Contacts of the helix formed by residues 194 - 207 (chain V) in PDB entry 3A68
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 GLY 194 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190M ARG* 3.3 35.5 - - - +
192V GLY 3.9 0.2 + - - -
193V LYS* 1.3 71.7 - - - +
195V HIS* 1.3 66.9 + - - -
196V GLY 3.2 1.5 + - - -
197V VAL* 3.3 5.9 + - - +
198V TRP* 3.1 22.3 + - - +
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Residues in contact with HIS 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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195F HIS* 3.7 22.0 + + + +
190M ARG 3.7 4.2 + - - -
191M VAL* 3.7 23.9 + - + +
195M HIS* 3.6 44.2 + + - +
196M GLY* 3.8 22.2 + - - -
199M HIS* 2.9 31.5 + - - +
193V LYS 3.6 3.0 + - - -
194V GLY* 1.3 71.2 - - - -
196V GLY* 1.3 63.2 + - - +
198V TRP* 3.3 13.5 + + - +
199V HIS* 2.9 20.5 + - + +
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Residues in contact with GLY 196 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195F HIS* 3.8 16.1 + - - -
191V VAL* 3.5 34.1 + - - +
192V GLY 3.5 10.9 + - - -
193V LYS 4.2 2.0 + - - -
194V GLY 3.2 0.8 - - - -
195V HIS* 1.3 79.1 - - - +
197V VAL* 1.3 61.2 + - - +
199V HIS* 3.2 4.0 + - - +
200V PHE 2.9 19.4 + - - -
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Residues in contact with VAL 197 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190M ARG* 4.0 20.4 - - - +
77V LEU* 4.3 9.2 - - + -
80V LEU* 5.9 0.4 - - + -
126V LYS 6.1 0.4 - - - +
127V GLY* 6.6 0.2 - - - -
128V ASP* 5.0 0.2 - - - +
129V ALA* 3.7 28.9 - - + -
130V LEU* 5.8 2.2 - - + +
188V LEU* 4.1 20.4 - - + +
191V VAL* 4.3 4.7 - - + -
192V GLY 3.1 19.4 + - - +
193V LYS* 3.8 17.3 - - + -
194V GLY 3.3 9.7 + - - +
196V GLY* 1.3 74.7 - - - +
198V TRP* 1.3 59.9 - - - +
200V PHE* 3.3 3.1 + - - +
201V ASP* 2.8 28.0 + - + +
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Residues in contact with TRP 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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187M GLN* 2.9 45.8 + - + +
190M ARG* 4.1 15.0 - - - +
191M VAL* 3.5 25.6 - - + -
199M HIS* 3.6 39.3 - + + -
200M PHE* 3.8 22.9 - + - -
203M MET* 3.8 29.6 - - + -
76V ALA 5.1 1.1 - - - -
77V LEU* 4.6 6.7 - - + -
194V GLY 3.1 13.0 + - - +
195V HIS* 3.6 13.5 - + - +
197V VAL* 1.3 77.0 - - - +
199V HIS* 1.3 72.2 + - - +
201V ASP* 3.2 10.4 + - - +
202V GLN* 2.9 55.8 + - + +
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Residues in contact with HIS 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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195F HIS* 2.9 25.3 + - + +
198F TRP* 3.5 21.7 - + + -
199F HIS* 3.5 43.4 + + - -
202F GLN* 5.6 1.4 - - - +
199M HIS* 3.5 31.7 + + + -
195V HIS 2.9 16.6 + - - +
196V GLY 3.5 4.3 - - - +
198V TRP* 1.3 81.1 - - + +
200V PHE* 1.3 65.2 + - - +
202V GLN* 3.1 10.7 + - + +
203V MET* 3.0 20.1 + - + +
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Residues in contact with PHE 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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198F TRP* 3.8 16.4 - + + -
80V LEU* 4.2 8.5 - - + -
133V MET* 4.7 1.6 - - + -
184V TYR* 3.6 38.1 - + + -
187V GLN* 3.8 35.7 - - + -
188V LEU* 3.5 36.1 - - + -
191V VAL* 4.4 7.2 - - + -
196V GLY 2.9 12.6 + - - +
197V VAL 3.6 6.5 - - - +
