Contacts of the strand formed by residues 206 - 210 (chain A) in PDB entry 2OT7
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 LYS 206 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A TYR* 3.1 15.0 + - - -
177A TYR* 5.0 0.8 - - - +
185A PHE* 3.9 15.9 - - + -
198A ASN* 4.0 1.8 - - - -
200A LEU* 4.0 8.4 - - + +
205A PRO* 1.3 73.8 - - - +
207A SER* 1.3 58.2 + - - +
208A TRP* 3.4 23.7 - - + +
261A THR* 3.6 0.4 - - - -
262A GLN* 2.7 60.5 + - - +
279A PHE 3.6 4.9 - - - +
280A ASN* 2.7 30.1 + - - +
284A ASN* 4.5 4.5 + - - +
286A ALA* 3.8 27.3 - - - +
500A OGA 2.7 28.8 + - - +
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Residues in contact with SER 207 (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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114A PHE* 3.1 18.6 - - - -
185A PHE* 3.8 4.7 - - - -
206A LYS* 1.3 69.2 - - - +
208A TRP* 1.3 65.4 + - - +
209A TYR* 5.4 2.2 - - - -
260A VAL 3.6 4.0 - - - -
261A THR* 2.7 25.4 + - - -
278A GLY* 3.1 6.4 - - - -
279A PHE* 2.9 49.2 + - - +
281A HIS* 2.9 24.4 + - - -
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Residues in contact with TRP 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 5.9 0.2 - - - -
44A LEU* 3.5 33.2 - - + -
185A PHE* 3.8 15.5 - + - -
198A ASN* 4.0 11.4 - - + -
206A LYS* 3.4 36.4 + - + +
207A SER* 1.3 78.0 - - - +
209A TYR* 1.3 67.1 + - - +
259A LYS* 3.4 5.2 - - - +
260A VAL* 2.8 41.3 + - + +
262A GLN* 3.2 28.8 + - + +
268A MET* 3.6 26.3 - - + +
270A THR* 3.8 14.1 - - + -
276A HIS* 3.7 29.4 - + + -
277A ALA 3.4 4.5 - - - -
500A OGA 3.6 27.6 - - - -
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Residues in contact with TYR 209 (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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114A PHE* 5.1 3.3 - + - -
118A GLU* 2.2 37.7 + - - +
122A TRP* 3.1 39.0 + + - -
187A TRP* 3.6 25.1 - + + -
207A SER* 5.4 1.3 - - - -
208A TRP* 1.3 79.3 - - - +
210A SER* 1.3 61.4 + - - +
245A ILE 5.9 0.7 - - - -
247A PRO* 3.7 25.3 - - + +
250A LEU* 6.4 0.2 - - + -
257A PHE* 4.4 5.2 - + + -
258A ASP 3.4 6.5 - - - +
259A LYS* 3.9 25.1 - - + -
276A HIS* 3.1 9.7 - - - +
277A ALA* 2.7 39.4 + - + +
278A GLY* 4.2 6.7 - - - -
279A PHE* 3.9 23.1 - + - -
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Residues in contact with SER 210 (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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14A ILE* 4.2 11.0 - - - -
42A ALA 3.0 23.3 + - - +
43A GLY* 3.7 6.6 - - - -
44A LEU* 3.4 33.0 - - - +
187A TRP* 3.9 1.1 - - - -
209A TYR* 1.3 77.2 - - - +
211A VAL* 1.3 63.5 + - - +
212A PRO* 4.1 1.4 - - - +
257A PHE* 3.0 5.9 - - - -
258A ASP* 2.8 31.0 + - - +
274A GLY 5.2 0.2 - - - -
275A TYR 3.3 11.2 + - - -
276A HIS* 4.8 1.7 - - - +
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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