Contacts of the helix formed by residues 312 - 317 (chain F) in PDB entry 4OR5
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 HIS 312 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287F TYR* 3.5 26.0 - + + -
290F ASP* 2.6 31.0 + - + -
291F LEU* 3.7 27.1 + - + -
294F LYS* 4.2 15.5 - - + -
304F ILE* 4.9 2.2 - - + -
308F ASP 3.3 10.6 + - - +
309F ALA 3.3 16.2 - - - +
310F LEU 3.3 1.4 - - - -
311F ASN* 1.3 83.8 - - - +
313F ASP* 1.3 87.8 + - + +
314F PHE* 2.8 25.0 + - + +
315F PHE* 3.3 15.0 + - + +
316F TRP* 3.6 9.0 - - - -
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Residues in contact with ASP 313 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287F TYR* 3.4 39.4 - - + -
290F ASP* 5.5 0.7 - - - +
311F ASN 3.7 2.5 + - - +
312F HIS* 1.3 83.1 + - - +
314F PHE* 1.3 63.5 + - - +
316F TRP* 2.8 19.8 + - - +
317F SER* 3.1 17.2 + - - +
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Residues in contact with PHE 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F LEU* 4.2 11.9 - - + -
126F ILE 4.5 2.7 - - - -
127F LYS* 3.0 89.0 + - + +
130F MET* 4.6 0.2 - - + -
219F MET* 3.6 27.8 - - + -
223F TRP* 4.2 11.0 - + - -
285F ASP* 4.5 2.9 - - - -
287F TYR* 3.7 18.1 - - + +
288F ALA* 3.6 33.7 - - + -
291F LEU* 4.1 6.3 - - + -
312F HIS* 2.8 24.2 + - + +
313F ASP* 1.3 73.4 - - - +
315F PHE* 1.3 78.5 + + + +
316F TRP 3.5 0.3 + - - -
317F SER* 3.9 1.5 + - - -
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Residues in contact with PHE 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127F LYS* 3.4 30.1 - - + -
130F MET* 3.9 5.8 - - + -
131F GLN* 3.6 34.4 + - + +
134F LEU* 3.7 24.9 - - + -
291F LEU* 3.9 18.6 - - + -
309F ALA 2.9 29.2 - - - -
310F LEU* 3.5 26.9 - - + +
312F HIS* 3.3 8.1 + - + +
313F ASP 3.0 1.2 + - - -
314F PHE* 1.3 92.1 - + - +
316F TRP* 1.3 73.8 + - + +
317F SER 3.7 1.1 - - - -
320F MET* 4.0 0.2 - - - +
321F PRO* 3.9 23.4 - - + +
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Residues in contact with TRP 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131F GLN* 4.4 16.4 - - - -
310F LEU 3.5 20.7 + - - -
311F ASN* 3.9 23.8 + - - +
312F HIS 3.6 18.8 - - - +
313F ASP* 2.8 16.4 + - - +
315F PHE* 1.3 92.0 - - + +
317F SER* 1.3 57.5 + - - +
320F MET* 4.1 29.7 - - + +
321F PRO* 6.0 1.6 - - + -
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Residues in contact with SER 317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127F LYS* 2.5 37.2 + - - -
287F TYR* 3.3 35.0 - - - -
313F ASP* 3.1 16.3 + - - -
314F PHE* 3.9 0.3 + - - -
315F PHE 3.7 0.8 - - - -
316F TRP* 1.3 79.7 - - - +
318F ASP* 1.3 62.7 + - - +
319F PRO 2.9 5.6 - - - +
320F MET* 3.8 5.8 + - - -
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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