Contacts of the strand formed by residues 207 - 213 (chain A) in PDB entry 2OM5
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 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A GLY 4.7 11.0 - - - -
119A TRP* 4.3 18.2 - + - -
120A GLY 6.0 0.7 - - - -
203A ASP* 3.5 32.3 - - + -
205A ARG* 3.9 27.1 - - + -
206A LEU* 1.3 81.3 - - - +
208A ALA* 1.3 61.9 + - - +
235A GLY* 3.9 4.9 - - - -
236A ASN* 3.0 30.8 + - + +
280A ASN* 2.7 27.2 + - - -
282A LYS* 4.4 2.5 - - - -
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Residues in contact with ALA 208 (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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207A PHE* 1.3 78.5 - - - +
209A PRO* 1.3 78.7 - - + +
210A SER* 3.5 4.2 + - - -
234A PHE 4.5 0.3 - - - +
235A GLY* 4.9 0.2 - - - -
280A ASN* 3.9 5.6 - - - +
282A LYS* 3.8 28.1 - - + +
283A GLY* 4.0 5.4 - - - -
284A ARG 5.0 0.7 - - - +
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Residues in contact with PRO 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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208A ALA* 1.3 86.8 - - + +
210A SER* 1.3 60.1 + - - +
233A ALA* 4.3 0.4 - - + -
234A PHE 3.1 13.7 - - - +
239A PRO* 3.9 14.8 - - + -
278A ALA* 3.3 43.7 - - + +
280A ASN* 3.3 20.3 - - - +
283A GLY 3.1 25.6 - - - +
284A ARG 4.1 0.6 - - - +
285A ASP* 3.1 21.1 + - - +
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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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208A ALA 3.5 4.3 + - - -
209A PRO* 1.3 72.6 - - - +
211A ILE* 1.3 61.5 + - - +
212A LYS* 3.4 27.0 + - - +
233A ALA* 3.8 2.5 - - - -
234A PHE* 2.8 43.3 + - - -
285A ASP* 3.4 5.9 + - - -
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Residues in contact with ILE 211 (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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210A SER* 1.3 73.6 + - - +
212A LYS* 1.3 68.6 + - - +
213A ALA 3.6 24.5 - - - +
214A ARG* 4.1 25.1 + - - +
231A CYS* 3.9 18.4 - - - -
232A PHE 3.7 5.2 - - - +
233A ALA* 3.7 5.8 - - + -
276A CYS 4.2 1.3 - - - +
278A ALA* 3.6 22.0 - - + -
285A ASP* 2.6 50.1 + - - +
286A THR* 3.8 5.2 - - - -
287A VAL* 3.7 24.7 - - + -
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Residues in contact with LYS 212 (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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163A TYR* 3.6 22.6 + - + -
210A SER* 3.4 31.6 + - - +
211A ILE* 1.3 74.4 - - - +
213A ALA* 1.3 61.2 + - - +
214A ARG* 3.9 6.5 + - - +
232A PHE 3.3 5.5 + - - +
234A PHE* 3.3 46.4 - - + +
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Residues in contact with ALA 213 (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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154A PHE* 4.6 8.5 - - + -
156A SER* 5.7 1.1 - - - -
163A TYR* 3.8 29.6 - - + +
211A ILE* 3.6 4.1 - - - +
212A LYS* 1.3 78.3 - - - +
214A ARG* 1.3 62.8 + - - +
230A GLU* 3.5 5.2 - - + +
231A CYS* 3.2 10.9 - - - +
232A PHE* 3.2 39.8 + - + +
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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