Contacts of the strand formed by residues 162 - 169 (chain A) in PDB entry 3VNG
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 ARG 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A GLY 3.4 8.1 - - - +
157A PHE* 3.2 39.2 - - + -
160A THR 4.2 3.8 + - - -
161A ASN* 1.3 76.2 - - - +
163A LEU* 1.3 62.0 + - - +
185A ILE* 3.3 33.3 - - + +
187A SER* 4.2 11.7 + - - +
204A TYR* 3.3 32.3 + - - -
205A ASP 3.8 1.8 - - - +
206A GLY* 3.4 31.7 - - - +
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Residues in contact with LEU 163 (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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137A THR* 3.6 24.0 - - + -
138A ARG 3.7 13.7 - - - +
139A ARG* 3.5 28.0 - - + +
155A GLY* 3.4 16.1 - - - +
156A GLY 2.7 19.7 + - - +
158A ASP* 3.4 28.3 - - - +
161A ASN* 3.5 17.7 - - + +
162A ARG* 1.3 76.5 - - - +
164A ASN* 1.3 59.6 + - - +
165A SER* 3.9 15.7 - - - +
185A ILE* 3.6 3.1 - - - -
186A ARG 3.0 21.5 + - - +
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Residues in contact with ASN 164 (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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163A LEU* 1.3 73.7 - - - +
165A SER* 1.3 68.0 + - - +
181A ALA* 3.5 15.4 - - - +
182A MET* 2.7 59.1 + - - +
183A ASN 5.0 2.2 + - - -
184A THR 3.2 25.1 - - - +
185A ILE* 3.1 25.4 - - + +
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Residues in contact with SER 165 (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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137A THR* 4.6 3.1 + - - +
139A ARG* 2.9 27.3 + - - -
155A GLY 2.9 24.9 + - - -
163A LEU* 3.5 11.3 - - - +
164A ASN* 1.3 86.7 + - - +
166A ALA* 1.3 59.9 + - - +
178A MET* 3.8 16.8 - - - +
179A ILE 5.9 0.2 - - - -
181A ALA* 4.0 13.2 - - - -
182A MET* 4.7 0.2 - - - +
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Residues in contact with ALA 166 (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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139A ARG* 3.8 3.8 - - - +
153A ALA 3.3 14.1 - - - +
154A VAL* 4.1 17.5 - - + -
164A ASN 4.9 1.1 - - - +
165A SER* 1.3 79.6 - - - +
167A GLU* 1.3 62.0 + - - +
178A MET* 3.2 9.9 - - - +
179A ILE* 2.9 45.4 + - + +
180A THR 4.2 7.1 + - - +
181A ALA* 4.6 0.6 - - - +
223A TRP* 4.2 10.1 - - + +
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Residues in contact with GLU 167 (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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135A MET* 3.4 13.0 - - - +
136A LEU* 2.6 35.4 + - - +
137A THR* 3.3 17.2 + - - -
139A ARG* 2.8 36.7 + - - +
152A TYR* 3.4 6.5 - - - +
153A ALA* 3.0 32.1 + - + +
166A ALA* 1.3 74.6 - - - +
168A CYS* 1.3 61.1 + - - +
176A TRP* 3.5 19.5 - - + +
177A ARG 3.2 14.4 - - - +
178A MET* 3.8 9.4 - - - +
179A ILE* 4.0 5.4 - - - +
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Residues in contact with CYS 168 (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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150A LEU* 3.5 41.7 - - - -
151A LEU 3.4 4.5 - - - -
152A TYR* 3.7 21.1 - - + -
167A GLU* 1.3 75.1 - - - +
169A TYR* 1.3 61.5 + - - +
170A TYR* 3.9 19.0 - - + +
175A GLU 3.7 1.2 - - - +
176A TRP* 3.1 6.5 - - - -
177A ARG 2.6 41.6 + - - +
179A ILE* 3.9 16.8 - - + -
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Residues in contact with TYR 169 (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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100A ILE* 5.4 0.2 - - + -
105A TYR* 3.7 25.8 + + - -
121A ARG* 5.5 0.9 + - - -
132A VAL* 3.6 16.7 - - + +
133A ALA* 4.1 5.4 - - + -
150A LEU* 3.6 6.2 - - - +
151A LEU* 2.7 45.4 + - + +
168A CYS* 1.3 72.1 - - - +
170A TYR* 1.3 59.7 + - - +
171A PRO* 3.3 35.0 + - + +
174A ASN* 2.7 52.8 + - - +
175A GLU 3.4 11.7 - - - -
176A TRP* 3.3 50.3 - + + -
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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