Contacts of the helix formed by residues 767 - 780 (chain B) in PDB entry 2O8C
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 767 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766B HIS* 1.3 80.3 - - - +
768B PRO* 1.4 64.9 - - - +
769B PHE* 3.4 33.9 - - + -
770B GLY* 2.9 24.3 + - - -
771B LYS* 3.0 16.4 + - - +
812B LEU* 3.8 36.6 - - + +
815B LEU* 3.9 11.9 - - + -
1054B ILE* 4.5 0.4 - - + -
1058B ASP* 2.8 20.6 + - - +
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Residues in contact with PRO 768 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B ASN* 3.6 31.4 - - - +
766B HIS 4.2 4.0 - - - +
767B THR* 1.4 86.5 - - - +
769B PHE* 1.3 59.3 + - + +
771B LYS* 3.5 5.6 + - + +
772B ARG* 3.4 28.8 + - - +
815B LEU 4.2 8.3 - - - +
816B PRO* 4.1 13.7 - - + +
817B ASP* 3.6 39.0 - - + +
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Residues in contact with PHE 769 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767B THR* 3.4 32.3 - - + -
768B PRO* 1.3 77.4 - - + +
770B GLY* 1.3 63.6 + - - +
772B ARG* 3.5 24.2 + - - +
773B LEU* 3.2 21.7 + - - +
815B LEU* 4.0 4.3 - - + -
816B PRO 3.6 21.1 - - - -
817B ASP* 4.1 5.4 - - - -
818B LEU* 4.0 23.6 - - + -
819B GLU* 4.1 13.2 - - + +
868B MET* 3.7 21.3 - - + -
1051B VAL* 3.5 34.3 - - + -
1054B ILE* 3.7 14.8 - - + -
1055B ALA* 3.7 13.9 - - + +
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Residues in contact with GLY 770 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765B CYS* 3.7 6.7 - - - -
767B THR* 2.9 23.1 + - - -
769B PHE* 1.3 76.0 - - - +
771B LYS* 1.3 63.6 - - - +
773B LEU 3.2 1.4 + - - -
774B LEU* 3.1 19.8 + - - +
1055B ALA* 4.2 18.2 - - - -
1058B ASP* 3.4 9.0 - - - -
1059B VAL* 3.3 10.8 - - - +
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Residues in contact with LYS 771 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B ASN* 3.7 26.4 + - + +
535B TYR* 3.4 37.2 + - + +
759B LEU* 5.3 0.3 - - - +
763B ASP* 3.4 35.3 + - - +
765B CYS* 3.9 24.2 - - + +
767B THR 3.0 14.0 + - - +
768B PRO* 3.7 8.7 - - + +
769B PHE 3.3 0.2 - - - -
770B GLY* 1.3 76.2 - - - +
772B ARG* 1.3 61.0 + - - +
774B LEU* 3.3 14.2 + - - +
775B LYS 3.4 5.5 + - - -
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Residues in contact with ARG 772 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B ASN* 2.8 43.4 + - - +
535B TYR* 4.0 15.9 - - + -
536B SER* 3.8 21.8 - - - +
565B LEU* 4.4 8.7 - - - +
768B PRO 3.4 14.6 + - - +
769B PHE* 3.5 16.3 - - - +
770B GLY 3.2 0.8 - - - -
771B LYS* 1.3 81.3 - - - +
773B LEU* 1.3 59.3 + - - +
775B LYS* 3.5 10.8 + - - +
776B GLN* 3.5 20.1 + - - +
817B ASP* 2.6 44.5 + - - -
819B GLU* 2.8 35.6 + - - +
820B ARG* 3.8 11.0 - - - +
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Residues in contact with LEU 773 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769B PHE 3.2 13.7 + - - +
770B GLY 3.2 8.0 + - - +
772B ARG* 1.3 74.1 - - - +
774B LEU* 1.3 65.5 + - - +
776B GLN* 3.2 14.6 + - + +
777B TRP* 3.1 51.5 + - + +
1055B ALA* 3.6 36.3 - - + +
1056B VAL* 3.6 21.8 - - + +
1059B VAL* 3.8 8.1 - - + -
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Residues in contact with LEU 774 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759B LEU* 4.3 7.6 - - + -
762B VAL* 4.5 10.8 - - + -
763B ASP* 3.7 46.0 - - + +
765B CYS* 3.8 10.1 - - - -
770B GLY 3.1 11.8 + - - +
771B LYS 3.3 10.5 + - - +
773B LEU* 1.3 75.6 - - - +
775B LYS* 1.3 63.0 + - - +
