4.0 23.6 - + - -
194B TRP* 4.0 18.6 - + - -
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Residues in contact with LYS 113 (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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109B VAL* 2.8 32.8 + - + +
110B ASP* 3.7 18.5 + - - +
112B PHE* 1.3 80.2 - - + +
114B ALA* 1.3 56.5 + - - +
116B PHE 3.4 0.3 + - - -
117B GLU* 2.9 41.0 + - - +
189B TRP* 3.7 68.3 + - + +
194B TRP* 5.4 5.8 - - - -
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Residues in contact with ALA 114 (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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110B ASP 3.1 17.3 + - - +
111B ASN* 3.6 9.2 - - - +
112B PHE 3.3 0.2 - - - -
113B LYS* 1.3 75.4 - - - +
115B GLU* 1.3 61.7 + - - +
117B GLU* 3.8 10.0 - - - +
118B LYS* 3.0 30.8 + - - +
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Residues in contact with GLU 115 (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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106B PHE* 4.7 13.2 - - + -
111B ASN* 3.1 19.5 + - + +
112B PHE* 3.1 9.6 + - - +
114B ALA* 1.3 78.4 - - - +
116B PHE* 1.3 62.8 + - - +
118B LYS* 2.9 37.7 + - - +
119B ALA* 3.1 22.7 + - - +
140B VAL* 3.8 16.8 - - + +
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Residues in contact with PHE 116 (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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112B PHE* 2.9 30.2 + + + +
113B LYS 3.7 4.5 - - - +
115B GLU* 1.3 74.7 - - - +
117B GLU* 1.3 58.5 + - - +
119B ALA* 3.2 4.3 + - - +
120B ALA* 2.9 30.1 + - + +
129B ALA* 3.7 24.1 - - + +
130B TRP 3.8 25.6 - - - -
131B LEU 4.0 0.4 - - - -
140B VAL* 4.0 24.1 - - + +
164B MET* 3.8 23.8 - - - -
166B LEU* 3.9 22.2 - - + -
185B ILE* 5.4 2.2 - - + -
188B PHE* 3.8 20.4 - + - -
189B TRP* 3.7 27.4 - + + -
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Residues in contact with GLU 117 (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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113B LYS* 2.9 24.3 + - - +
114B ALA* 3.8 9.2 - - - +
115B GLU 3.4 0.2 - - - -
116B PHE* 1.3 75.7 - - - +
118B LYS* 1.3 57.5 + - - +
120B ALA* 3.8 1.0 - - - +
121B ALA* 2.9 33.4 + - - +
185B ILE* 3.6 31.4 - - + +
186B LYS* 4.6 16.9 - - - +
189B TRP* 2.8 31.7 + - + +
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Residues in contact with LYS 118 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114B ALA 3.0 14.7 + - - +
115B GLU* 2.9 43.9 + - - +
117B GLU* 1.3 76.9 - - - +
119B ALA* 1.3 50.2 + - - +
121B ALA* 4.1 3.4 - - - +
122B SER* 2.7 44.0 + - - +
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Residues in contact with ALA 119 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115B GLU 3.1 7.4 + - - +
116B PHE 3.2 8.3 + - - +
118B LYS* 1.3 76.9 - - - +
120B ALA* 1.3 61.6 + - - +
122B SER* 3.4 6.6 + - - -
123B ARG* 3.3 23.4 + - - +
129B ALA* 4.4 9.0 - - + -
140B VAL* 3.5 28.7 - - + -
141B VAL* 4.9 2.2 - - - +
142B SER* 4.3 15.4 + - - -
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Residues in contact with ALA 120 (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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116B PHE* 2.9 17.5 + - + +
117B GLU 3.8 1.3 - - - +
119B ALA* 1.3 80.0 - - - +
121B ALA* 1.3 57.7 + - - +
123B ARG* 3.9 2.6 + - - -
129B ALA* 3.7 21.5 - - + +
166B LEU* 4.2 7.6 - - + -
168B VAL* 4.0 14.6 - - + +
181B ARG* 2.7 28.6 + - - -
185B ILE* 3.6 25.8 - - + -
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Residues in contact with ALA 121 (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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117B GLU 2.9 18.2 + - - +
118B LYS* 4.1 4.0 - - - +
120B ALA* 1.3 78.5 - - - +
122B SER* 1.3 62.4 + - - +
123B ARG 3.5 1.4 + - - +
181B ARG* 3.6 15.2 + - - +
182B PRO* 5.2 12.6 - - + -
185B ILE* 3.7 13.4 - - + +
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Residues in contact with SER 122 (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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118B LYS* 2.7 28.5 + - - +
119B ALA* 3.4 9.5 + - - -
121B ALA* 1.3 76.5 - - - +
123B ARG* 1.3 58.7 + - - +
124B PHE* 3.0 12.9 + - - +
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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