Contacts of the helix formed by residues 773 - 784 (chain B) in PDB entry 6V3O
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 ARG 773 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294B ASP* 3.0 49.2 + - - -
295B GLY* 3.5 7.6 - - - -
456B ARG* 3.3 15.6 - - - +
606B LYS* 4.6 1.6 - - - -
759B ARG* 3.1 42.0 - - - +
760B PRO 4.2 6.5 - - - -
761B ALA 3.3 21.7 + - - +
762B LYS* 4.0 8.3 - - - +
763B ARG* 3.1 33.5 - - + +
771B THR 4.2 2.7 - - - +
772B LEU* 1.3 104.9 - - - +
774B ALA* 1.3 66.1 + - - +
775B ILE 3.4 0.7 - - - -
776B PRO* 3.1 7.2 - - + +
777B TRP* 3.1 1.3 + - - +
1001B SO4 4.0 4.2 + - - -
1002B SO4 3.5 21.4 + - - +
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Residues in contact with ALA 774 (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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602B SER* 4.4 24.9 - - - +
603B ASP* 4.5 15.0 - - - +
606B LYS* 4.6 6.9 - - + +
773B ARG* 1.3 72.0 - - - +
775B ILE* 1.3 65.2 + - + +
777B TRP* 3.0 10.9 + - - +
778B ILE* 3.0 27.4 + - - +
1001B SO4 3.6 15.4 + - - +
1002B SO4 2.8 20.1 + - - +
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Residues in contact with ILE 775 (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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178B PRO* 4.8 15.5 - - + -
641B ARG* 3.2 47.1 - - - +
751B TYR* 4.5 15.5 - - - +
759B ARG* 3.7 19.1 - - - +
774B ALA* 1.3 74.6 - - + +
776B PRO* 1.3 64.7 - - + +
778B ILE* 3.3 4.2 + - - +
779B PHE* 2.8 36.3 + - + +
1001B SO4 3.5 20.6 - - - +
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Residues in contact with PRO 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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742B PHE* 4.7 0.6 - - - -
748B GLU* 3.4 21.7 - - - +
751B TYR* 4.4 15.9 - - + -
759B ARG* 4.1 3.8 - - - +
761B ALA* 3.5 33.0 - - + +
772B LEU* 3.8 11.9 - - + -
773B ARG* 3.1 19.7 - - + +
775B ILE* 1.3 95.0 - - + +
777B TRP* 1.3 55.0 + - - +
779B PHE* 4.2 6.5 - - + -
780B SER* 2.9 35.6 + - - +
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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
----------------------------------------------------------
602B SER 5.4 0.9 - - - -
606B LYS* 3.5 29.9 - - + +
728B TYR* 3.5 27.0 + + - -
732B VAL* 4.2 6.1 - - + -
738B PHE* 3.8 25.6 - + - -
742B PHE* 4.0 15.3 - + - -
769B ILE* 3.8 34.3 - - + -
772B LEU* 3.5 8.5 - - + +
773B ARG 3.1 14.0 + - - +
774B ALA* 3.0 13.1 + - - +
776B PRO* 1.3 79.2 - - - +
778B ILE* 1.3 67.6 + - + +
780B SER* 4.3 0.5 - - - -
781B TRP* 3.3 54.3 + - - -
788B LEU* 4.1 17.7 - - + -
789B PRO* 3.3 29.1 - - + +
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Residues in contact with ILE 778 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602B SER* 3.0 40.8 - - - +
774B ALA* 3.0 15.1 + - - +
775B ILE* 4.1 3.6 - - - +
777B TRP* 1.3 85.9 - - + +
779B PHE* 1.3 59.0 + - - +
781B TRP* 3.5 1.4 + - - +
782B THR* 2.4 40.9 + - + +
789B PRO* 4.5 13.5 - - + -
790B VAL* 5.5 2.7 - - + -
969B THR* 3.6 23.8 - - - +
