Contacts of the strand formed by residues 193 - 200 (chain A) in PDB entry 2C1H
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 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A ASP 3.1 10.7 + - - -
166A PHE* 3.4 24.5 - - - -
167A VAL* 2.9 30.0 + - - +
181A ARG* 3.8 1.1 - - - -
191A ASP 3.6 4.4 + - - -
192A VAL* 1.3 75.2 - - - +
194A ILE* 1.3 60.9 - - - -
248A ASP* 3.4 13.2 - - - -
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Residues in contact with ILE 194 (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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166A PHE* 3.3 4.3 - - - -
167A VAL* 3.4 21.3 - - + +
169A PRO* 4.1 8.7 - - + -
177A ILE* 3.9 42.8 - - + +
180A ILE* 3.9 9.2 - - + -
181A ARG* 3.4 57.4 - - + +
184A LEU* 4.1 2.5 - - + -
193A GLY* 1.3 76.9 - - - +
195A LEU* 1.3 60.2 + - - +
196A SER* 3.6 3.1 + - - +
246A GLY 5.3 2.5 - - - +
247A ALA* 4.0 3.5 - - - -
248A ASP* 2.9 33.1 + - - +
249A ILE 3.4 7.1 + - - +
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Residues in contact with LEU 195 (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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121A MET* 3.6 32.3 - - + -
166A PHE* 3.5 12.9 - - + -
167A VAL 2.9 8.3 + - - -
168A SER* 3.3 32.4 - - - -
169A PRO* 3.4 4.3 - - - +
194A ILE* 1.3 69.4 - - - +
196A SER* 1.3 65.0 + - - +
197A TYR* 3.6 2.6 + - + -
249A ILE* 3.4 33.9 - - + -
251A MET* 3.7 42.0 - - + +
274A ALA* 4.2 4.5 - - + -
314A ILE* 4.5 2.0 - - + -
316A PHE* 3.7 18.6 - - + -
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Residues in contact with SER 196 (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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169A PRO* 4.4 0.4 - - - -
176A ARG* 3.9 1.6 + - - -
177A ILE* 3.3 32.4 - - - +
194A ILE 3.6 3.2 + - - -
195A LEU* 1.3 73.5 - - - +
197A TYR* 1.3 59.9 + - - +
198A ALA 3.0 4.4 + - - -
242A ASP* 2.7 29.5 + - - -
247A ALA* 3.9 17.3 - - - -
249A ILE 2.8 10.3 + - - -
250A VAL* 3.5 3.3 - - - -
251A MET* 2.7 34.7 + - - +
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Residues in contact with TYR 197 (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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82A ASP* 3.4 14.7 + - - -
84A PHE* 4.2 5.0 - - - -
123A ASP* 4.6 1.2 + - - -
168A SER* 3.4 30.7 - - - -
169A PRO 3.3 25.6 + - - +
170A SER* 3.6 19.1 - - - -
172A MET* 3.6 9.5 - - - +
176A ARG* 2.9 18.3 + - - +
195A LEU* 3.9 8.5 - - + -
196A SER* 1.3 68.9 + - - +
198A ALA* 1.3 64.2 + - - +
199A ALA 3.5 2.0 - - - -
200A LYS* 3.6 29.0 + - + -
251A MET* 3.7 32.8 - - - -
253A LYS* 3.8 26.2 - - + -
276A TYR* 3.2 23.9 - + - -
316A PHE* 4.1 3.2 - + - -
1330A DSB 4.7 0.4 - - + -
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Residues in contact with ALA 198 (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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172A MET* 3.6 7.1 - - - +
196A SER* 3.0 5.3 + - - +
197A TYR* 1.3 76.5 - - - +
199A ALA* 1.3 59.6 + - - +
238A GLU* 3.6 27.2 - - - +
239A VAL* 3.7 29.2 - - + -
242A ASP* 3.3 23.6 - - - +
250A VAL* 4.0 20.0 - - + -
251A MET 3.1 8.7 + - - +
1329A MG 4.3 0.3 - - - -
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Residues in contact with ALA 199 (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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172A MET* 4.7 0.2 - - - -
198A ALA* 1.3 77.8 - - - +
200A LYS* 1.3 58.4 + - - +
201A TYR* 3.5 14.3 - - + -
227A MET* 4.0 12.8 - - - -
235A ALA* 4.0 29.6 - - + +
239A VAL* 4.5 11.0 - - + -
251A MET 3.2 7.5 + - - +
252A VAL* 3.7 4.2 - - + -
253A LYS 3.1 26.6 + - - +
261A ILE* 4.6 7.2 - - + -
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Residues in contact with LYS 200 (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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135A ASP* 5.0 0.2 + - - -
170A SER 3.4 23.1 + - - +
172A MET* 3.5 26.5 - - + +
197A TYR* 3.6 27.8 - - + +
199A ALA* 1.3 73.1 - - - +
201A TYR* 1.3 61.8 + - - +
206A TYR* 3.8 11.4 - - - +
226A GLN* 3.5 22.0 - - - +
227A MET* 3.0 20.7 + - - +
253A LYS* 3.4 19.7 - - + +
1330A DSB 1.3 85.0 - - - +
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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