Contacts of the helix formed by residues 192 - 203 (chain V) in PDB entry 3J7Y
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 LYS 192 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190V CYS* 3.5 14.4 - - + +
191V LEU* 1.3 83.1 - - - +
193V THR* 1.3 80.2 + - - +
196V GLU* 3.3 28.1 - - + +
197V GLU* 4.7 11.2 - - + +
200V GLU* 3.7 35.9 + - - +
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Residues in contact with THR 193 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1269 LYS* 5.2 0.5 + - - -
1289 PHE* 5.6 2.1 - - + +
1309 LEU* 3.6 19.9 - - + +
1359 PHE* 4.9 1.3 - - + -
190V CYS 5.3 1.0 + - - -
192V LYS* 1.3 87.1 + - - +
194V LEU* 1.3 67.3 + - - +
195V GLN* 3.1 30.3 - - - +
196V GLU* 3.6 9.6 + - - -
197V GLU* 3.3 20.3 - - - +
95Y ASN* 3.6 7.5 - - - +
150Y GLU* 3.3 24.5 - - + +
153Y LEU* 3.1 28.5 - - + +
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Residues in contact with LEU 194 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20U PHE* 4.5 6.1 - - + -
21U ARG* 4.0 15.0 - - + +
193V THR* 1.3 78.0 - - - +
195V GLN* 1.3 83.8 + - + +
197V GLU* 3.9 1.7 - - - +
198V VAL* 3.1 46.8 + - + +
95Y ASN* 3.5 47.0 - - + +
98Y LEU* 4.5 4.5 - - + -
99Y HIS* 4.3 15.7 - - + +
146Y VAL* 3.8 39.5 - - + -
150Y GLU* 4.3 1.3 + - - +
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Residues in contact with GLN 195 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1289 PHE* 3.5 21.5 - - + -
1359 PHE* 3.1 32.7 - - + -
1369 LEU 5.1 1.8 - - - +
1379 ARG 3.8 15.4 + - - -
20U PHE* 3.4 29.1 - - + -
21U ARG* 4.1 3.6 - - - +
193V THR* 3.1 16.3 - - - +
194V LEU* 1.3 90.8 - - + +
196V GLU* 1.3 62.6 + - - +
198V VAL* 3.2 4.7 + - - +
199V MET* 2.9 33.8 + - - +
150Y GLU* 2.7 32.7 + - - +
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Residues in contact with GLU 196 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1269 LYS* 3.6 30.4 + - - +
1279 LEU* 5.9 0.5 - - - +
1289 PHE* 3.3 44.0 - - + +
192V LYS* 3.3 28.2 + - + +
193V THR* 3.6 10.1 + - - -
195V GLN* 1.3 77.7 - - - +
197V GLU* 1.3 58.8 + - - +
199V MET* 3.2 10.4 + - - +
200V GLU* 2.9 43.4 + - - +
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Residues in contact with GLU 197 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188V VAL 5.7 1.8 - - - +
190V CYS* 5.2 12.2 - - - +
192V LYS* 4.0 12.5 + - + +
193V THR 3.3 10.0 + - - +
194V LEU 3.8 7.3 + - - +
195V GLN 3.2 0.8 - - - -
196V GLU* 1.3 79.2 - - - +
198V VAL* 1.3 60.6 + - - +
200V GLU* 3.2 17.7 + - - +
201V ALA* 2.9 28.1 + - - +
94Y SER* 4.6 4.3 + - - -
95Y ASN* 2.7 43.9 + - + +
96Y GLU* 3.4 36.6 + - + +
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Residues in contact with VAL 198 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619 VAL* 4.7 0.2 - - + -
20U PHE* 4.2 15.3 - - + -
194V LEU* 3.1 36.4 + - + +
195V GLN* 3.2 7.2 + - - +
197V GLU* 1.3 77.6 - - - +
199V MET* 1.3 58.0 + - - +
201V ALA* 3.2 8.8 + - - +
202V MET* 2.9 37.5 + - + +
95Y ASN 4.3 0.2 - - - +
96Y GLU* 4.3 16.2 - - - +
99Y HIS* 3.6 50.0 - - + +
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Residues in contact with MET 199 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1279 LEU* 4.5 2.2 - - + -
1289 PHE* 3.8 28.5 - - + -
18U ARG* 4.3 11.0 - - + +
20U PHE* 3.5 26.2 - - + -
195V GLN 2.9 17.0 + - - +
196V GLU* 3.3 10.1 - - - +
198V VAL* 1.3 75.9 - - - +
200V GLU* 1.3 57.9 + - + +
202V MET* 3.2 7.2 + - - +
203V GLY 2.9 24.4 + - - -
204V ILE* 3.1 56.6 + - + +
206V GLU* 4.2 21.5 - - + +
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Residues in contact with GLU 200 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192V LYS* 3.7 35.9 + - - +
196V GLU* 2.9 30.4 + - - +
197V GLU* 3.2 17.5 + - - +
199V MET* 1.3 77.2 - - + +
201V ALA* 1.3 60.9 - - - +
203V GLY* 3.2 13.5 + - - +
204V ILE 5.4 2.0 - - - -
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Residues in contact with ALA 201 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197V GLU 2.9 12.4 + - - +
198V VAL* 3.2 9.8 + - - +
200V GLU* 1.3 78.1 - - - +
202V MET* 1.3 63.7 + - + +
203V GLY 3.4 0.2 + - - -
96Y GLU* 3.7 31.2 - - + +
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Residues in contact with MET 202 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619 VAL* 3.7 31.9 - - + -
629 VAL 3.7 23.6 - - - +
639 PRO* 4.3 14.4 - - - -
649 ASP* 5.5 2.0 - - - +
198V VAL* 2.9 23.5 + - + +
199V MET 3.4 7.9 - - - +
201V ALA* 1.3 79.4 - - + +
203V GLY* 1.3 58.4 + - - +
204V ILE* 3.7 21.5 - - + -
99Y HIS* 5.9 0.7 - - - -
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Residues in contact with GLY 203 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199V MET 2.9 5.3 + - - -
200V GLU* 3.2 10.9 + - - -
202V MET* 1.3 78.1 - - - +
204V ILE* 1.3 63.9 - - - +
205V LYS* 3.7 4.5 + - - +
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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