Contacts of the strand formed by residues 182 - 186 (chain A) in PDB entry 5CVE
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 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A PHE* 3.8 4.0 - - - -
139A GLY* 3.2 19.7 - - - -
140A HIS* 3.6 18.2 - - - -
176A LEU* 3.6 5.1 - - - +
177A ASP* 2.8 28.4 + - - +
180A ASP* 2.6 21.3 + - - -
181A SER* 1.3 78.0 - - - +
183A VAL* 1.3 67.8 + - - +
1D PBE 6.2 0.3 - - - -
3D LYS* 3.2 15.9 + - - -
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Residues in contact with VAL 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A THR* 3.8 22.0 - - + -
5A VAL* 3.9 28.3 - - + -
6A ILE* 4.5 2.5 - - + -
12A PHE* 4.3 9.9 - - + -
139A GLY* 2.8 37.9 + - - +
141A LEU 4.6 1.3 - - - +
174A VAL* 4.0 7.2 - - + -
175A ILE 3.2 7.9 - - - +
176A LEU* 4.2 9.6 - - + -
177A ASP* 6.1 0.4 - - - -
182A SER* 1.3 82.5 + - - +
184A CYS* 1.3 60.0 + - - +
185A ARG* 3.7 29.5 + - + +
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Residues in contact with CYS 184 (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 ASN* 3.8 28.7 - - + +
169A MET 3.6 7.9 - - - -
170A ALA* 3.3 30.8 - - + +
174A VAL* 3.3 2.4 - - - -
175A ILE* 2.9 36.3 + - + +
183A VAL* 1.3 73.1 - - - +
185A ARG* 1.3 62.7 + - - +
215A TYR* 3.8 33.4 - - + +
3D LYS* 6.1 1.3 - - + -
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Residues in contact with ARG 185 (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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2A THR* 3.5 5.1 - - - +
138A ILE* 3.0 34.1 + - + +
139A GLY* 3.9 1.2 - - - -
141A LEU 2.7 24.5 + - - -
142A THR 3.4 2.8 + - - -
143A ASP* 2.9 40.4 + - - +
146A LEU* 3.8 16.6 - - - +
168A ASN 4.2 2.5 + - - +
169A MET* 3.3 13.9 - - - +
170A ALA 3.0 15.4 + - - -
173A GLY 3.6 4.9 - - - -
174A VAL* 4.1 10.5 - - + -
183A VAL* 3.7 20.9 + - + +
184A CYS* 1.3 76.2 - - - +
186A ASP* 1.3 64.1 + - - +
189A VAL* 3.8 23.6 - - + -
190A VAL* 3.9 19.5 - - + -
193A ILE* 3.5 9.7 - - - +
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Residues in contact with ASP 186 (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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0A HIS* 5.7 1.0 - - - +
169A MET* 4.7 0.7 - - - -
170A ALA* 3.2 21.1 - - - +
171A GLN 4.0 3.5 - - - +
172A GLU* 3.6 10.4 - - - +
173A GLY* 2.7 43.2 + - - +
185A ARG* 1.3 78.9 - - - +
187A LEU* 1.3 65.8 + - - +
188A ASP* 3.0 11.3 + - - +
189A VAL* 2.9 29.0 + - - +
190A VAL* 3.1 19.6 + - - +
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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