Contacts of the helix formed by residues 778 - 795 (chain B) in PDB entry 2P0C
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 778 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720B LEU* 3.7 11.4 - - - +
770B GLU* 5.0 1.6 + - - -
776B VAL* 4.6 14.6 - - + -
777B TYR* 1.3 88.0 - - - +
779B SER* 1.3 65.8 + - - +
780B LYS* 3.2 24.1 + - - +
781B SER* 3.1 25.0 + - - +
782B ASP 3.4 2.4 + - - -
841B PRO* 5.0 3.3 - - - +
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Residues in contact with SER 779 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715B SER* 4.0 20.2 - - - -
720B LEU* 3.6 17.0 - - - +
778B THR* 1.3 76.1 + - - +
780B LYS* 1.3 71.9 + - - +
782B ASP* 3.1 10.7 + - - +
783B VAL* 2.9 31.8 + - - +
847B PHE* 3.9 4.4 - - - -
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Residues in contact with LYS 780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778B THR* 3.5 13.7 - - - +
779B SER* 1.3 86.8 + - - +
781B SER* 1.3 62.4 + - - +
783B VAL* 3.5 6.0 + - + +
784B TRP 3.2 14.0 + - - -
841B PRO* 3.4 41.3 - - + +
842B LEU* 4.7 12.7 + - + +
844B ARG* 2.9 51.9 + - + +
845B PRO 3.7 4.0 - - - +
846B THR* 3.6 33.3 - - - +
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Residues in contact with SER 781 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766B TRP 4.9 1.2 - - - +
768B ALA* 4.2 9.0 + - - +
770B GLU* 3.4 15.3 + - - +
771B SER* 3.3 16.9 + - - -
776B VAL 3.9 0.9 + - - -
777B TYR* 3.3 35.3 + - - -
778B THR* 3.1 26.3 + - - +
780B LYS* 1.3 77.4 - - - +
782B ASP* 1.3 63.8 + - - +
784B TRP* 3.3 6.4 + - - +
785B ALA* 3.2 17.5 + - - +
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Residues in contact with ASP 782 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711B MET* 3.9 16.9 - - + +
719B PHE 4.8 0.7 - - - +
720B LEU* 3.7 13.5 - - - +
721B HIS* 2.8 35.1 + - - +
722B ARG 2.9 16.1 + - - -
723B ASP 4.6 0.7 + - - -
724B LEU* 3.9 5.6 - - + +
777B TYR* 2.6 31.9 + - - -
778B THR 3.4 1.7 + - - -
779B SER* 3.1 11.1 + - - +
781B SER* 1.3 75.0 - - - +
783B VAL* 1.3 63.9 + - - +
785B ALA* 3.2 6.1 + - - +
786B PHE* 2.9 18.7 + - - +
847B PHE* 3.6 10.9 - - + -
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Residues in contact with VAL 783 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779B SER* 2.9 19.5 + - - +
780B LYS* 3.6 16.2 - - + +
781B SER 3.3 0.4 - - - -
782B ASP* 1.3 75.9 - - - +
784B TRP* 1.3 62.2 + - - +
786B PHE* 3.2 4.5 + - - +
787B GLY 3.2 16.1 + - - -
836B CYS* 3.5 19.6 - - + +
844B ARG* 4.0 14.8 - - + -
845B PRO* 3.3 29.6 - - + +
846B THR* 4.6 1.8 - - - -
847B PHE* 3.6 29.2 - - + +
850B LEU* 3.9 16.4 - - + -
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Residues in contact with TRP 784 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765B LYS 4.9 1.2 + - - -
766B TRP 3.3 24.5 + - - -
767B ILE 3.8 6.1 + - - -
768B ALA* 3.5 24.0 - - + -
769B ILE* 3.4 31.6 - - + -
780B LYS 3.2 11.3 + - - +
781B SER 3.3 9.9 - - - +
782B ASP 3.2 0.2 - - - -
783B VAL* 1.3 76.3 - - - +
785B ALA* 1.3 61.1 + - - +
787B GLY 3.0 12.1 + - - -
788B VAL* 3.2 23.1 + - + +
801B TYR* 4.2 7.9 + - - -
813B LEU* 3.8 30.5 - - + -
818B ARG* 3.8 19.7 - - - -
836B CYS 3.4 11.7 - - - +
837B TRP* 3.3 49.6 + + + -
844B ARG* 3.8 16.2 - - - +
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Residues in contact with ALA 785 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724B LEU* 3.7 30.7 - - + +
766B TRP* 3.7 22.6 - - + +
777B TYR* 4.5 6.1 - - - +
781B SER 3.2 8.4 + - - +
782B ASP* 3.2 10.3 + - - +
784B TRP* 1.3 79.3 - - - +
786B PHE* 1.3 52.3 + - - +
788B VAL* 3.4 7.7 + - - +
789B THR* 2.8 37.2 + - - -
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Residues in contact with PHE 786 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704B MET* 3.6 12.8 - - - -
707B ILE* 3.6 24.2 - - + -
708B ALA* 3.6 25.6 - - + -
724B LEU* 3.6 12.2 - - + +
782B ASP 2.9 7.8 + - - +
783B VAL 3.3 9.0 - - - +
784B TRP 3.2 0.2 - - - -
785B ALA* 1.3 77.2 - - - +
787B GLY* 1.3 51.9 + - - +
789B THR* 3.2 5.7 + - + -
790B MET* 2.7 62.4 + - + +
836B CYS* 4.3 3.1 - - - -
847B PHE* 3.6 23.3 - + + -
850B LEU* 4.0 29.4 - - + -
854B LEU* 3.6 26.9 - - + -
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Residues in contact with GLY 787 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783B VAL 3.2 4.2 + - - -
