Contacts of the helix formed by residues 290 - 296 (chain B) in PDB entry 1OH7
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 THR 290 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278B GLU* 2.8 16.5 + - - -
279B ILE 2.8 30.1 + - - -
280B THR 3.4 14.7 - - - +
281B GLN 4.5 3.6 - - - -
287B ALA 2.9 33.2 - - - +
288B GLU 3.5 4.3 - - - -
289B ASN* 1.3 80.2 - - - +
291B LEU* 1.3 59.8 + - - +
292B ALA* 4.1 1.6 - - + +
293B SER* 2.3 43.5 + - - +
294B VAL* 3.5 4.5 + - - +
587B VAL* 3.6 12.0 - - - +
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Residues in contact with LEU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B LEU 4.8 0.7 - - - +
278B GLU 2.9 10.0 + - - +
279B ILE* 3.5 20.0 - - + +
290B THR* 1.3 76.2 + - - +
292B ALA* 1.3 58.8 + - - +
294B VAL* 3.3 3.6 + - + +
295B LEU* 3.1 46.5 + - + +
311B LEU* 3.9 24.2 - - + -
586B PRO* 4.0 29.4 - - + -
587B VAL* 3.7 12.2 - - + +
629B LEU* 4.0 24.0 - - + -
632B LEU* 4.2 14.1 - - + -
633B MET* 4.0 10.3 - - + -
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B ILE 2.9 17.6 + - - +
280B THR* 4.2 19.3 - - + +
290B THR* 3.2 3.1 - - + +
291B LEU* 1.3 77.1 - - - +
293B SER* 1.3 53.4 + - - +
295B LEU 4.6 0.2 - - - +
296B ASP* 2.7 45.1 + - + +
308B LYS* 4.5 12.8 - - + +
311B LEU* 4.2 21.5 - - + -
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Residues in contact with SER 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B ALA 3.9 8.1 - - - -
288B GLU* 4.4 18.1 + - - -
289B ASN* 3.8 3.1 + - - -
290B THR* 2.3 51.1 + - - +
292B ALA* 1.3 78.2 - - - +
294B VAL* 1.3 66.7 + - - +
296B ASP* 4.1 6.8 + - - +
297B CYS* 5.2 3.1 - - - -
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Residues in contact with VAL 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B THR 3.8 11.9 - - - +
291B LEU* 3.3 7.6 + - + +
293B SER* 1.3 88.2 + - - +
295B LEU* 1.3 62.9 + - + +
296B ASP 3.6 0.3 + - - -
297B CYS* 4.1 2.1 - - - -
561B ARG* 3.2 25.6 + - - +
565B LEU* 4.3 15.5 - - + -
567B TYR* 4.6 5.6 - - - +
586B PRO* 3.9 9.9 - - + +
587B VAL* 3.9 29.8 - - + -
590B GLN* 3.7 31.6 - - + -
591B VAL* 5.3 3.6 - - + -
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B LEU* 3.1 37.1 + - + +
292B ALA* 4.6 1.6 - - - +
294B VAL* 1.3 82.0 - - + +
296B ASP* 1.3 58.3 + - - +
297B CYS 3.3 2.9 + - - -
307B LEU* 3.6 8.6 - - + +
311B LEU* 3.9 26.2 - - + -
557B ASN* 3.1 24.6 + - - +
558B LEU* 5.0 17.4 - - + +
561B ARG* 3.8 20.0 - - + +
565B LEU* 5.6 0.2 - - + -
567B TYR* 3.8 36.3 - - + +
586B PRO* 5.9 0.2 - - + -
633B MET* 3.9 15.5 - - + -
636B ILE* 5.2 1.1 - - + -
638B SER* 5.1 1.6 - - - +
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Residues in contact with ASP 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ARG* 3.3 17.0 + - - +
292B ALA* 2.7 29.1 + - + +
293B SER* 4.1 4.9 + - - +
294B VAL 3.4 2.8 - - - -
295B LEU* 1.3 70.3 - - - +
297B CYS* 1.3 62.0 + - - +
298B THR* 2.6 27.2 + - - +
304B SER* 2.5 28.6 + - - +
307B LEU* 3.4 23.9 - - + +
308B LYS* 4.4 8.9 + - - -
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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