Contacts of the strand formed by residues 171 - 181 (chain B) in PDB entry 6VVT
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 VAL 171 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B LEU* 2.8 38.6 - - + +
43B LEU* 3.3 30.0 - - + +
46B ILE* 4.0 17.5 - - + -
167B ILE* 5.1 0.2 - - - +
169B SER* 3.4 20.6 - - - +
170B PRO* 1.3 77.1 - - + +
172B LEU* 1.3 61.5 + - - +
174B VAL* 4.3 6.1 - - + -
196B VAL* 4.3 11.0 - - + -
197B GLU 4.0 4.9 - - - -
198B THR* 4.6 4.0 - - + -
207B ALA* 4.2 15.3 - - + -
620D MET* 4.6 9.7 - - - +
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Residues in contact with LEU 172 (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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43B LEU* 5.2 3.6 - - - +
167B ILE* 4.7 26.0 - - + -
170B PRO 3.3 5.1 + - - +
171B VAL* 1.3 73.2 - - - +
173B LYS* 1.3 57.6 + - + +
197B GLU* 2.9 30.9 + - + +
198B THR 5.2 0.9 - - - -
199B LYS* 5.0 19.1 - - + +
614D SER* 4.7 7.0 - - - +
616D ALA* 3.2 32.1 - - + +
617D GLU 4.9 0.2 - - - +
620D MET* 4.3 16.1 - - - +
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Residues in contact with LYS 173 (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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18B ARG* 5.3 13.1 - - - +
43B LEU* 5.0 1.3 - - - -
171B VAL 3.9 0.2 - - - -
172B LEU* 1.3 81.2 - - - +
174B VAL* 1.3 71.3 + - - +
175B THR* 5.0 15.5 - - + +
195B ASP 3.6 0.9 - - - +
196B VAL* 3.4 1.6 - - - -
197B GLU* 2.8 52.5 + - + +
615D PRO* 6.2 1.6 - - - +
616D ALA* 4.2 11.9 - - + +
619D ILE* 4.4 27.7 - - + +
674D GLU* 3.6 29.1 + - - -
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Residues in contact with VAL 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ARG* 3.1 53.0 + - + -
42B LEU* 4.5 8.7 - - + -
43B LEU* 3.2 33.8 - - + +
171B VAL* 4.3 6.7 - - + -
173B LYS* 1.3 83.5 - - - +
175B THR* 1.3 66.0 + - - +
194B ILE* 4.1 18.2 - - + -
195B ASP 3.0 7.9 - - - +
196B VAL* 3.7 23.3 - - + -
619D ILE* 5.9 1.4 - - - +
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Residues in contact with THR 175 (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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39B ARG* 4.5 6.3 - - - +
173B LYS* 5.0 16.6 - - + -
174B VAL* 1.3 77.3 - - - +
176B TYR* 1.3 65.4 + - - +
194B ILE* 3.4 3.1 - - - +
195B ASP* 2.5 66.3 + - + +
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Residues in contact with TYR 176 (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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31B GLY 4.7 4.5 - - - -
32B TYR* 4.4 25.7 + + - -
35B GLY* 3.4 22.7 - - - -
36B ASN* 3.0 54.6 + - - +
39B ARG* 4.7 17.7 - - + -
175B THR* 1.3 83.7 + - - +
177B LYS* 1.3 61.9 + - - +
178B VAL* 5.5 3.1 - - + -
192B LEU* 3.9 11.7 - - + -
193B ILE 2.9 15.7 - - - +
194B ILE* 4.0 14.8 - - + -
1006C SER* 4.8 4.9 - - - -
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Residues in contact with LYS 177 (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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176B TYR* 1.3 76.3 - - - +
178B VAL* 1.3 92.0 + - - +
179B GLU* 3.8 17.7 - - + +
192B LEU* 3.7 2.3 - - - +
193B ILE* 2.7 57.7 + - + +
435D GLN* 5.5 10.5 + - - +
717D ASP* 5.2 10.3 + - - -
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Residues in contact with VAL 178 (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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31B GLY* 3.8 31.0 - - - -
32B TYR* 3.1 52.4 + - + +
176B TYR* 5.5 3.8 - - + -
177B LYS* 1.3 97.1 + - - +
179B GLU* 1.3 64.1 + - - +
190B ASP* 4.8 4.9 - - + +
191B LYS 3.2 21.8 - - - +
192B LEU* 4.0 9.6 - - + -
435D GLN* 6.1 0.5 - - - +
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Residues in contact with GLU 179 (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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177B LYS* 3.8 23.0 - - + +
178B VAL* 1.3 82.0 - - - +
180B ALA* 1.3 62.5 + - - +
181B THR* 5.3 0.2 - - - +
190B ASP* 3.4 11.1 - - - +
191B LYS* 3.0 64.0 + - - -
193B ILE* 4.6 7.8 - - + +
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Residues in contact with ALA 180 (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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179B GLU* 1.3 77.7 - - - +
181B THR* 1.3 69.9 + - - +
187B THR 3.6 19.1 - - - +
188B ASP* 4.4 7.0 - - - -
189B PHE 3.0 10.5 - - - +
190B ASP* 5.7 0.9 - - - +
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Residues in contact with THR 181 (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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24B GLU* 2.7 39.3 + - - +
25B PRO* 4.9 2.3 - - - +
179B GLU* 5.2 0.4 - - + +
180B ALA* 1.3 84.7 - - - +
182B ARG* 1.3 77.8 + - - +
183B VAL* 3.7 2.9 - - - -
187B THR* 4.0 6.8 - - - +
189B PHE* 3.1 22.3 + - - +
191B LYS* 3.5 29.2 + - - +
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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