Contacts of the helix formed by residues 169 - 174 (chain A) in PDB entry 4GWR
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 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A GLU 4.6 1.6 + - - -
165A LEU* 3.6 13.2 - - - +
166A THR* 2.9 34.5 + - - +
168A ASP* 1.3 76.6 - - - +
170A PHE* 1.3 64.1 + - - +
171A ASP 3.5 2.0 + - - -
172A LYS* 3.7 5.2 + - - +
173A ASN* 2.9 40.5 + - - +
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Residues in contact with PHE 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LEU* 3.8 25.6 - - + -
166A THR 2.9 16.4 + - - +
167A ASP 4.1 2.7 + - - +
168A ASP 3.6 1.0 - - - -
169A SER* 1.3 79.9 + - - +
171A ASP* 1.3 73.3 + - - +
173A ASN* 4.7 3.1 - - - -
174A VAL* 2.7 64.9 + - + +
175A LEU* 4.3 4.7 - - + -
183A VAL* 4.3 11.2 - - + -
185A PHE* 4.4 11.4 - + - -
220A VAL* 4.4 1.1 - - + -
228A LEU* 3.7 30.1 - - + -
231A ARG* 4.3 0.2 - - - -
232A TYR* 3.6 24.5 - + - -
243A PHE* 3.5 30.3 - + - -
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Residues in contact with ASP 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ASP 5.1 5.9 + - - -
168A ASP 5.1 1.4 + - - -
169A SER 3.5 0.6 + - - -
170A PHE* 1.3 84.5 - - - +
172A LYS* 1.3 59.0 + - - +
175A LEU* 3.0 37.2 + - + +
176A ASP* 3.1 14.3 + - - +
228A LEU* 4.7 0.5 - - - +
231A ARG* 2.8 45.6 + - - -
171B ASP* 2.7 33.3 - - - +
231B ARG* 4.6 2.0 - - - +
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Residues in contact with LYS 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ASP 5.6 1.7 + - - +
169A SER* 3.7 6.7 + - - +
170A PHE 3.4 0.2 - - - -
171A ASP* 1.3 78.4 - - - +
173A ASN* 1.3 68.3 + - - +
176A ASP* 3.7 36.9 + - + +
177A SER* 5.0 0.3 - - - -
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Residues in contact with ASN 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ILE* 4.9 6.0 - - - +
165A LEU* 3.8 23.1 - - + +
169A SER* 2.9 42.0 + - - +
170A PHE 3.9 0.9 - - - +
172A LYS* 1.3 84.1 - - - +
174A VAL* 1.3 58.8 + - - +
177A SER* 3.2 21.0 - - - -
181A TRP* 3.3 27.4 - - + -
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Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LEU* 3.6 31.4 - - + -
170A PHE* 2.7 40.2 + - + +
173A ASN* 1.3 75.1 - - + +
175A LEU* 1.3 67.1 + - + +
176A ASP 3.2 1.6 - - - -
177A SER* 3.3 17.0 + - - +
179A ASP 4.8 0.9 - - - +
181A TRP* 3.7 32.5 - - + +
183A VAL* 4.9 0.2 - - + -
243A PHE* 3.6 39.3 - - + -
244A GLN 6.1 0.3 - - - -
245A LYS* 5.8 2.3 - - - -
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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