Contacts of the strand formed by residues 197 - 206 (chain A) in PDB entry 2O0L
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 LEU 197 (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* 3.4 15.2 - - - +
167A PHE 3.4 14.1 - - - +
168A ASP 4.0 4.5 - - - +
170A ILE* 3.7 23.6 - - + -
193A MET 2.9 17.8 + - - +
194A LYS* 4.5 2.2 - - - -
195A THR 3.2 4.0 - - - +
196A ALA* 1.3 78.3 - - - +
198A LYS* 1.3 72.2 + - - +
201A GLY* 3.6 20.9 - - - +
202A VAL* 3.4 34.1 - - - +
203A LEU* 4.3 16.8 - - + +
228A PHE* 4.6 2.0 - - + -
251A CYS 5.1 0.7 - - - +
253A LYS* 3.1 33.2 + - + -
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Residues in contact with LYS 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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95A ARG* 5.7 7.6 - - - +
96A LYS* 4.9 8.5 - - - -
165A ASP* 3.2 39.1 + - - +
166A ALA* 3.6 18.1 + - - +
167A PHE 2.7 24.6 + - - +
168A ASP* 3.6 22.0 - - - +
197A LEU* 1.3 78.5 - - - +
199A GLU* 1.3 66.9 + - + +
200A ASP* 3.3 13.5 - - - +
201A GLY* 3.0 12.7 + - - +
253A LYS* 3.3 11.3 + - - +
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Residues in contact with GLU 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ASP* 3.9 8.3 + - - +
198A LYS* 1.3 73.2 - - - +
200A ASP* 1.3 62.9 + - + +
253A LYS* 3.4 33.2 - - - +
254A ASN* 4.9 0.2 - - - -
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Residues in contact with ASP 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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91A HIS* 3.6 29.0 + - - -
92A PRO* 5.6 6.5 - - + +
168A ASP* 4.8 2.4 - - - +
198A LYS* 4.2 12.5 - - - +
199A GLU* 1.3 78.8 + - + +
201A GLY* 1.3 65.5 + - - +
202A VAL* 4.0 5.0 - - - +
254A ASN* 3.9 37.7 + - + +
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Residues in contact with GLY 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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91A HIS* 4.5 0.7 - - - -
167A PHE 4.4 1.6 - - - -
168A ASP* 3.4 16.8 - - - -
197A LEU* 3.6 18.8 - - - +
198A LYS 3.0 18.8 + - - -
199A GLU 3.5 0.8 + - - -
200A ASP* 1.3 81.8 + - - +
202A VAL* 1.3 60.9 + - - +
252A SER* 3.7 0.2 - - - -
253A LYS* 3.0 26.4 + - - +
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Residues in contact with VAL 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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87A PRO* 3.6 35.4 - - + +
90A SER 4.3 14.6 - - - +
91A HIS* 4.1 9.9 - - + -
92A PRO* 6.2 0.2 - - + -
168A ASP 2.9 7.4 + - - +
169A VAL* 3.1 41.6 - - + +
170A ILE 3.1 3.1 + - - -
197A LEU* 3.4 7.5 - - - +
200A ASP 4.0 7.6 - - - +
201A GLY* 1.3 78.5 - - - -
203A LEU* 1.3 61.8 + - - +
251A CYS 3.4 9.9 - - - +
252A SER* 3.5 22.4 - - - +
257A THR* 4.4 3.6 - - - +
259A PHE* 4.3 10.8 - - + -
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Residues in contact with LEU 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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87A PRO* 4.5 4.9 - - - +
170A ILE* 3.2 7.6 - - + +
190A TYR* 3.8 16.2 - - + -
193A MET* 3.3 40.8 - - + -
197A LEU* 4.4 6.7 - - + -
202A VAL* 1.3 76.2 - - - +
204A CYS* 1.3 64.2 + - - +
205A CYS* 3.8 23.6 - - - -
228A PHE* 3.6 33.4 - - + -
249A MET 4.1 5.8 - - - +
250A LEU* 3.3 10.0 - - - +
251A CYS* 2.9 49.1 + - + +
259A PHE* 4.6 0.5 - - - -
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Residues in contact with CYS 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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83A ILE* 3.8 31.4 - - - +
86A LEU* 4.9 1.6 - - - -
87A PRO* 3.6 26.2 - - + +
170A ILE 2.8 9.1 + - - +
171A ILE* 3.2 8.0 - - + +
172A THR 3.0 22.9 + - - +
203A LEU* 1.3 76.7 - - - +
205A CYS* 1.3 64.4 + - - +
248A PHE* 3.9 24.0 - - - -
249A MET 3.2 3.4 - - - -
250A LEU* 3.7 17.9 - - + -
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Residues in contact with CYS 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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83A ILE* 4.6 2.7 - - - -
172A THR* 3.6 27.8 - - + -
189A TYR* 4.5 3.1 - - - -
190A TYR* 3.1 39.5 - - + +
193A MET* 3.8 13.0 - - - -
203A LEU* 3.8 14.6 - - - -
204A CYS* 1.3 74.7 - - - +
206A GLN* 1.3 70.1 - - - +
207A GLY 3.1 0.5 + - - -
248A PHE* 3.4 4.3 - - - -
249A MET 2.9 29.0 + - - +
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Residues in contact with GLN 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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79A TYR* 3.0 37.8 + - + +
83A ILE* 4.1 5.0 - - - +
172A THR* 3.3 14.3 + - - +
173A ASP* 4.5 0.7 - - - +
174A SER* 3.3 38.9 + - - +
175A SER 5.8 1.8 - - - -
190A TYR* 4.8 2.1 + - - -
205A CYS* 1.3 78.8 - - - +
207A GLY* 1.3 65.7 + - - +
241A TYR* 5.0 4.7 + - - -
246A ILE* 3.6 32.6 - - + +
247A GLY 4.0 3.6 - - - +
248A PHE* 4.5 2.2 - - - -
249A MET* 5.2 0.3 - - - +
501A S4M 5.4 1.2 - - - +
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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