Contacts of the helix formed by residues 782 - 799 (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 PRO 782 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678A ALA* 5.1 0.7 - - - -
681A LEU* 4.0 22.2 - - + +
682A HIS* 3.8 24.2 - - + +
714A ASN* 5.4 2.0 - - - +
780B GLY 3.3 6.7 - - - +
781B VAL* 1.3 94.2 - - + +
783B LYS* 1.3 65.8 + - - +
784B GLU* 2.8 7.8 + - + +
785B VAL* 3.0 27.6 + - + +
786B ILE* 3.2 8.3 + - - +
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Residues in contact with LYS 783 (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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781B VAL 3.3 3.7 + - - -
782B PRO* 1.3 68.9 - - - +
784B GLU* 1.3 58.5 - - + +
786B ILE* 3.4 12.1 - - - +
787B LYS* 3.2 31.3 + - + +
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Residues in contact with GLU 784 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A ASN* 5.5 6.5 - - - +
718A LYS* 5.1 13.6 - - - -
782B PRO* 2.8 7.3 + - + +
783B LYS* 1.3 74.6 - - + +
785B VAL* 1.3 68.6 + - + +
786B ILE 3.3 0.9 - - - -
787B LYS* 3.4 22.4 + - - +
788B ARG* 3.1 37.1 + - + +
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Residues in contact with VAL 785 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A LEU* 4.3 2.9 - - + -
707A LEU* 4.9 2.9 - - + -
710A ALA* 3.3 40.8 - - + +
711A CYS* 3.9 13.5 - - - +
714A ASN* 3.7 36.6 - - + +
781B VAL* 3.9 19.3 - - + -
782B PRO* 3.0 28.6 + - + +
784B GLU* 1.3 78.5 - - + +
786B ILE* 1.3 61.4 + - - +
788B ARG* 3.4 2.1 + - - -
789B ALA* 3.0 18.4 + - - +
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Residues in contact with ILE 786 (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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707A LEU* 5.9 1.3 - - + -
773B LEU* 4.3 19.5 - - + +
776B ALA* 4.4 4.9 - - + -
777B ALA* 4.2 29.4 - - + +
781B VAL* 3.1 51.6 - - + +
782B PRO 3.2 4.7 + - - +
783B LYS* 3.4 13.5 - - - +
785B VAL* 1.3 76.4 - - - +
787B LYS* 1.3 60.0 + - + +
789B ALA* 3.3 7.5 + - - +
790B ARG* 3.0 30.0 + - + +
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Residues in contact with LYS 787 (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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783B LYS* 3.2 22.6 + - + +
784B GLU* 3.5 26.0 - - - +
785B VAL 3.2 0.4 - - - -
786B ILE* 1.3 77.5 - - + +
788B ARG* 1.3 66.0 + - - +
790B ARG* 3.1 17.3 + - - +
791B GLN* 3.1 12.8 + - - +
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Residues in contact with ARG 788 (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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709A TRP* 5.9 0.7 - - - -
710A ALA* 4.0 12.8 - - + +
713A GLU* 2.8 58.2 + - - +
784B GLU* 3.1 28.4 + - + +
785B VAL* 3.6 10.3 - - - +
787B LYS* 1.3 81.8 - - - +
789B ALA* 1.3 57.4 + - - +
791B GLN* 3.3 34.5 + - - +
792B LYS* 3.1 27.6 + - - +
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Residues in contact with ALA 789 (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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706A SER* 3.4 32.6 - - - +
707A LEU* 4.2 4.5 - - + -
710A ALA* 3.7 5.4 - - + -
773B LEU* 3.6 25.4 - - + -
785B VAL 3.0 16.8 + - - +
786B ILE* 3.5 7.0 - - - +
788B ARG* 1.3 73.8 - - - +
790B ARG* 1.3 60.6 + - - +
792B LYS* 4.5 1.1 - - - -
793B LEU* 3.0 29.6 + - - +
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Residues in contact with ARG 790 (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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773B LEU* 3.6 19.4 - - + +
786B ILE* 3.0 15.5 + - + +
787B LYS* 3.4 11.7 - - - +
789B ALA* 1.3 75.1 - - - +
791B GLN* 1.3 65.5 + - - +
793B LEU* 3.7 17.9 - - - +
794B ARG* 3.4 37.7 + - - +
797B GLU* 5.4 3.2 + - - -
