Contacts of the helix formed by residues 189 - 198 (chain V) in PDB entry 1P7G
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 ASP 189 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186V TYR* 3.1 25.9 + - + +
187V LYS 3.2 2.7 - - - -
188V ASN* 1.3 82.4 - - - +
190V ARG* 1.3 63.3 + - - +
191V GLY* 3.5 5.0 + - - -
192V SER* 2.9 43.7 + - - -
193V TYR 3.4 8.0 + - - -
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Residues in contact with ARG 190 (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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133V ALA 3.3 28.0 + - - -
134V LYS* 3.3 21.1 + - - +
136V VAL* 2.6 28.2 + - - +
138V GLY 2.8 27.9 + - - +
139V VAL* 5.7 0.4 - - - +
177V VAL* 3.7 25.6 + - + -
179V GLU* 5.8 2.4 - - - +
182V TYR* 3.5 43.6 + - + +
188V ASN 2.8 11.4 + - - +
189V ASP* 1.3 72.0 - - - +
191V GLY* 1.3 63.9 + - - +
193V TYR* 3.1 4.6 + - + +
194V VAL* 3.0 28.8 + - + +
178X TRP* 6.2 0.2 - - - -
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Residues in contact with GLY 191 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134V LYS* 3.6 29.9 - - - +
189V ASP* 3.2 5.3 + - - -
190V ARG* 1.3 79.7 - - - +
192V SER* 1.3 59.5 + - - +
194V VAL 3.4 0.5 + - - -
195V ASP* 3.1 30.7 + - - -
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Residues in contact with SER 192 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186V TYR* 3.5 13.0 - - - -
189V ASP* 2.9 34.7 + - - -
190V ARG 3.2 0.2 - - - -
191V GLY* 1.3 73.6 - - - +
193V TYR* 1.3 64.0 + - - +
195V ASP* 3.4 6.5 + - - +
196V ASN* 2.7 43.9 + - - -
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Residues in contact with TYR 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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33V TYR 4.9 2.5 - - - -
34V ILE* 4.4 20.7 - - + +
93V PHE* 3.7 16.6 - - - -
175V LEU* 3.4 22.9 - - + +
176V ASP 2.8 29.2 + - - -
177V VAL* 4.2 6.3 - - + -
181V ALA* 3.6 22.2 + - - +
182V TYR* 3.3 43.3 - + + -
186V TYR* 3.6 29.5 - + + -
189V ASP 3.4 3.8 + - - +
190V ARG* 3.1 10.7 + - + +
192V SER* 1.3 79.2 - - - +
194V VAL* 1.3 67.9 + - + +
196V ASN* 3.3 2.6 + - - +
197V TRP* 3.0 25.6 + - + +
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Residues in contact with VAL 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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130V SER* 3.4 37.9 - - - +
133V ALA* 3.9 20.2 - - + -
134V LYS* 3.9 17.7 - - + +
175V LEU* 3.9 22.2 - - + -
177V VAL* 4.2 11.9 - - + -
190V ARG* 3.0 19.1 + - + +
191V GLY 3.6 7.6 - - - +
192V SER 3.3 0.2 - - - -
193V TYR* 1.3 80.7 - - + +
195V ASP* 1.3 63.2 + - - +
197V TRP* 3.4 12.6 + - - +
198V TRP* 3.4 17.4 + - + +
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Residues in contact with ASP 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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130V SER* 4.0 5.9 + - - -
134V LYS* 3.1 26.6 + - - -
191V GLY 3.1 20.5 + - - +
192V SER* 3.8 7.5 - - - +
193V TYR 3.3 0.2 - - - -
194V VAL* 1.3 74.9 - - - +
196V ASN* 1.3 63.9 + - - +
198V TRP* 3.4 25.8 + - - +
199V ASN* 4.1 4.0 - - - +
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Residues in contact with ASN 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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33V TYR* 3.6 31.6 - - + +
186V TYR* 3.3 35.0 - - - +
192V SER* 2.7 31.5 + - - +
193V TYR 3.8 1.8 - - - +
195V ASP* 1.3 76.8 - - - +
197V TRP* 1.3 55.5 + - - +
199V ASN* 2.8 41.6 + - - +
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Residues in contact with TRP 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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33V TYR* 5.3 2.5 - - - -
34V ILE* 4.6 8.1 - - + -
93V PHE* 4.0 4.9 - + - -
96V ASN* 5.4 0.9 - - + -
97V MSE 3.7 38.3 - - + +
129V PHE* 3.5 32.1 - + - -
173V LEU* 3.7 36.3 - - + -
174V ALA 3.8 14.6 - - - -
175V LEU* 3.5 36.3 - - + +
193V TYR* 3.0 20.2 + - + +
194V VAL 3.4 10.3 - - - +
195V ASP 3.3 0.2 - - - -
196V ASN* 1.3 75.6 - - - +
198V TRP* 1.3 101.0 + + - +
199V ASN 2.9 0.2 - - - -
200V VAL* 2.8 29.5 + - + +
201V VAL* 3.6 15.2 + - + +
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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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104V GLY* 3.2 16.8 - - - -
105V GLY 4.2 3.3 + - - +
122V PHE* 4.6 2.0 - + + -
125V PHE* 3.9 18.8 - + - -
126V LYS* 3.6 67.0 - - + +
129V PHE* 3.5 39.0 - + + -
130V SER* 4.2 15.6 + - - -
173V LEU* 4.5 2.2 - - + -
194V VAL* 3.4 15.7 + - + +
195V ASP* 3.4 27.2 + - - +
196V ASN 3.1 0.8 + - - -
197V TRP* 1.3 102.9 - + - +
199V ASN* 1.3 59.7 + - - +
200V VAL 3.1 4.7 + - - -
201V VAL* 3.4 22.5 + - + +
203V TRP* 4.2 15.9 + + - -
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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