Contacts of the strand formed by residues 186 - 192 (chain B) in PDB entry 1VE3
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 186 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B GLU* 4.5 2.3 - - - +
162B TYR* 4.3 2.2 - - - -
179B GLU* 4.3 11.3 + - - -
180B PHE 3.2 14.8 - - - -
181B LYS* 3.6 18.2 - - - -
182B SER 4.0 0.7 - - - +
185B ASP* 1.3 89.5 + - - +
187B PHE* 1.3 66.4 + - - +
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Residues in contact with PHE 187 (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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3B PHE* 3.3 37.2 - + + -
5B GLU* 3.3 35.0 - - + +
6B TYR* 3.8 10.5 - - - -
9B VAL* 3.9 19.1 - - + -
10B PHE* 4.8 1.8 - + - -
162B TYR* 3.5 34.3 - + + -
179B GLU* 3.6 3.3 - - - +
180B PHE* 2.6 83.9 + + + +
186B SER* 1.3 76.4 + - - +
188B ARG* 1.3 61.5 + - - +
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Residues in contact with ARG 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B PHE* 3.5 22.2 - - - -
168B ILE* 5.0 13.1 - - - +
177B VAL* 3.8 19.9 - - + +
178B ILE 2.9 21.1 - - - +
179B GLU* 3.4 33.3 + - - +
180B PHE* 4.2 0.7 - - - -
187B PHE* 1.3 81.8 - - - +
189B VAL* 1.3 60.2 + - - +
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Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B GLY* 3.6 38.6 - - - +
3B PHE* 4.2 18.6 - - + +
6B TYR* 4.1 5.6 - - + -
176B VAL 3.8 1.0 - - - +
177B VAL* 3.4 5.0 - - - +
178B ILE* 3.0 29.3 + - + +
180B PHE* 3.6 25.1 - - + -
188B ARG* 1.3 76.9 - - - +
190B ARG* 1.3 64.3 + - - +
191B PHE* 3.6 32.2 + - + -
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Residues in contact with ARG 190 (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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2B GLY 4.0 10.6 + - - -
114B VAL 4.7 1.4 - - - +
170B ASP* 5.8 4.4 + - - +
175B THR* 4.0 32.4 + - + -
176B VAL 3.3 11.4 - - - +
177B VAL* 3.2 27.5 - - + +
189B VAL* 1.3 76.4 - - - +
191B PHE* 1.3 69.2 + - - +
192B ASN* 4.3 1.0 + - - -
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Residues in contact with PHE 191 (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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2B GLY* 3.8 17.7 - - - -
6B TYR* 3.5 38.4 - + - -
114B VAL* 3.7 34.8 - - + -
145B LEU* 4.5 9.9 - - + -
148B LEU* 4.5 13.0 - - + -
152B LEU* 4.7 2.0 - - + -
175B THR* 3.1 10.5 - - - -
176B VAL* 2.9 44.9 + - + -
178B ILE* 3.5 33.9 - - + -
189B VAL* 3.6 24.2 - - + -
190B ARG* 1.3 76.0 - - - +
192B ASN* 1.3 65.5 + - - +
193B VAL* 3.6 1.5 + - + -
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Residues in contact with ASN 192 (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 ILE* 5.4 0.2 - - - +
114B VAL* 2.9 48.7 + - - +
115B HIS* 3.4 6.3 + - - +
116B PHE 3.3 38.7 - - - +
117B GLU* 3.4 20.4 - - - +
118B PRO* 5.1 0.9 - - + +
120B GLU* 4.9 0.6 + - - -
173B GLU 5.2 1.0 - - - +
174B ARG 3.6 5.4 - - - +
175B THR* 3.7 15.0 - - - +
190B ARG 5.5 1.2 + - - -
191B PHE* 1.3 73.1 - - - +
193B VAL* 1.3 61.6 + - - +
194B TRP* 3.7 10.2 + - + +
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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