Contacts of the helix formed by residues 291 - 300 (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 CYS 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A PHE* 5.5 5.2 - - + -
45A PHE* 3.7 31.8 - - + -
48A ASN* 4.9 2.4 - - - +
288A THR* 3.3 14.2 + - - +
290A CYS* 1.3 78.8 - - - +
292A ILE* 1.3 67.5 + - + +
294A PRO* 3.8 9.4 - - - +
295A ILE* 3.7 14.2 - - - +
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Residues in contact with ILE 292 (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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246A LEU* 4.1 31.9 - - + +
250A PRO* 6.1 1.1 - - + -
288A THR* 4.1 5.8 - - - +
289A HIS* 3.5 42.6 - - + +
290A CYS 3.7 0.2 - - - -
291A CYS* 1.3 82.5 - - + +
293A ASN* 1.3 66.3 + - - +
295A ILE* 3.4 12.1 + - + +
296A ILE* 3.0 45.5 + - + +
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Residues in contact with ASN 293 (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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70A LEU* 3.4 23.5 - - + +
73A ALA* 5.6 4.2 - - + +
74A ILE* 5.8 1.1 - - + -
77A LEU* 4.2 23.1 - - + +
116A ILE* 3.7 22.1 - - - +
243A VAL* 4.4 18.2 - - - +
289A HIS* 3.0 50.2 + - - +
290A CYS 4.7 0.7 - - - +
291A CYS 3.7 0.4 - - - -
292A ILE* 1.3 77.4 - - - +
294A PRO* 1.4 70.4 - - + +
296A ILE* 3.8 13.6 + - - +
297A TYR 3.9 5.4 + - - -
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Residues in contact with PRO 294 (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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48A ASN* 3.3 26.9 - - - +
49A MET* 3.7 25.4 - - + -
52A ILE* 3.8 22.5 - - + +
70A LEU* 4.3 7.8 - - + -
74A ILE* 4.0 19.7 - - + -
290A CYS 3.7 11.4 - - - +
291A CYS 3.8 8.3 - - - +
293A ASN* 1.4 94.1 - - + +
295A ILE* 1.3 56.4 + - - +
297A TYR* 3.6 3.6 + - - +
298A ALA* 3.1 26.9 + - - +
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Residues in contact with ILE 295 (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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48A ASN* 4.8 17.5 - - - +
52A ILE* 4.4 1.7 - - + +
291A CYS* 3.7 17.3 - - - +
292A ILE* 3.4 22.9 + - + +
294A PRO* 1.3 74.9 - - - +
296A ILE* 1.4 59.1 + - + +
298A ALA* 4.0 6.5 - - + +
299A PHE* 3.1 51.4 + - + +
300A VAL* 4.0 2.6 + - - +
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Residues in contact with ILE 296 (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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235A ARG* 3.3 15.6 + - - +
238A PHE* 5.9 0.2 - - + -
239A THR* 3.6 23.3 - - - +
242A ILE* 3.8 32.5 - - + +
243A VAL* 4.1 23.3 - - + -
246A LEU* 3.8 26.5 - - + -
292A ILE* 3.0 41.2 + - + +
293A ASN* 4.0 8.7 - - - +
294A PRO 3.5 0.4 - - - -
295A ILE* 1.4 73.2 - - + +
297A TYR* 1.3 59.5 + - - +
298A ALA 3.6 0.2 + - - -
300A VAL* 3.4 24.4 + - + +
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Residues in contact with TYR 297 (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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52A ILE* 5.2 8.5 - - + -
56A ILE* 3.8 28.0 - - + +
60A ARG* 4.4 12.8 + - - -
62A LYS* 4.9 5.7 + - - -
67A ILE* 3.2 35.7 + - + +
70A LEU* 3.7 44.9 - - + -
235A ARG* 3.0 58.1 + - + +
239A THR* 4.1 16.5 + - + +
293A ASN 3.9 2.0 + - - +
294A PRO 3.6 8.5 + - - +
296A ILE* 1.3 78.1 - - - +
298A ALA* 1.3 59.5 + - - +
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Residues in contact with ALA 298 (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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52A ILE* 3.7 29.6 - - + -
235A ARG* 4.7 1.3 - - - -
294A PRO 3.1 18.1 + - - +
295A ILE* 4.5 3.1 - - + -
296A ILE 3.5 0.4 - - - -
297A TYR* 1.3 78.3 - - - +
299A PHE* 1.3 59.5 + - + +
301A GLY 4.5 6.4 - - - +
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Residues in contact with PHE 299 (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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295A ILE* 3.1 43.4 + - + +
298A ALA* 1.3 73.9 - - + +
300A VAL* 1.3 65.4 + - + +
301A GLY 3.0 14.2 + - - +
304A PHE* 5.4 6.4 - + - -
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Residues in contact with VAL 300 (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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235A ARG* 3.0 21.6 + - - +
238A PHE* 3.6 32.9 - - + -
242A ILE* 5.1 4.7 - - + -
295A ILE 4.0 1.0 + - - +
296A ILE* 3.4 34.9 + - + +
298A ALA 4.2 0.2 - - - -
299A PHE* 1.3 78.7 - - + +
301A GLY* 1.3 55.9 + - - +
304A PHE* 3.9 31.4 - - + -
313A GLN* 3.0 10.5 + - - +
314A LYS* 5.4 3.4 - - + -
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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