777B TRP* 3.7 1.2 + - - +
778B LEU* 3.1 35.1 + - + +
1059B VAL* 3.8 22.8 - - + +
1062B CYS* 3.8 7.6 - - - -
1063B LEU* 4.6 3.8 - - + -
1156B MET* 3.8 22.9 - - + -
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Residues in contact with LYS 775 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B TYR* 4.5 18.8 - - + -
536B SER* 6.3 1.6 - - - +
538B TYR* 5.6 4.5 - - - -
588B HIS* 3.1 28.7 + - - +
589B TYR* 5.0 4.4 - - - -
590B PRO* 5.7 2.0 - - + -
746B PHE* 3.5 42.8 - - + -
759B LEU* 4.7 8.0 - - + +
771B LYS 3.4 7.7 + - - +
772B ARG 3.6 9.2 - - - +
773B LEU 3.2 0.2 - - - -
774B LEU* 1.3 78.6 - - - +
776B GLN* 1.3 88.1 + - - +
778B LEU* 3.2 5.5 + - - +
779B CYS* 2.9 52.6 + - - +
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Residues in contact with GLN 776 (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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538B TYR* 4.7 5.9 + - - -
569B PHE* 6.0 1.8 - - - -
589B TYR* 3.8 28.4 + - - -
732B ARG* 4.5 5.1 + - - +
772B ARG 3.5 14.3 + - - +
773B LEU* 3.4 17.9 - - + +
775B LYS* 1.3 106.9 + - - +
777B TRP* 1.3 63.4 + - + +
779B CYS* 3.4 3.0 + - - +
780B ALA* 3.0 32.4 + - - +
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Residues in contact with TRP 777 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732B ARG* 5.1 6.8 - - - +
773B LEU* 3.1 49.1 + - + +
774B LEU* 4.0 3.4 - - - +
776B GLN* 1.3 81.5 - - + +
778B LEU* 1.3 60.9 + - - +
780B ALA 3.4 21.6 - - - +
781B PRO* 3.5 7.4 - - - +
791B ARG* 3.3 58.2 + - + +
886B ILE* 5.5 6.1 - - + -
1056B VAL* 4.3 20.0 - - + -
1059B VAL* 3.7 20.2 - - + -
1060B LEU* 3.8 24.0 - - + -
1063B LEU* 3.8 23.6 - - + -
1156B MET* 3.5 21.0 - - + +
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Residues in contact with LEU 778 (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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735B LEU* 3.6 14.0 - - - +
745B ILE* 3.9 18.6 - - + +
758B LEU* 3.8 29.2 - - + -
759B LEU* 3.7 39.5 - - + +
762B VAL* 4.9 11.0 - - + -
774B LEU* 3.1 30.9 + - + +
775B LYS* 3.7 4.0 - - - +
777B TRP* 1.3 76.8 - - - +
779B CYS* 1.3 62.2 + - - +
781B PRO* 4.1 1.6 - - - +
1152B VAL* 4.0 12.4 - - + +
1153B MET* 4.5 8.1 - - + -
1156B MET* 3.6 24.9 - - + -
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Residues in contact with CYS 779 (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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588B HIS* 3.2 40.5 - - + +
712B LEU* 5.1 1.6 - - - +
733B MET 4.3 2.4 - - - +
735B LEU* 3.6 17.7 + - - +
740B LEU* 4.3 12.8 - - - -
745B ILE* 5.3 0.4 - - - -
746B PHE* 4.0 27.4 - - - -
775B LYS* 2.9 36.5 + - - +
776B GLN* 4.1 3.1 - - - +
778B LEU* 1.3 82.5 - - - +
780B ALA* 1.3 59.6 + - + +
781B PRO* 3.6 3.6 - - - +
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Residues in contact with ALA 780 (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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588B HIS* 5.8 0.4 - - + -
712B LEU* 4.5 11.7 - - + -
732B ARG* 3.5 41.5 + - + +
733B MET 4.2 4.7 - - - -
776B GLN* 3.0 13.9 + - - +
777B TRP* 3.4 9.4 - - - +
779B CYS* 1.3 81.3 - - - +
781B PRO* 1.3 66.8 - - - +
782B LEU* 3.8 1.7 + - - +
791B ARG* 5.3 1.2 + - - -
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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
------------------------------------------------------------
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