Contacts of the strand formed by residues 175 - 181 (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 ASN 175 (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 3.5 4.9 + - - -
101A LEU* 2.8 45.4 + - - +
102A SER 3.5 1.0 - - - -
103A GLN* 3.4 19.2 - - - +
106A CYS* 3.7 19.5 - - + -
122A VAL* 4.5 2.8 - - + +
123A GLY 3.3 10.3 - - - +
124A THR* 4.4 0.6 - - - +
125A SER 3.7 2.9 - - - +
170A CYS* 3.3 17.5 + - - -
171A THR 3.5 0.3 + - - -
172A ALA* 2.8 47.2 + - - +
173A THR 4.1 1.0 - - - -
174A VAL* 1.3 75.4 - - - +
176A SER* 1.3 64.0 + - - +
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Residues in contact with SER 176 (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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97A GLU* 4.0 8.6 + - - -
98A LEU 3.1 14.6 - - - -
99A ASN* 4.0 1.3 - - - -
101A LEU* 4.1 2.2 - - - -
122A VAL* 3.2 10.4 - - - +
123A GLY* 2.9 37.1 + - - -
124A THR 3.2 0.2 + - - -
125A SER* 2.9 43.8 + - - -
175A ASN* 1.3 76.4 - - - +
177A ILE* 1.3 65.3 + - - +
178A THR* 5.5 0.5 + - - -
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Residues in contact with ILE 177 (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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96A MET 3.7 1.0 - - - +
97A GLU* 3.3 3.0 - - - -
98A LEU* 2.8 47.7 + - + +
101A LEU* 3.7 17.3 - - + -
106A CYS* 3.7 30.3 - - - +
109A ILE* 3.7 28.5 - - + -
110A LEU* 3.8 21.3 - - + -
120A VAL* 4.4 1.1 - - + -
121A ALA 3.3 7.9 - - - +
122A VAL* 4.3 3.4 - - + -
176A SER* 1.3 80.7 - - - +
178A THR* 1.3 64.7 + - - +
179A LEU* 3.6 31.4 - - + -
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Residues in contact with THR 178 (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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95A ALA* 4.1 21.5 - - + -
96A MET 3.3 10.8 - - - +
97A GLU* 3.7 16.5 + - - +
119A TYR* 3.8 20.9 - - + +
120A VAL* 3.3 5.7 - - - -
121A ALA* 2.8 40.7 + - - +
123A GLY 5.6 1.1 + - - +
132A ALA* 3.7 16.2 - - + +
133A LEU* 4.7 4.5 - - + -
138A VAL* 4.1 11.4 - - + -
176A SER* 5.5 0.7 + - - -
177A ILE* 1.3 73.4 - - - +
179A LEU* 1.3 65.0 + - - +
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Residues in contact with LEU 179 (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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14A THR* 4.2 24.2 - - + -
94A PHE 4.0 0.2 - - - +
95A ALA* 3.2 2.5 - - - -
96A MET* 2.8 42.1 + - + +
98A LEU* 4.2 10.8 - - + -
113A VAL* 4.1 21.3 - - + -
117A TRP* 3.7 44.9 - - + +
119A TYR 3.4 2.7 - - - -
120A VAL* 4.0 22.2 - - + -
177A ILE* 3.6 24.0 - - + +
178A THR* 1.3 76.5 - - - +
180A ALA* 1.3 60.8 + - - +
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Residues in contact with ALA 180 (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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82A ALA* 4.2 2.5 - - + -
94A PHE 3.1 14.8 - - - +
95A ALA* 3.9 12.6 - - + -
117A TRP* 3.6 8.8 - - - -
118A GLU 3.7 2.6 + - - -
119A TYR* 2.9 54.3 + - + +
138A VAL* 4.6 1.6 - - + -
140A MET* 3.8 17.1 - - + +
179A LEU* 1.3 75.6 - - - +
181A SER* 1.3 63.7 + - - +
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Residues in contact with SER 181 (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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18A ARG* 4.6 9.4 + - - -
22A LYS* 4.3 5.0 + - - -
93A GLY* 3.1 2.6 - - - -
94A PHE* 2.9 42.6 + - - -
117A TRP* 3.8 21.7 - - - -
118A GLU* 5.2 9.5 + - - +
140A MET* 3.7 9.9 - - - -
180A ALA* 1.3 78.5 - - - +
182A ARG* 1.3 79.2 + - - +
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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