Contacts of the strand formed by residues 163 - 167 (chain B) in PDB entry 2VM8
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 163 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B HIS* 2.8 30.2 + - - -
139B VAL 3.4 18.0 + - - -
161B VAL* 3.6 11.4 - - - +
162B ASN* 1.3 79.5 - - - +
164B PHE* 1.3 70.7 + - - +
194B ILE* 3.2 16.4 - - - +
196B GLN* 4.2 5.4 - - - -
392B PHE* 4.0 16.4 - - - -
471B ARG* 2.9 18.7 + - - -
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Residues in contact with PHE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 4.5 0.4 - - + -
139B VAL* 3.0 36.3 - - + +
141B ILE* 3.8 18.4 - - + -
152B MET* 3.4 55.9 - - + -
155B LEU* 4.0 9.9 - - + -
156B VAL* 3.4 33.7 - - + -
161B VAL* 4.0 10.8 - - + -
163B SER* 1.3 78.1 - - - +
165B LEU* 1.3 60.6 + - - +
188B ILE* 4.3 13.8 - - + +
191B ILE* 4.6 1.6 - - + -
193B ALA* 4.0 17.5 - - + -
194B ILE 3.1 5.6 + - - +
195B ALA* 3.8 1.6 - - - -
196B GLN* 2.8 31.3 + - - +
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ARG* 3.9 9.0 - - - +
107B HIS* 3.5 24.2 - - + -
139B VAL 2.9 8.5 + - - -
140B ASP* 3.6 15.3 - - - +
141B ILE* 2.8 35.5 + - - +
164B PHE* 1.3 75.0 - - - +
166B VAL* 1.3 72.1 + - - +
167B TYR* 3.1 51.1 - - + +
196B GLN* 3.3 14.8 + - + +
198B HIS* 4.1 8.3 - - + +
253B THR* 3.8 30.1 - - + +
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Residues in contact with VAL 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ILE* 4.1 13.2 - - + -
164B PHE 5.6 0.2 - - - -
165B LEU* 1.3 79.0 - - - +
167B TYR* 1.4 61.5 + - - +
176B LEU* 3.4 28.3 - - + -
181B ILE* 4.7 15.0 - - + -
184B VAL* 3.7 26.0 - - + -
185B LEU* 4.8 13.0 - - + -
188B ILE* 5.4 2.5 - - + -
195B ALA* 6.0 0.2 - - + -
196B GLN 3.0 12.8 + - - +
197B VAL* 3.2 15.6 - - + +
198B HIS 2.8 29.8 + - - -
250B LEU* 6.5 0.2 - - + -
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Residues in contact with TYR 167 (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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75B ARG* 4.0 10.7 + - - -
109B VAL* 4.9 5.0 - - + +
140B ASP* 3.0 29.6 + - + +
141B ILE 3.7 22.2 + - - -
142B SER* 6.0 0.2 - - - -
165B LEU* 3.1 25.6 - - + +
166B VAL* 1.4 75.0 - - - +
168B MET* 1.3 60.9 + - - +
169B ALA 3.2 14.1 - - - +
170B PHE* 3.3 37.2 - + - -
174B PHE* 3.7 39.4 + + + +
175B GLN* 3.6 0.2 - - - -
176B LEU* 3.1 30.7 + - - +
181B ILE* 4.8 0.4 - - - +
198B HIS* 3.7 20.2 - + + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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