Contacts of the helix formed by residues 278 - 287 (chain A) in PDB entry 1OPT
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 ALA 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257A LEU* 4.4 2.0 - - - -
276A ASP 3.5 17.5 - - - +
277A GLN* 1.3 72.6 + - - +
279A MET* 1.3 56.3 + - - +
280A GLN* 4.7 5.4 - - + +
281A VAL* 3.4 23.6 - - + +
282A THR* 2.7 37.3 + - - -
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Residues in contact with MET 279 (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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189A PHE* 6.4 2.9 - - + -
191A LYS* 5.3 11.9 - - - +
192A ASN* 4.6 23.1 - - + +
194A GLN* 3.9 48.7 - - + +
257A LEU* 3.6 30.4 - - + +
258A ASN* 3.9 26.7 - - - +
278A ALA* 1.3 72.2 - - - +
280A GLN* 1.3 55.6 + - - +
282A THR* 4.2 8.5 - - - -
283A GLU* 3.0 35.9 + - - +
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Residues in contact with GLN 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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29A ALA* 3.9 28.9 - - - +
30A ALA 5.1 3.0 + - - -
31A ARG* 3.9 34.2 - - - +
34A PRO* 5.6 6.0 - - + +
192A ASN* 4.0 28.1 + - - +
278A ALA* 3.5 4.9 - - + +
279A MET* 1.3 74.2 - - - +
281A VAL* 1.3 58.7 + - + +
283A GLU* 3.6 12.1 - - - +
284A THR* 2.7 32.0 + - - -
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ALA* 3.4 34.9 - - + +
280A GLN* 1.3 74.3 - - + +
282A THR* 1.3 58.6 + - - +
284A THR* 3.5 7.8 - - + -
285A LEU* 3.0 29.8 + - - +
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Residues in contact with THR 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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253A ILE* 4.1 17.8 - - + +
254A VAL* 3.6 43.2 - - + +
257A LEU* 3.5 26.1 - - + +
258A ASN* 4.9 2.7 - - - +
277A GLN 4.9 0.2 - - - -
278A ALA 2.7 27.5 + - - -
279A MET* 3.4 11.4 + - - -
281A VAL* 1.3 70.8 - - - +
283A GLU* 1.4 59.6 + - - +
285A LEU* 3.5 5.7 + - - +
286A GLY 2.9 24.3 + - - -
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Residues in contact with GLU 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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31A ARG* 3.5 28.4 + - - -
34A PRO* 6.2 2.9 - - + -
88A HIS* 4.4 3.5 + - - -
109A PHE* 3.8 27.1 - - + -
113A PHE* 5.9 0.2 - - - -
192A ASN* 5.1 4.3 - - - +
193A PHE* 5.0 4.9 - - - -
194A GLN* 3.6 31.4 - - - +
254A VAL* 5.7 1.1 - - - -
279A MET* 3.0 22.8 + - - +
280A GLN* 3.6 18.0 - - - +
282A THR* 1.4 70.8 - - - +
284A THR* 1.3 65.1 + - - +
286A GLY* 3.8 2.4 - - - +
287A MET* 3.1 41.0 + - + +
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Residues in contact with THR 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 LEU* 6.4 3.1 - - + -
34A PRO* 4.8 15.3 - - + +
37A TYR* 2.6 60.8 + - + +
280A GLN 2.7 25.8 + - - -
281A VAL* 3.5 11.1 - - + -
282A THR 3.4 0.2 - - - -
283A GLU* 1.3 78.0 - - - +
285A LEU* 1.3 59.6 + - - +
287A MET* 3.8 6.9 + - - +
288A THR* 3.8 0.6 - - - +
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Residues in contact with LEU 285 (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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249A ALA 4.4 4.0 - - - +
250A PRO* 3.6 31.9 - - + +
253A ILE* 4.0 41.7 - - + -
254A VAL* 5.7 0.4 - - + -
281A VAL 3.0 19.5 + - - +
282A THR* 3.8 4.5 - - - +
284A THR* 1.3 71.7 - - - +
286A GLY* 1.3 59.3 + - - +
288A THR* 2.6 40.3 + - + +
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Residues in contact with GLY 286 (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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113A PHE* 3.3 16.6 - - - -
250A PRO* 4.7 0.7 - - - -
251A TYR* 2.7 36.9 + - - -
254A VAL* 3.8 21.7 - - - +
282A THR 2.9 16.6 + - - -
283A GLU* 3.5 3.9 + - - -
285A LEU* 1.3 70.3 - - - +
287A MET* 1.3 57.6 + - - +
288A THR 3.5 0.7 + - - -
289A HIS 4.2 0.5 + - - -
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Residues in contact with MET 287 (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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34A PRO* 5.8 0.9 - - + -
37A TYR* 4.3 20.0 - - + -
38A SER* 5.6 1.1 - - - -
41A PHE* 3.6 14.4 - - + -
80A LEU* 5.5 6.7 - - + +
85A PHE* 3.7 32.9 - - + -
88A HIS* 3.8 31.0 - - + -
109A PHE* 3.7 31.2 - - + -
113A PHE* 4.8 8.1 - - + -
283A GLU* 3.1 35.6 + - + +
284A THR* 4.0 13.5 - - - +
285A LEU 3.5 0.6 - - - -
286A GLY* 1.3 72.0 - - - +
288A THR* 1.3 61.0 + - - +
289A HIS 3.5 1.1 + - - -
290A CYS* 4.0 15.0 + - - +
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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