Contacts of the helix formed by residues 102 - 114 (chain A) in PDB entry 3VOR
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 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A GLY 3.9 1.2 + - - -
101A LEU* 1.3 76.4 - - - +
103A GLN* 1.3 65.4 + - - +
104A GLU* 3.4 8.3 + - - +
105A GLN* 2.9 41.3 + - - +
106A CYS* 2.9 21.8 + - - +
173A THR 4.1 10.8 - - - -
175A ASN* 3.5 0.4 - - - -
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Residues in contact with GLN 103 (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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102A SER* 1.3 73.6 - - - +
104A GLU* 1.3 61.4 + - + +
106A CYS* 3.6 1.8 - - - +
107A ARG* 2.9 65.7 + - - +
170A CYS 3.1 16.1 - - - +
171A THR* 4.0 12.4 + - - +
172A ALA 3.0 28.3 + - - +
173A THR* 4.6 9.4 + - - +
175A ASN* 3.4 4.7 - - - +
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Residues in contact with GLU 104 (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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102A SER* 3.2 6.9 + - - +
103A GLN* 1.3 79.1 - - + +
105A GLN* 1.3 60.2 + - + +
107A ARG* 3.4 9.9 + - - +
108A SER* 2.9 30.3 + - - -
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Residues in contact with GLN 105 (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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4A SER* 5.0 2.4 + - - +
6A THR* 4.1 7.3 + - - -
7A VAL* 3.6 24.7 - - + +
72A ILE* 3.4 43.7 - - + +
100A GLY 4.1 0.9 - - - +
101A LEU* 4.3 4.5 - - + -
102A SER* 2.9 40.8 + - - +
104A GLU* 1.3 76.2 - - + +
106A CYS* 1.3 63.6 + - - +
108A SER* 3.3 2.5 + - - -
109A ILE* 2.9 31.5 + - - +
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Residues in contact with CYS 106 (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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101A LEU* 4.0 15.6 - - + +
102A SER 2.9 17.8 + - - +
105A GLN* 1.3 75.4 - - - +
107A ARG* 1.3 60.3 + - - +
109A ILE 3.3 1.0 + - - -
110A LEU* 3.0 28.1 + - - +
122A VAL* 4.3 6.5 - - - -
170A CYS* 2.1 49.8 - - + -
175A ASN* 3.7 21.1 - - + -
177A ILE* 3.7 22.5 - - - +
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Residues in contact with ARG 107 (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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103A GLN* 2.9 47.1 + - - +
104A GLU* 3.9 9.7 - - - +
106A CYS* 1.3 76.1 - - - +
108A SER* 1.3 59.0 + - - +
110A LEU* 3.4 1.7 + - - +
111A GLY* 2.9 25.8 + - - -
166A ILE* 3.4 36.5 + - + +
167A LEU* 3.8 34.4 + - - +
169A THR 3.0 17.1 + - - -
170A CYS* 3.0 34.0 + - + -
171A THR* 3.8 6.5 - - - +
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Residues in contact with SER 108 (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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1A GLY* 3.3 26.5 + - - -
2A SER* 4.5 3.5 + - - -
7A VAL* 3.6 13.3 - - - +
104A GLU 2.9 17.8 + - - -
105A GLN* 3.7 5.2 - - - -
107A ARG* 1.3 77.5 - - - +
109A ILE* 1.3 63.2 + - - +
111A GLY* 3.2 3.0 + - - -
112A GLN* 3.2 41.0 + - - +
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Residues in contact with ILE 109 (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 VAL* 3.8 17.7 - - + +
10A LEU* 3.9 19.1 - - + -
11A VAL* 4.1 20.9 - - + -
14A THR* 5.8 0.2 - - + -
72A ILE* 4.5 6.1 - - + -
98A LEU* 4.0 18.4 - - + -
101A LEU* 3.9 34.3 - - + -
105A GLN 2.9 22.6 + - - +
106A CYS 3.8 3.6 - - - +
108A SER* 1.3 76.4 - - - +
110A LEU* 1.3 63.3 + - - +
112A GLN* 3.0 3.8 + - - +
113A VAL* 2.9 35.1 + - + +
177A ILE* 3.7 14.8 - - + -
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Residues in contact with LEU 110 (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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106A CYS 3.0 16.8 + - - +
107A ARG 3.9 2.0 - - - +
109A ILE* 1.3 76.2 - - - +
111A GLY* 1.3 58.6 + - - +
113A VAL* 4.5 2.9 - - + -
114A GLY* 2.9 31.0 + - - +
120A VAL* 3.6 30.5 - - + -
122A VAL* 4.0 3.6 - - + -
150A LEU* 3.8 12.1 - - + -
161A LEU* 4.7 7.6 - - + +
166A ILE* 3.8 23.8 - - + +
169A THR* 3.6 21.3 - - + -
170A CYS* 3.6 25.6 - - - -
177A ILE* 3.8 23.6 - - + -
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Residues in contact with GLY 111 (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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107A ARG 2.9 14.6 + - - -
108A SER* 3.2 6.0 + - - -
109A ILE 3.2 0.2 - - - -
110A LEU* 1.3 77.8 - - - +
112A GLN* 1.3 60.2 + - - +
114A GLY 4.9 0.2 - - - -
161A LEU 5.2 1.1 - - - -
166A ILE* 3.6 15.6 - - - +
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Residues in contact with GLN 112 (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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1A GLY* 4.3 14.7 - - - +
7A VAL* 3.9 7.9 - - - +
8A SER* 4.9 7.2 - - - +
11A VAL* 3.7 41.6 - - + +
108A SER* 3.2 32.9 + - - +
109A ILE 3.0 7.0 + - - +
111A GLY* 1.3 80.5 - - - +
113A VAL* 1.3 60.9 + - - +
114A GLY 3.8 0.4 - - - -
116A ASN* 3.7 13.0 + - - -
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Residues in contact with VAL 113 (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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11A VAL* 3.7 29.8 - - + -
14A THR* 4.0 16.2 - - + +
15A ASN* 5.3 5.2 - - - +
109A ILE* 2.9 31.0 + - + +
110A LEU* 4.5 4.0 - - + -
112A GLN* 1.3 80.5 - - - +
114A GLY* 1.3 73.3 + - - +
115A ASP 3.3 2.0 - - - -
116A ASN* 3.0 20.9 + - + +
117A TRP* 3.4 19.9 - - + +
179A LEU* 4.1 27.1 - - + -
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Residues in contact with GLY 114 (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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110A LEU* 2.9 23.4 + - - -
111A GLY 4.9 0.2 - - - -
112A GLN 3.8 0.4 - - - -
113A VAL* 1.3 84.1 - - - +
115A ASP* 1.3 63.8 + - - +
116A ASN 3.4 0.7 + - - -
117A TRP 3.7 2.1 + - - +
120A VAL* 3.4 15.4 - - - +
151A ARG* 3.2 20.9 + - - -
161A LEU* 4.1 15.7 - - - -
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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
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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