784B TRP 3.0 8.2 + - - -
786B PHE* 1.3 76.1 - - - +
788B VAL* 1.3 64.9 + - - +
790B MET* 3.4 11.7 + - - +
791B TRP* 3.1 17.0 + - - +
833B MET* 4.0 3.6 - - - +
836B CYS* 3.9 18.4 - - - -
837B TRP* 3.3 25.6 - - - -
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Residues in contact with VAL 788 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765B LYS 3.9 12.6 - - - +
766B TRP* 3.2 32.1 - - + +
784B TRP* 3.2 32.1 + - + +
785B ALA 3.5 7.0 - - - +
786B PHE 3.3 0.2 - - - -
787B GLY* 1.3 76.8 - - - +
789B THR* 1.3 51.3 + - - +
791B TRP* 3.0 5.4 + - - +
792B GLU* 2.8 32.2 + - - +
800B PRO* 3.7 25.6 - - + -
801B TYR* 4.7 2.9 - - - +
819B LEU* 4.1 16.6 - - + -
837B TRP* 3.7 10.1 - - + +
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Residues in contact with THR 789 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707B ILE* 4.2 15.5 - - + -
724B LEU* 3.8 6.8 - - + +
725B ALA* 3.4 25.4 + - - -
726B ALA* 3.6 27.6 - - + +
729B CYS* 4.4 3.6 - - - -
766B TRP* 4.2 0.3 - - - -
785B ALA 2.8 19.8 + - - -
786B PHE* 3.4 12.8 - - + -
788B VAL* 1.3 73.7 - - - +
790B MET* 1.3 66.0 + - - +
792B GLU* 3.2 10.4 + - - +
793B ILE* 3.0 38.7 + - + +
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Residues in contact with MET 790 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704B MET* 3.7 15.6 - - + +
786B PHE* 2.7 58.1 + - + +
787B GLY* 3.4 10.8 - - - +
789B THR* 1.3 71.5 - - - +
791B TRP* 1.3 53.0 + - - +
793B ILE* 3.2 12.4 + - - +
794B ALA* 2.8 33.6 + - - +
829B LEU* 3.2 35.0 - - + +
832B ILE* 3.7 27.4 - - + -
833B MET* 3.7 26.5 - - + -
836B CYS* 4.9 1.1 - - - -
854B LEU* 3.7 9.0 - - + -
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Residues in contact with TRP 791 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A LEU* 3.7 23.1 - - + -
787B GLY 3.1 12.6 + - - +
788B VAL 3.0 11.6 + - - +
790B MET* 1.3 74.0 - - - +
792B GLU* 1.3 71.5 + - - +
794B ALA* 3.2 1.3 + - - -
795B THR* 2.9 43.0 + - + +
798B MET* 3.2 44.4 - - + -
799B THR 3.7 10.1 - - - -
800B PRO* 3.5 21.8 - - + -
801B TYR 4.4 1.6 - - - -
802B PRO* 4.4 6.7 - - + -
819B LEU* 3.6 39.6 - - + +
820B LYS 2.9 27.7 + - - -
822B PRO* 4.1 8.6 - - + +
830B TYR* 5.4 0.2 - + - -
833B MET* 4.0 24.5 - - - -
837B TRP* 4.4 1.6 - + + -
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Residues in contact with GLU 792 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680B HIS* 3.2 30.0 + - + -
683B LEU* 3.9 2.1 - - - +
725B ALA* 5.0 0.3 - - - +
726B ALA* 3.0 34.1 + - + +
727B ARG* 4.9 1.4 + - - +
766B TRP* 2.8 45.7 + - + +
788B VAL 2.8 16.3 + - - +
789B THR* 3.4 11.8 - - - +
791B TRP* 1.3 76.6 - - - +
793B ILE* 1.3 60.9 + - - +
795B THR* 3.2 6.5 + - - -
796B ARG 3.1 2.4 + - - -
797B GLY* 2.7 29.9 + - - -
798B MET 4.3 14.2 - - - +
800B PRO* 4.5 6.0 - - + +
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Residues in contact with ILE 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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679B LEU* 3.9 18.8 - - + -
683B LEU* 3.8 14.9 - - + +
700B LEU* 3.8 40.4 - - + +
703B PHE* 4.5 4.0 - - + -
704B MET* 3.7 36.3 - - + +
707B ILE* 3.8 29.2 - - + -
726B ALA* 4.9 1.6 - - + -
786B PHE* 6.3 0.4 - - + -
789B THR* 3.0 25.6 + - + +
790B MET* 3.4 7.0 - - - +
791B TRP 3.1 0.2 - - - -
792B GLU* 1.3 75.4 - - - +
794B ALA* 1.3 65.2 + - - +
796B ARG* 2.9 14.6 + - - -
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Residues in contact with ALA 794 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700B LEU* 4.5 10.5 - - - +
704B MET* 4.5 2.5 - - + -
790B MET 2.8 18.5 + - - +
791B TRP 3.2 3.8 + - - +
793B ILE* 1.3 74.0 - - - +
795B THR* 1.3 59.3 + - - +
796B ARG* 3.5 15.1 + - - +
822B PRO* 4.0 18.1 - - + +
825B CYS* 4.7 3.8 - - + -
829B LEU* 4.4 13.2 - - + -
833B MET* 3.8 23.3 - - + -
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Residues in contact with THR 795 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A ARG* 3.7 19.6 + - - +
688A LEU* 4.5 2.5 - - + -
791B TRP* 2.9 46.3 + - + +
792B GLU 3.2 7.3 + - - -
794B ALA* 1.3 74.5 - - - +
796B ARG* 1.3 69.0 + - - +
797B GLY 3.4 0.2 + - - -
798B MET* 3.3 36.1 + - - +
822B PRO* 3.6 28.5 - - + -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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