Contacts of the helix formed by residues 192 - 201 (chain s) in PDB entry 5GJQ
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 192 (chain s).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203c ARG* 4.2 0.7 - - + +
204c MET 4.4 8.1 - - - +
205c ASP* 3.6 33.9 - - + +
161s TYR* 3.8 21.2 - - + -
164s THR* 4.0 18.6 - - + +
172s GLY 3.2 28.8 + - - +
173s ALA 4.3 0.4 - - - +
174s VAL* 4.1 20.6 - - + -
190s ASP 3.9 0.2 + - - -
191s ASN* 1.3 75.8 + - - +
193s ALA* 1.3 58.1 + - - +
195s LEU* 3.2 8.5 + - - +
196s HIS* 2.9 28.1 + - + +
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Residues in contact with ALA 193 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201c LYS* 5.2 5.9 + - - +
203c ARG* 4.1 28.3 - - + +
204c MET 5.9 0.2 - - - +
191s ASN* 2.8 17.6 + - - +
192s VAL* 1.3 79.1 - - - +
194s ASP* 1.3 65.3 - - - +
196s HIS* 3.3 20.1 - - - +
197s GLU* 3.6 12.6 + - - +
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Residues in contact with ASP 194 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190s ASP* 5.4 1.7 - - + -
191s ASN* 3.3 30.0 + - - +
192s VAL 3.2 0.4 - - - -
193s ALA* 1.3 78.9 - - - +
195s LEU* 1.3 69.0 + - + +
197s GLU* 3.1 15.0 + - - +
198s LYS* 3.1 22.2 + - - +
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Residues in contact with LEU 195 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157s ARG* 3.8 33.2 - - + -
161s TYR* 3.9 19.3 - - + -
174s VAL* 3.7 30.5 - - + -
190s ASP* 3.9 23.1 - - + +
191s ASN 3.2 12.4 + - - +
192s VAL* 3.5 8.5 - - - +
194s ASP* 1.3 80.1 - - + +
196s HIS* 1.3 57.3 + - - +
198s LYS* 4.2 14.6 - - + -
199s TYR* 2.9 53.5 + - + +
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Residues in contact with HIS 196 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201c LYS* 5.9 4.0 - - + -
202c ALA 4.5 9.3 + - - -
203c ARG* 5.9 0.4 - - - -
204c MET* 3.8 36.1 - - + +
161s TYR* 3.2 23.6 + - + +
165s TYR* 6.0 2.7 - + - -
192s VAL* 2.9 13.4 + - + +
193s ALA* 3.3 15.5 - - - +
194s ASP 3.0 0.6 - - - -
195s LEU* 1.3 76.9 - - - +
197s GLU* 1.3 58.9 + - + +
200s SER* 2.5 61.2 + - - -
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Residues in contact with GLU 197 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201c LYS* 3.1 32.8 + - - +
193s ALA 3.9 11.0 - - - +
194s ASP* 3.1 13.8 + - - +
196s HIS* 1.3 80.8 - - + +
198s LYS* 1.3 63.2 + - - +
200s SER* 4.2 3.1 - - - -
201s GLY 2.9 32.1 + - - +
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Residues in contact with LYS 198 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154s ASP* 5.4 6.1 + - - -
157s ARG* 5.9 3.1 - - - +
194s ASP 3.1 15.6 + - - +
195s LEU* 3.7 17.3 - - + +
197s GLU* 1.3 81.5 - - - +
199s TYR* 1.3 81.7 + - + +
201s GLY 4.1 8.4 - - - -
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Residues in contact with TYR 199 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154s ASP* 4.2 7.0 + - + +
157s ARG* 3.6 28.4 + - - +
158s ARG* 3.4 61.8 + - + +
161s TYR* 3.7 37.2 - + + -
195s LEU* 2.9 44.8 + - + +
196s HIS 4.4 0.4 - - - +
198s LYS* 1.3 98.3 - - + +
200s SER* 1.3 64.0 + - - +
201s GLY 3.5 0.6 + - - -
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Residues in contact with SER 200 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161s TYR* 5.4 1.7 + - - -
196s HIS* 2.5 47.3 + - - -
197s GLU* 4.2 2.8 - - - -
199s TYR* 1.3 77.8 - - - +
201s GLY* 1.4 58.4 + - - +
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Residues in contact with GLY 201 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197s GLU 2.9 21.6 + - - +
198s LYS* 4.1 9.4 - - - -
199s TYR 3.5 0.6 - - - -
200s SER* 1.4 84.8 + - - +
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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