Contacts of the helix formed by residues 195 - 206 (chain B) in PDB entry 2VCK
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 TYR 195 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72B LEU* 3.5 28.0 - - + -
92B TYR* 3.7 25.8 - + + -
93B PRO* 2.7 41.3 + - + +
94B LYS 4.3 1.0 + - - -
95B THR* 3.6 13.7 - - + +
99B LEU 4.3 3.8 + - - -
101B CYS* 3.6 21.3 - - - -
123B PRO* 3.7 30.3 - - + -
192B THR* 3.0 12.2 + - - +
194B VAL* 1.3 84.8 - - + +
196B SER* 1.3 57.3 + - - +
197B ASP 3.4 2.2 - - - -
198B PHE* 3.3 10.9 + + + +
199B ASP* 2.9 30.8 + - - +
232B TYR* 3.7 24.0 - + + -
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Residues in contact with SER 196 (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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193B THR* 3.2 23.5 + - - -
194B VAL 3.4 0.2 - - - -
195B TYR* 1.3 77.0 - - - +
197B ASP* 1.3 60.6 + - - +
199B ASP* 3.9 0.3 - - - -
200B THR* 2.7 41.3 + - - -
232B TYR 3.3 21.7 + - - -
233B LYS* 3.1 20.3 + - - +
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Residues in contact with ASP 197 (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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123B PRO 4.4 12.5 - - - +
125B GLU* 4.1 28.3 + - + +
149B HIS* 4.2 2.6 + - - -
193B THR 4.8 0.2 + - - -
194B VAL 4.7 3.2 + - - +
195B TYR 3.4 0.4 - - - -
196B SER* 1.3 81.2 + - - +
198B PHE* 1.3 57.7 + - - +
200B THR* 3.6 6.1 + - - +
201B TYR* 2.9 31.5 + - - +
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Residues in contact with PHE 198 (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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90B ILE* 3.8 16.2 - - + -
92B TYR* 3.7 24.9 - + - -
101B CYS* 4.2 13.5 - - - -
121B GLN* 3.4 53.2 - - + -
122B HIS 4.6 1.6 - - - -
123B PRO* 4.3 14.0 + - + -
149B HIS* 3.6 38.9 - + + +
194B VAL 5.3 0.2 + - - -
195B TYR* 3.3 12.7 + + - +
196B SER 3.3 0.6 - - - -
197B ASP* 1.3 78.2 - - - +
199B ASP* 1.3 81.3 + - - +
201B TYR* 3.3 4.2 + - - +
202B MSE 2.9 48.4 + - + +
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Residues in contact with ASP 199 (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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73B LYS* 5.0 0.5 + - - -
92B TYR* 2.7 28.9 + - - -
195B TYR 2.9 19.3 + - - +
198B PHE* 1.3 82.7 - - - +
200B THR* 1.3 57.2 + - - +
202B MSE 4.5 2.0 - - - -
203B THR* 2.6 38.8 + - - -
230B PHE* 3.5 18.1 - - - +
231B SER 3.2 6.6 + - - -
232B TYR* 2.8 33.1 + - - +
233B LYS* 3.7 22.2 - - + +
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Residues in contact with THR 200 (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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196B SER* 2.7 26.0 + - - -
197B ASP* 3.6 7.0 - - - +
199B ASP* 1.3 77.8 - - - +
201B TYR* 1.3 52.1 + - - +
203B THR* 3.3 1.4 + - - -
204B GLU* 2.7 59.0 + - + +
233B LYS* 3.5 24.5 + - + +
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Residues in contact with TYR 201 (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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125B GLU* 4.5 6.3 - - - +
144B PHE* 3.3 15.6 - + + +
145B GLU* 2.7 32.9 + - + -
148B ASN* 2.9 48.2 + - + -
149B HIS* 3.5 25.8 - + + +
150B PHE* 3.7 3.9 - + - -
197B ASP 2.9 18.9 + - - +
198B PHE 3.4 3.8 - - - +
200B THR* 1.3 72.0 - - - +
202B MSE 1.3 89.3 + - + +
204B GLU* 3.5 6.1 + - - -
205B LEU* 3.1 53.5 + - + +
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Residues in contact with MSE 202 (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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121B GLN* 3.8 18.8 - - - +
144B PHE* 3.6 25.1 - - + -
150B PHE* 4.2 1.3 - - + -
198B PHE* 2.9 36.5 + - + +
199B ASP 4.0 0.4 - - - +
201B TYR* 1.3 92.0 - - + +
203B THR* 1.3 56.2 + - - +
206B ASP* 2.8 63.5 + - - +
230B PHE* 3.3 35.9 - - + -
1234B BLA 3.5 33.2 - - + +
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Residues in contact with THR 203 (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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199B ASP 2.6 23.3 + - - -
200B THR 3.3 4.9 + - - -
202B MSE 1.3 78.2 - - - +
204B GLU* 1.3 69.9 + - - +
205B LEU 3.5 0.2 + - - -
206B ASP* 4.3 8.4 + - - +
209B ARG* 5.9 3.1 - - - +
225B VAL* 4.0 15.1 - - + +
226B ASN* 3.5 22.7 - - - +
230B PHE* 3.2 16.2 - - - +
233B LYS* 3.0 24.3 + - - +
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Residues in contact with GLU 204 (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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200B THR* 2.7 46.8 + - + +
201B TYR* 4.0 6.3 - - - +
202B MSE 3.4 0.2 - - - -
203B THR* 1.3 89.1 - - - +
205B LEU* 1.3 72.2 + - + +
206B ASP 5.3 0.3 - - - +
233B LYS* 4.7 2.8 - - - +
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Residues in contact with LEU 205 (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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143B PHE* 3.6 40.3 - - - +
144B PHE* 3.9 14.6 - - + -
145B GLU* 4.5 2.9 - - + +
201B TYR* 3.1 56.7 + - + +
204B GLU* 1.3 92.5 - - + +
206B ASP* 1.3 63.3 + - - +
207B PRO* 3.4 8.0 - - - +
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Residues in contact with ASP 206 (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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88B ASN* 5.4 0.4 - - - -
144B PHE* 3.8 13.1 - - + -
202B MSE 2.8 26.9 + - - +
203B THR* 4.5 6.8 - - - +
204B GLU 3.8 0.5 - - - +
205B LEU* 1.3 72.9 - - - +
207B PRO* 1.4 74.2 - - - +
208B VAL* 3.0 30.3 + - + +
209B ARG* 4.4 6.1 + - - +
225B VAL* 6.2 0.4 - - + -
229B LEU* 5.6 0.2 - - - -
230B PHE* 3.1 25.0 - - + -
1234B BLA 2.4 40.5 + - - +
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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