Contacts of the strand formed by residues 183 - 191 (chain s) in PDB entry 5GJQ
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 183 (chain s).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39s PRO 3.6 13.2 - - - -
40s TYR* 4.4 13.7 - - - -
73s ARG* 5.9 0.4 - - - -
178s HIS 4.1 0.2 - - - +
179s VAL* 4.4 3.4 - - - -
180s ARG* 2.7 40.8 + - - +
181s GLU 3.3 1.8 + - - -
182s ASP* 1.3 81.1 - - - +
184s TRP* 1.3 60.2 + - - -
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Residues in contact with TRP 184 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36s GLU* 3.4 41.3 - - + +
38s ASN 2.5 27.6 + - - -
39s PRO* 3.1 30.8 + - + +
40s TYR* 3.9 3.7 - - - +
41s LEU 4.1 5.2 - - - -
42s LEU* 3.7 41.1 - - + +
177s TYR* 3.9 15.3 - + + -
178s HIS 3.0 10.8 - - - +
179s VAL* 3.9 9.3 - - + +
180s ARG* 5.9 0.2 - - - -
183s GLY* 1.3 74.4 - - - -
185s ILE* 1.3 72.1 + - + +
186s ARG* 3.5 26.7 - - - -
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Residues in contact with ILE 185 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153s TYR* 4.8 2.0 - - - +
177s TYR* 3.5 2.3 - - - -
178s HIS* 2.7 47.2 + - + +
180s ARG* 3.8 36.6 - - - +
184s TRP* 1.3 84.6 - - + +
186s ARG* 1.3 77.4 + - + +
187s VAL* 3.0 13.9 + - + -
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Residues in contact with ARG 186 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32s LYS* 4.8 5.6 - - - +
36s GLU* 2.4 36.6 + - - -
175s ASN* 5.7 4.9 - - + +
176s LEU 4.2 4.9 - - - +
177s TYR* 3.5 30.3 + - + -
184s TRP* 3.5 23.1 - - - -
185s ILE* 1.3 82.1 - - + +
187s VAL* 1.3 67.3 + - - +
188s SER 4.9 8.7 - - - +
189s SER* 6.0 4.3 - - - -
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Residues in contact with VAL 187 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153s TYR* 3.3 55.6 - - + +
157s ARG* 4.4 4.5 - - - +
176s LEU* 2.9 21.0 + - + +
177s TYR 4.5 0.7 - - - -
178s HIS* 3.7 19.1 - - + +
185s ILE* 3.0 11.4 + - + +
186s ARG* 1.3 75.5 - - - +
188s SER* 1.3 73.1 + - - +
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Residues in contact with SER 188 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157s ARG* 3.0 28.0 + - - -
174s VAL 4.3 0.6 + - - -
175s ASN* 3.5 3.1 - - - +
176s LEU* 3.0 39.4 + - - +
186s ARG* 3.7 6.6 - - - +
187s VAL* 1.3 84.7 - - - +
189s SER* 1.3 64.5 + - - +
190s ASP* 3.1 18.8 + - - -
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Residues in contact with SER 189 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173s ALA* 4.7 5.9 - - - +
174s VAL 3.4 6.3 - - - -
175s ASN* 2.7 25.8 + - - -
186s ARG* 6.0 5.6 - - - -
188s SER* 1.3 78.0 - - - +
190s ASP* 1.3 63.5 + - - +
191s ASN 3.9 0.5 + - - -
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Residues in contact with ASP 190 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157s ARG* 3.0 34.1 + - - +
173s ALA* 3.3 4.9 - - - +
174s VAL* 2.8 35.5 + - + +
188s SER* 3.1 19.3 + - - -
189s SER* 1.3 73.4 - - - +
191s ASN* 1.3 60.5 + - - +
194s ASP* 5.4 1.8 - - + -
195s LEU* 3.9 28.5 - - + +
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Residues in contact with ASN 191 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203c ARG* 3.0 24.1 + - - +
172s GLY 3.8 10.0 + - - -
173s ALA* 4.3 5.7 - - + +
189s SER 3.9 1.8 + - - -
190s ASP* 1.3 76.0 - - - +
192s VAL* 1.3 66.7 + - - +
193s ALA* 2.8 32.2 + - - +
194s ASP* 3.3 27.3 + - - +
195s LEU* 3.2 22.9 + - - +
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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