970B GLY* 3.3 22.9 - - - +
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Residues in contact with PHE 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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178B PRO* 4.6 15.9 - - + -
179B THR* 3.5 31.0 - - + -
747B PRO* 5.4 2.0 - - + -
751B TYR* 3.5 45.1 - + + -
775B ILE* 2.8 29.9 + - + +
776B PRO* 4.0 4.7 - - + +
778B ILE* 1.3 74.2 - - - +
780B SER* 1.3 67.0 + - - +
782B THR* 2.6 19.1 + - - -
783B GLN* 3.1 54.8 + - + +
959B MET* 4.1 15.9 - - + -
963B ALA* 4.3 6.7 - - + -
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Residues in contact with SER 780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742B PHE* 3.8 10.8 - - - -
746B THR* 3.5 25.1 - - - -
747B PRO* 3.9 4.2 - - - +
748B GLU* 2.6 40.6 + - - +
751B TYR* 5.1 1.0 - - - +
776B PRO* 2.9 15.7 + - - +
779B PHE* 1.3 85.3 - - - +
781B TRP* 1.3 61.9 + - - +
783B GLN* 3.6 7.9 + - - +
784B THR* 3.5 20.4 - - - +
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Residues in contact with TRP 781 (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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738B PHE* 4.2 14.1 - + - -
741B TYR* 3.9 28.5 - + - -
742B PHE* 3.3 41.4 - + + -
745B ALA* 4.8 5.8 - - + -
746B THR* 3.6 23.6 - - + -
777B TRP* 3.3 39.4 + + - +
778B ILE 3.5 1.7 + - - +
779B PHE 3.3 0.4 - - - -
780B SER* 1.3 74.7 - - - +
782B THR* 1.3 65.0 + - - +
784B THR* 3.1 18.1 + - - -
786B PHE* 3.3 38.3 + + + -
787B HIS* 3.2 14.9 + - - +
788B LEU* 4.0 19.4 - - + +
789B PRO* 3.4 34.5 - - + -
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Residues in contact with THR 782 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778B ILE* 2.4 31.0 + - + +
779B PHE* 2.6 19.4 + - - -
781B TRP* 1.3 73.5 - - - +
783B GLN* 1.3 66.7 + - - +
785B ARG* 3.2 12.1 + - - -
787B HIS* 3.2 29.8 + - + -
789B PRO* 6.5 0.4 - - + -
790B VAL* 5.8 0.7 - - + -
962B ILE* 4.3 1.1 - - - +
966B MET* 4.2 19.9 - - - +
969B THR* 3.0 36.6 - - + +
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Residues in contact with GLN 783 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747B PRO* 4.1 11.2 - - + -
779B PHE* 3.1 56.5 + - + +
780B SER 3.8 7.0 - - - +
781B TRP 3.3 0.6 - - - -
782B THR* 1.3 79.0 + - - +
784B THR* 1.3 53.0 + - - +
785B ARG* 3.2 1.1 + - - +
844B TYR* 3.6 2.1 + - - -
902B ASN* 2.7 32.2 + - - -
905B GLN* 3.0 35.1 + - - +
959B MET* 3.3 28.8 + - - +
962B ILE* 3.7 18.9 - - - +
963B ALA* 3.6 16.2 - - - +
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Residues in contact with THR 784 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745B ALA 3.3 24.9 - - - +
746B THR* 3.8 12.3 - - + -
747B PRO* 3.9 6.5 - - + -
780B SER 3.5 16.2 - - - +
781B TRP* 3.1 18.2 + - - -
783B GLN* 1.3 75.9 - - - +
785B ARG* 1.3 68.8 + - - +
786B PHE* 3.3 15.6 + - - +
840B ILE* 3.9 2.6 - - - +
841B ALA* 3.6 23.0 + - - +
844B TYR* 3.8 25.4 - - + -
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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