Contacts of the strand formed by residues 197 - 206 (chain A) in PDB entry 2GP0
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 PHE 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A GLN* 3.9 15.3 - - + -
156A SER 5.1 0.7 - - - -
159A TRP* 4.0 15.3 - - + -
160A GLU* 3.6 33.0 - - + -
163A TRP* 3.5 38.8 - + + -
193A THR* 3.1 6.1 - - - +
194A TYR* 2.8 45.1 + - - +
195A GLY 3.2 0.2 - - - -
196A PRO* 1.3 97.1 - - + +
198A GLN* 1.3 60.6 + - - +
199A ILE* 4.0 7.1 + - + -
217A ILE* 3.9 29.4 - - + -
218A GLN 3.5 1.3 - - - -
219A TYR* 3.8 26.5 - + + -
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Residues in contact with GLN 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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191A GLU* 2.9 39.4 + - + +
192A GLU 3.7 2.5 - - - +
193A THR* 4.0 10.5 + - - +
196A PRO 4.0 1.2 + - - -
197A PHE* 1.3 73.9 - - - +
199A ILE* 1.3 62.3 + - - +
200A ARG* 3.0 39.6 + - + +
216A THR* 3.7 1.4 + - - +
217A ILE* 3.4 2.8 - - - -
218A GLN* 2.9 52.9 + - + +
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Residues in contact with ILE 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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159A TRP* 3.7 39.5 - - + -
188A PRO* 3.5 22.3 - - + +
191A GLU* 3.3 4.7 - - - +
192A GLU 2.8 31.3 + - - +
194A TYR* 3.3 35.2 - - + -
197A PHE* 4.4 4.7 - - + +
198A GLN* 1.3 74.7 - - - +
200A ARG* 1.3 69.6 + - - +
215A LEU* 4.4 11.7 - - + -
216A THR 3.2 9.4 - - - +
217A ILE* 3.6 33.2 - - + -
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Residues in contact with ARG 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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188A PRO* 4.4 3.4 - - - -
190A GLU 3.5 7.2 - - - +
191A GLU* 3.8 23.9 + - + +
198A GLN* 3.0 39.2 + - + +
199A ILE* 1.3 79.7 - - - +
201A ILE* 1.3 63.7 + - - +
202A GLN* 3.8 3.0 + - + -
215A LEU* 3.1 8.8 - - - +
216A THR* 2.9 47.0 + - - +
218A GLN* 5.6 1.8 + - - -
223A ARG* 5.4 6.7 - - - +
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Residues in contact with ILE 201 (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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187A TRP* 5.1 0.2 - - + -
188A PRO* 3.9 12.7 - - + +
189A THR 3.0 34.8 - - - +
190A GLU* 3.0 19.5 + - - +
200A ARG* 1.3 74.6 - - - +
202A GLN* 1.3 60.1 + - - +
203A ASP* 3.6 18.2 - - - +
204A MET* 4.3 13.2 - - + -
213A ARG* 3.8 39.7 - - + +
214A GLN 3.7 5.2 - - - +
215A LEU* 4.0 10.1 - - + -
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Residues in contact with GLN 202 (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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200A ARG* 4.4 7.0 - - + +
201A ILE* 1.3 75.7 - - - +
203A ASP* 1.3 61.9 + - + +
214A GLN* 2.8 24.4 + - + +
215A LEU 4.4 1.6 - - - -
216A THR* 3.7 31.9 - - + +
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Residues in contact with ASP 203 (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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201A ILE* 3.6 11.8 - - - +
202A GLN* 1.3 83.0 - - + +
204A MET* 1.3 76.2 + - - +
205A LYS* 4.4 15.0 - - - +
212A VAL 4.6 0.2 - - - -
213A ARG* 3.4 4.0 - - - -
214A GLN* 2.9 42.2 + - + +
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Residues in contact with MET 204 (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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201A ILE* 4.3 10.8 - - + -
203A ASP* 1.3 85.2 + - - +
205A LYS* 1.3 61.8 + - - +
206A GLU* 4.3 11.2 + - + +
211A THR* 3.9 21.3 - - + +
212A VAL 3.5 3.8 - - - -
213A ARG* 3.2 42.8 - - + +
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Residues in contact with LYS 205 (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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203A ASP* 4.4 11.2 - - - +
204A MET* 1.3 73.7 - - - +
206A GLU* 1.3 65.4 + - - +
207A CYS* 3.7 27.6 + - - -
211A THR* 3.5 2.4 - - - -
212A VAL* 2.8 54.3 + - + +
252A GLU* 5.2 7.3 + - - -
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Residues in contact with GLU 206 (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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204A MET* 4.3 11.3 + - + -
205A LYS* 1.3 74.5 - - - +
207A CYS* 1.3 66.7 + - - +
210A TYR 4.1 2.2 - - - -
211A THR* 3.9 22.7 - - + +
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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