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Residues in contact with GLN 791 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787B LYS 3.1 10.9 + - - +
788B ARG* 3.3 43.8 + - - +
789B ALA 3.2 0.6 - - - -
790B ARG* 1.3 73.9 - - - +
792B LYS* 1.3 65.6 + - - +
793B LEU 3.1 1.0 + - - -
794B ARG* 3.2 33.8 + - - +
795B GLU* 3.1 26.3 + - + +
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Residues in contact with LYS 792 (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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706A SER* 3.6 10.3 - - - +
709A TRP* 3.2 71.3 - - + +
738A LYS* 5.4 7.9 - - - +
788B ARG 3.1 13.6 + - - +
789B ALA* 3.8 6.7 - - - +
790B ARG 3.5 0.2 - - - -
791B GLN* 1.3 80.4 - - - +
793B LEU* 1.3 61.6 + - - +
795B GLU* 3.2 36.4 + - + +
796B LEU* 3.1 44.6 + - + +
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Residues in contact with LEU 793 (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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702A TYR* 3.1 41.1 - - + +
703A ASP* 3.3 11.9 - - - +
706A SER* 3.1 12.1 - - - +
770B SER* 4.0 19.7 - - - +
773B LEU* 4.1 18.6 - - + -
789B ALA 3.0 14.8 + - - +
790B ARG* 3.7 21.3 - - - +
791B GLN 3.1 0.2 - - - -
792B LYS* 1.3 73.4 - - - +
794B ARG* 1.3 66.6 + - - +
795B GLU 3.1 0.3 + - - -
796B LEU* 3.2 3.0 + - - +
797B GLU* 3.0 52.9 + - - +
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Residues in contact with ARG 794 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790B ARG* 3.4 27.5 + - - +
791B GLN* 3.2 39.8 + - - +
793B LEU* 1.3 79.2 - - - +
795B GLU* 1.3 50.0 + - - +
797B GLU* 4.8 5.6 - - - -
798B SER* 2.7 40.3 + - - +
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Residues in contact with GLU 795 (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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738A LYS* 5.9 2.4 - - - -
791B GLN* 3.1 17.3 + - + +
792B LYS* 3.3 47.5 + - + +
793B LEU 3.1 0.8 - - - -
794B ARG* 1.3 78.6 - - - +
796B LEU* 1.3 61.4 + - + +
798B SER* 3.1 19.5 - - - -
799B ILE* 3.8 18.0 - - + +
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Residues in contact with LEU 796 (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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702A TYR* 3.7 45.3 + - + -
705A LEU* 3.7 30.7 - - + -
706A SER* 4.0 14.8 - - - +
709A TRP* 6.0 2.0 - - + -
731A GLU* 4.7 12.3 - - + -
792B LYS* 3.1 40.9 + - + +
793B LEU 3.8 2.0 - - - +
795B GLU* 1.3 78.8 - - + +
797B GLU* 1.3 64.6 + - - +
799B ILE* 3.8 12.7 + - - +
800B SER* 4.2 4.0 - - - -
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Residues in contact with GLU 797 (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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700A SER* 4.6 10.9 + - - -
702A TYR* 4.0 23.2 + - + +
730B PHE* 4.2 18.9 - - + -
770B SER* 4.8 5.9 + - - -
790B ARG* 5.4 3.5 + - - -
793B LEU* 3.0 43.4 + - - +
794B ARG* 4.5 4.9 + - - +
796B LEU* 1.3 72.4 - - - +
798B SER* 1.3 67.6 + - - +
799B ILE 3.1 2.0 - - - -
800B SER* 2.8 26.1 + - - -
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Residues in contact with SER 798 (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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794B ARG* 2.7 27.5 + - - +
795B GLU* 3.1 16.1 - - - -
797B GLU* 1.3 71.6 - - - +
799B ILE* 1.3 62.5 + - - -
800B SER* 3.4 1.2 + - - +
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Residues in contact with ILE 799 (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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799A ILE* 3.2 38.7 - - + +
702B TYR* 6.0 0.2 - - - +
795B GLU* 3.8 20.2 - - + +
796B LEU* 3.8 9.3 + - - +
797B GLU 2.8 4.2 + - - -
798B SER* 1.3 77.9 - - - +
800B SER* 1.3 63.5 + - - +
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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