Contacts of the helix formed by residues 705 - 713 (chain A) in PDB entry 2OR4
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 705 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604A LEU* 4.1 23.6 - - + -
607A TYR* 3.6 41.7 - + + -
608A ALA* 3.6 15.9 - - + -
611A ILE* 4.1 14.8 - - + -
632A LEU* 3.8 19.7 - - + -
636A VAL* 5.0 1.8 - - + -
690A VAL 3.9 10.8 - - - -
691A ILE* 2.8 35.6 + - + -
704A SER* 1.3 71.5 - - - +
706A PRO* 1.3 68.7 - - - +
707A GLY 3.2 2.7 - - - -
708A ILE* 3.1 20.0 + - + -
709A TYR* 2.8 20.1 + - - +
735A ALA* 3.9 27.4 - - + -
739A VAL* 4.1 4.7 - - + -
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Residues in contact with PRO 706 (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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681A LEU* 3.7 15.5 - - + -
684A ARG* 4.4 6.7 - - - +
689A HIS 4.2 1.3 - - - +
690A VAL 3.4 12.3 - - - +
691A ILE 3.4 13.2 - - - +
692A TYR 3.8 2.9 - - - +
693A ALA* 3.5 37.0 - - + +
694A PRO 5.6 0.2 - - - +
703A GLU* 3.8 14.8 - - + +
704A SER 3.1 7.1 - - - +
705A PHE* 1.3 90.6 - - - +
707A GLY* 1.3 57.5 + - - +
709A TYR* 4.1 5.2 - - + -
710A ASP* 2.9 37.5 + - - +
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Residues in contact with GLY 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A LEU* 4.2 15.0 - - - +
682A PRO* 4.8 7.3 - - - +
690A VAL 5.1 1.2 + - - -
705A PHE 3.2 1.4 - - - -
706A PRO* 1.3 82.2 - - - +
708A ILE* 1.3 62.9 + - - +
710A ASP* 4.2 3.2 - - - +
711A ALA* 3.2 16.5 + - - +
731A GLN* 3.4 35.2 - - - +
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Residues in contact with ILE 708 (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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611A ILE* 3.5 23.6 - - + -
629A PHE* 4.2 10.3 - - + -
632A LEU* 4.0 20.9 - - + -
705A PHE* 3.1 19.4 + - + +
707A GLY* 1.3 74.7 - - - +
709A TYR* 1.3 65.8 + - - +
711A ALA* 3.2 3.7 + - - +
712A LEU* 3.0 32.0 + - + +
728A VAL* 4.4 9.0 - - + +
731A GLN* 3.6 26.9 - - - +
732A ILE* 3.9 18.6 - - + +
735A ALA* 3.9 22.9 - - + -
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Residues in contact with TYR 709 (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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610A LYS* 6.0 1.8 - - - -
611A ILE* 3.6 11.8 - - + +
614A ILE* 3.8 33.9 - - + -
695A SER* 5.8 1.3 - - - -
697A HIS* 4.7 10.6 - + - -
703A GLU* 3.8 44.2 + - + -
704A SER 4.0 3.4 - - - +
705A PHE 2.8 20.2 + - - +
706A PRO 3.7 3.8 - - - +
708A ILE* 1.3 71.7 - - - +
710A ASP* 1.3 71.9 + - - +
712A LEU* 3.1 5.0 + - - +
713A PHE* 2.9 61.3 + + - +
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Residues in contact with ASP 710 (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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684A ARG* 3.4 15.1 + - - -
696A SER* 2.7 37.4 + - - -
697A HIS* 4.6 5.4 + - - -
703A GLU* 5.8 0.7 - - - +
706A PRO* 2.9 22.1 + - - +
707A GLY* 4.2 3.4 - - - +
709A TYR* 1.3 89.1 - - - +
711A ALA* 1.3 63.7 + - - +
712A LEU 3.3 0.3 + - - -
713A PHE* 3.3 18.1 + - - +
718A LYS* 5.2 4.3 + - - -
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Residues in contact with ALA 711 (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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707A GLY 3.2 19.1 + - - +
708A ILE 3.2 5.6 + - - +
710A ASP* 1.3 77.0 - - - +
712A LEU* 1.3 59.5 + - - +
713A PHE 3.8 1.6 + - - +
715A ILE* 3.7 18.9 - - - +
718A LYS* 4.9 6.9 + - - +
724A ALA* 4.6 3.3 - - - +
727A GLU* 4.2 11.0 - - + +
728A VAL* 3.7 34.7 - - + +
731A GLN* 4.2 9.2 - - + -
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Residues in contact with LEU 712 (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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611A ILE* 3.9 15.7 - - + +
614A ILE* 4.0 24.9 - - + +
615A SER* 4.0 24.2 - - - +
618A HIS* 4.9 6.4 - - + +
629A PHE* 4.7 0.7 - - + -
708A ILE* 3.0 31.2 + - + +
709A TYR 3.6 7.2 - - - +
711A ALA* 1.3 76.3 - - - +
713A PHE* 1.3 66.5 + - - +
714A ASP 3.2 0.9 + - - -
715A ILE* 3.1 25.2 + - + +
716A GLU* 5.0 0.2 - - - +
725A TRP* 3.6 38.4 - - + -
728A VAL* 3.8 16.2 - - + -
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Residues in contact with PHE 713 (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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182A THR* 3.9 21.1 - - + -
186A PHE* 4.0 13.0 - + - -
614A ILE* 6.4 0.2 - - - -
697A HIS* 3.4 39.9 - + - +
709A TYR* 2.9 49.1 + + + +
710A ASP* 3.3 16.8 + - - +
711A ALA 4.6 0.3 - - - +
712A LEU* 1.3 76.5 - - - +
714A ASP* 1.3 85.8 + - + +
715A ILE* 3.0 2.4 + - - -
718A LYS* 4.4 10.9 + - - -
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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