199V HIS* 1.3 74.8 - - - +
201V ASP* 1.3 67.8 + - - +
203V MET* 3.0 30.7 + - + +
204V LEU* 2.9 39.2 + - + +
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Residues in contact with ASP 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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76V ALA 4.9 0.3 - - - +
77V LEU* 3.2 27.8 - - + +
78V ARG* 3.1 9.9 + - - +
79V GLY* 2.8 21.0 + - - -
80V LEU* 2.7 39.4 + - + +
197V VAL* 2.8 14.7 + - + +
198V TRP* 3.3 11.2 - - - +
200V PHE* 1.3 82.5 - - - +
202V GLN* 1.3 63.4 + - - +
204V LEU* 3.2 3.8 + - - +
205V LEU* 2.8 27.5 + - - +
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Residues in contact with GLN 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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199M HIS* 5.7 2.0 - - - +
203M MET* 3.3 27.1 - - - +
78V ARG* 3.0 26.6 + - - +
198V TRP* 2.9 48.9 + - + +
199V HIS* 3.1 13.9 + - + +
201V ASP* 1.3 80.4 - - - +
203V MET* 1.3 63.4 + - - +
205V LEU* 3.3 10.1 + - - +
206V HIS* 3.1 52.9 + - - +
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Residues in contact with MET 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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78F ARG* 3.7 9.0 - - - +
198F TRP* 3.9 11.7 - - + -
202F GLN* 3.4 30.7 - - - +
184V TYR* 4.8 1.8 - - + -
187V GLN* 3.7 14.4 - - - +
199V HIS* 3.0 13.2 + - + +
200V PHE* 3.0 43.5 + - + +
202V GLN* 1.3 75.3 - - - +
204V LEU* 1.3 60.0 - - + +
206V HIS* 3.1 5.0 + - - +
207V GLU* 2.8 62.7 + - - +
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Residues in contact with LEU 204 (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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79V GLY* 3.8 22.0 - - - +
80V LEU* 3.9 22.0 - - + -
82V LYS* 5.1 5.2 - - - +
83V PHE* 3.8 21.8 - - + -
133V MET* 4.0 16.2 - - + -
180V ARG* 5.1 1.6 - - - +
184V TYR* 3.3 37.7 - - + +
200V PHE* 2.9 19.8 + - + +
201V ASP* 3.6 8.3 - - - +
203V MET* 1.3 77.4 - - + +
205V LEU* 1.3 66.7 - - - +
207V GLU* 3.2 27.1 + - + +
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Residues in contact with LEU 205 (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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78V ARG* 3.8 59.9 - - + +
79V GLY* 3.7 8.4 - - - +
82V LYS* 3.7 33.3 - - + -
201V ASP* 2.8 17.7 + - - +
202V GLN* 3.4 16.8 - - - +
204V LEU* 1.3 78.4 - - - +
206V HIS* 1.3 80.1 + - + +
207V GLU 5.0 0.5 - - - +
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Residues in contact with HIS 206 (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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203M MET* 6.0 0.4 - - + -
202V GLN* 3.1 41.7 + - - +
203V MET* 3.1 5.9 + - - +
204V LEU 3.1 0.2 - - - -
205V LEU* 1.3 94.4 - - + +
207V GLU* 1.3 67.4 + - - +
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Residues in contact with GLU 207 (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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78F ARG* 3.3 27.0 + - - +
82V LYS* 5.7 3.5 - - - -
180V ARG* 4.3 5.9 + - - -
184V TYR* 2.6 37.9 + - - -
203V MET* 2.8 33.5 + - - +
204V LEU* 3.2 20.6 + - + +
205V LEU 3.5 1.2 - - - +
206V HIS* 1.3 83.3 - - - +
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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