Contacts of the strand formed by residues 175 - 180 (chain B) in PDB entry 6C1V
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 SER 175 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163B GLU* 2.7 40.0 + - - -
164B VAL 3.4 13.7 - - - -
165B ILE* 4.0 11.7 - - - -
166B ARG* 4.4 4.3 - - - +
174B LYS* 1.3 79.3 - - - +
176B ASP* 1.3 59.7 + - - +
209B ARG* 2.8 49.7 + - - +
305B UNX 4.0 0.9 - - - -
306B UNX 3.8 5.4 - - - -
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Residues in contact with ASP 176 (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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162B GLU 3.8 0.9 - - - +
163B GLU* 3.5 2.6 - - - +
164B VAL* 3.0 34.1 + - + +
166B ARG* 2.9 36.5 + - - +
175B SER* 1.3 73.0 - - - +
177B VAL* 1.3 62.7 + - - +
178B TYR* 3.6 35.5 + - + +
209B ARG* 4.8 0.9 - - - +
306B UNX 2.8 24.1 - - - -
1C C 3.8 15.3 + - - -
10D C 5.1 0.5 - - - -
11D C 4.3 5.4 + - - -
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Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LYS* 3.6 17.7 - - - -
162B GLU 3.4 5.8 - - - +
163B GLU* 4.3 15.5 - - + +
175B SER 4.3 0.4 + - - -
176B ASP* 1.3 77.7 - - - +
178B TYR* 1.3 71.4 + - - +
179B TYR* 3.6 15.9 - - + -
187B PHE 4.3 0.3 - - - +
188B ARG* 4.4 3.8 - - - +
208B PHE* 3.3 48.0 - - + +
209B ARG* 3.5 44.2 - - - +
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Residues in contact with TYR 178 (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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161B LYS* 3.4 6.1 - - - +
162B GLU* 2.8 47.5 + - + +
164B VAL* 4.0 32.6 - - + +
176B ASP* 3.6 31.4 + - + +
177B VAL* 1.3 78.6 - - - +
179B TYR* 1.3 68.2 + - - +
180B PHE* 4.1 18.8 - + + -
186B LYS* 4.3 21.3 - - + -
187B PHE 3.5 4.3 - - - +
188B ARG* 4.0 38.0 + - + -
1C C 4.8 8.0 + - - -
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Residues in contact with TYR 179 (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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152B CYS* 4.3 6.1 - - - -
155B LEU* 3.6 28.5 - - + -
159B TRP* 4.3 10.8 - + + -
160B LYS 3.5 14.1 - - - -
161B LYS* 3.7 24.1 - - + +
177B VAL* 3.6 7.9 - - + -
178B TYR* 1.3 74.7 - - - +
180B PHE* 1.3 64.7 + - - +
185B LYS 4.1 0.2 - - - -
186B LYS* 3.3 6.4 - - - -
187B PHE* 2.7 45.7 + - + +
193B LEU* 4.3 6.7 - - + -
206B PHE* 3.4 10.8 - + - -
208B PHE* 2.8 63.4 + + - -
211B GLY* 3.1 21.8 + - - -
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Residues in contact with PHE 180 (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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149B ARG* 3.2 62.4 - - + +
159B TRP* 3.0 16.6 - - - -
160B LYS* 3.0 36.0 + - + +
162B GLU* 4.0 19.1 - - + -
178B TYR* 4.1 19.7 - + + -
179B TYR* 1.3 78.2 - - - +
181B SER* 1.3 68.6 + - - +
184B GLY* 3.9 20.6 - - - -
185B LYS 3.3 4.3 - - - +
186B LYS* 3.9 36.6 - - + -
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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