Contacts of the strand formed by residues 279 - 284 (chain A) in PDB entry 1OLS
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 279 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A ILE 3.0 8.4 + - - +
216A ILE* 3.4 4.9 - - + -
217A PHE* 2.8 28.5 + - - +
248A ILE* 3.9 2.7 - - - -
249A MET* 3.3 30.7 - - + -
267A GLU* 6.1 0.7 - - + -
268A ALA* 3.8 40.8 - - + -
271A ARG* 3.3 46.2 - - + -
272A ALA* 3.6 19.1 - - + -
277A GLN* 3.4 37.0 - - + -
278A PRO* 1.3 76.6 - - - +
280A LEU* 1.3 61.6 + - - +
281A ILE* 5.5 0.9 - - + -
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Residues in contact with LEU 280 (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 PHE* 4.4 5.8 - - + -
205A PHE* 4.3 19.3 - - + -
217A PHE* 3.5 27.6 - - + +
219A CYS* 4.6 1.6 - - + -
239A ILE* 3.6 35.2 - - + +
240A ALA* 4.0 9.9 - - - -
243A GLY* 3.7 22.9 - - - +
248A ILE* 3.7 9.4 - - + +
249A MET 2.8 8.7 + - - -
250A SER* 3.2 14.6 - - - +
251A ILE* 2.9 28.8 + - - +
279A PHE* 1.3 72.7 - - - +
281A ILE* 1.3 75.1 + - - +
282A GLU* 4.8 0.4 - - - +
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Residues in contact with ILE 281 (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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216A ILE* 3.7 25.4 - - + -
217A PHE 2.9 10.1 + - - +
218A PHE* 3.5 24.4 - - + -
219A CYS* 2.9 27.0 + - - +
251A ILE* 3.4 23.3 - - + -
253A VAL* 4.2 24.0 - - + -
261A VAL 6.0 0.2 - - - +
264A ALA* 3.8 10.8 - - + +
265A THR* 3.7 36.1 - - - +
268A ALA* 4.0 8.1 - - + -
279A PHE* 5.5 0.9 - - + -
280A LEU* 1.3 80.0 - - - +
282A GLU* 1.3 62.7 + - - +
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Residues in contact with GLU 282 (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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219A CYS* 3.4 13.9 - - + +
221A ASN* 2.9 32.1 + - + +
238A GLY* 3.9 0.9 - - - -
239A ILE* 2.9 29.0 + - + +
240A ALA* 2.8 35.2 + - + +
251A ILE 2.9 10.4 + - - +
252A ARG* 2.9 29.8 + - - +
253A VAL 2.8 26.3 + - - +
280A LEU* 4.1 1.3 - - + +
281A ILE* 1.3 72.8 - - - +
283A ALA* 1.3 60.5 + - - +
284A MET* 3.8 17.9 - - - -
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Residues in contact with ALA 283 (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 THR* 3.7 28.7 - - + -
218A PHE* 3.7 24.7 - - + -
219A CYS 2.8 10.0 + - - +
220A ARG* 3.8 2.8 - - - -
221A ASN 3.0 24.3 + - - -
253A VAL* 3.5 17.5 - - + -
255A GLY* 4.1 2.2 - - - -
261A VAL* 4.8 0.2 - - + -
281A ILE 3.9 1.2 - - - -
282A GLU* 1.3 70.3 - - - +
284A MET* 1.3 64.1 + - - +
285A THR* 3.5 3.3 + - - -
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Residues in contact with MET 284 (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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33A ILE* 4.0 21.1 - - + -
221A ASN* 3.6 32.3 - - - +
234A TYR* 5.5 0.9 - - - +
252A ARG* 3.7 28.7 - - + +
253A VAL 2.9 18.8 + - - +
254A ASP* 4.3 3.1 - - - +
255A GLY* 2.7 27.9 + - - +
256A ASN* 4.0 2.6 + - - +
282A GLU* 3.8 31.2 - - - +
283A ALA* 1.3 69.9 - - - +
285A THR* 1.3 59.2 + - - +
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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