Contacts of the strand formed by residues 159 - 167 (chain B) in PDB entry 2VT5
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 LEU 159 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B GLY* 3.6 11.7 - - - -
138B ILE 3.4 31.2 - - - +
139B TYR* 3.4 28.2 - - + +
156B GLY* 2.9 27.7 + - - +
157B ARG 3.3 4.0 - - - +
158B ASN* 1.3 77.7 - - - +
160B VAL* 1.3 60.3 + - - +
161B ALA 3.8 5.2 - - - +
162B ALA* 4.3 3.4 - - + -
178B ASP* 5.4 2.4 - - - +
278B LEU 6.0 0.2 - - - +
282B ASN* 3.9 17.9 - - + +
283B PRO* 5.6 0.2 - - + -
286B TYR* 3.6 51.1 + - + -
303B LEU* 4.1 0.2 - - + -
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Residues in contact with VAL 160 (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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30B LEU* 3.7 32.5 - - + +
113B TYR* 4.2 13.0 - - + -
138B ILE* 2.9 14.1 + - + +
140B ARG* 3.9 50.9 - - + +
158B ASN 3.4 4.2 + - - +
159B LEU* 1.3 74.5 - - - +
161B ALA* 1.3 61.5 + - - +
177B MET* 4.3 7.1 - - - +
178B ASP* 4.6 6.1 + - - +
286B TYR* 3.3 12.1 + - - -
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Residues in contact with ALA 161 (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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30B LEU* 4.9 6.7 - - + -
34B LEU* 5.0 2.0 - - + -
138B ILE* 2.7 51.1 + - + +
159B LEU* 3.5 3.3 - - - +
160B VAL* 1.3 87.5 - - + +
162B ALA* 1.3 61.6 + - - +
175B LEU* 4.5 7.2 - - + -
176B ALA 3.4 14.8 - - - +
177B MET* 3.8 14.6 - - + -
286B TYR* 4.0 4.7 - - - -
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Residues in contact with ALA 162 (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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136B PHE* 3.3 27.1 - - - +
137B GLY* 4.0 3.1 - - - -
159B LEU* 4.3 3.6 - - + -
161B ALA* 1.3 78.9 - - - +
163B GLY* 1.3 54.5 + - - +
175B LEU* 3.8 2.3 - - - +
176B ALA* 2.7 38.3 + - - +
283B PRO* 3.8 21.1 - - + +
286B TYR* 3.5 22.6 - - + -
287B VAL* 4.4 0.4 - - - -
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Residues in contact with GLY 163 (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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135B ILE* 3.8 5.2 - - - +
136B PHE* 3.0 37.2 + - - +
162B ALA* 1.3 78.9 - - - +
164B TYR* 1.3 65.2 + - - +
174B VAL 3.1 14.4 - - - -
283B PRO* 4.2 2.7 - - - +
287B VAL* 3.8 15.6 - - - +
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Residues in contact with TYR 164 (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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134B THR 3.0 17.0 - - - +
135B ILE* 4.2 1.6 - - - -
136B PHE* 3.5 9.1 - - - -
163B GLY* 1.3 77.0 - - - +
165B ALA* 1.3 66.1 + - - +
166B LEU* 4.4 3.8 - - + -
173B LEU* 3.4 3.0 - - - +
174B VAL* 2.8 62.3 + - + +
249B VAL* 3.4 21.5 - - + -
252B VAL* 4.5 4.1 - - + +
253B HIS* 2.7 51.1 + + + -
256B LEU* 3.6 12.0 - - - +
284B MET* 3.4 39.3 - - + -
287B VAL* 4.3 13.2 - - + -
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Residues in contact with ALA 165 (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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41B VAL* 3.6 37.7 - - + -
133B GLY* 3.2 6.9 - - - -
134B THR* 2.8 31.5 + - - +
136B PHE* 4.7 1.8 - - - -
164B TYR* 1.3 75.5 - - - +
166B LEU* 1.3 60.0 + - - +
167B TYR* 3.8 17.0 - - + +
171B THR* 4.9 1.1 - - + -
172B MET 3.2 9.4 - - - +
173B LEU* 4.2 6.7 - - + +
249B VAL* 3.8 2.6 - - - +
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Residues in contact with LEU 166 (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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128A CYS 4.0 9.4 - - - +
129A LEU* 4.0 11.9 - - + +
131B SER* 3.9 23.3 - - - -
132B VAL 3.6 11.0 - - - +
164B TYR* 4.1 7.9 - - + -
165B ALA* 1.3 73.9 - - - +
167B TYR* 1.3 64.8 + - - +
168B GLY* 3.9 7.2 - - - +
170B ALA 3.3 2.3 - - - +
171B THR* 3.0 8.0 - - - +
172B MET* 2.7 41.2 + - + +
249B VAL* 3.7 18.4 - - + -
250B ALA* 4.1 13.7 - - + +
253B HIS* 3.5 42.4 - - + -
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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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169A SER* 4.0 6.1 - - - -
41B VAL* 3.9 12.1 - - + +
44B ILE* 3.3 27.4 - - + +
45B SER* 3.8 25.4 - - - -
48B VAL* 4.2 9.9 - - + -
49B ARG* 3.7 15.2 + - - +
120B LEU* 4.0 3.4 - - + -
131B SER* 3.5 3.8 - - - -
132B VAL* 2.9 60.8 + - + +
133B GLY* 3.7 13.2 - - - -
134B THR* 2.6 32.2 + - - -
165B ALA* 3.8 16.8 - - + +
166B LEU* 1.3 70.5 - - - +
168B GLY* 1.3 61.4 + - - +
171B THR* 3.6 31.0 - - + -
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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