Contacts of the helix formed by residues 855 - 871 (chain B) in PDB entry 1QXP
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 ILE 855 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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764B PHE* 4.3 12.1 - - + -
772B MET* 3.8 11.6 - - + +
796B ILE* 5.4 12.3 - - + -
799B TRP* 5.6 8.5 - - + -
851B PHE* 3.3 39.6 + - + +
853B ASN 2.9 1.2 - - - -
854B PHE* 1.3 72.3 - - - +
856B SER* 1.3 68.0 + - - +
858B LEU* 3.1 8.5 - - - +
859B VAL* 3.0 17.8 + - - +
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Residues in contact with SER 856 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768B THR* 3.6 32.1 - - - -
771B SER* 5.7 4.5 - - - -
772B MET* 3.8 12.9 - - - +
851B PHE 4.1 3.2 + - - -
853B ASN* 2.9 15.9 + - - -
855B ILE* 1.3 76.9 - - - +
857B CYS* 1.4 52.6 + - - -
858B LEU* 2.5 16.3 + - - -
859B VAL* 3.0 11.8 + - - +
860B ARG* 3.5 13.0 + - - +
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Residues in contact with CYS 857 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580B ARG* 4.8 6.1 - - - -
701B VAL* 5.9 5.7 - - - +
823B PHE* 3.9 12.2 - - + -
838B ILE* 3.6 27.2 - - + +
839B ILE 4.6 1.3 - - - -
840B ARG 3.3 25.4 - - - -
853B ASN* 2.3 46.3 + - - +
854B PHE* 3.6 11.4 - - + +
856B SER* 1.4 63.5 - - - +
858B LEU* 1.4 54.0 - - - -
860B ARG* 5.5 5.8 - - - +
861B LEU* 4.1 12.0 + - - +
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Residues in contact with LEU 858 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799B TRP* 3.2 38.8 - - + -
823B PHE* 3.8 4.9 - - + -
854B PHE 3.0 10.5 + - - +
855B ILE 3.1 10.5 - - - +
856B SER 2.5 7.3 + - - -
857B CYS* 1.4 72.5 - - - +
859B VAL* 1.3 63.1 + - - +
860B ARG 2.7 8.7 - - - -
861B LEU* 3.1 11.2 + - - +
862B ASP* 2.8 23.6 + - - +
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Residues in contact with VAL 859 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771B SER 6.0 0.9 - - - +
772B MET* 3.4 35.7 - - + -
775B VAL* 4.4 8.2 - - + +
792B LEU* 4.8 17.5 - - + -
799B TRP* 5.9 0.9 - - - -
855B ILE 3.0 2.9 + - - +
856B SER 3.0 5.4 + - - +
858B LEU* 1.3 76.3 - - - +
860B ARG* 1.3 56.1 + - + +
862B ASP* 3.6 8.6 - - - +
863B ALA* 3.0 21.3 + - - +
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Residues in contact with ARG 860 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670B ARG* 4.6 1.2 - - - +
700B SER 2.6 32.1 + - - -
701B VAL* 2.8 52.9 - - + +
702B LEU* 3.9 23.7 - - - +
771B SER* 5.1 20.0 - - - +
775B VAL* 5.5 4.7 - - + -
856B SER 3.5 11.6 + - - +
857B CYS* 5.5 4.3 - - - +
858B LEU 2.7 1.0 - - - -
859B VAL* 1.3 80.5 - - + +
861B LEU* 1.3 58.0 + - - -
862B ASP 3.2 0.2 - - - -
863B ALA* 3.8 7.4 - - - -
864B MET* 3.1 33.0 - - + +
889B LEU 5.8 0.8 + - - -
890B THR* 5.5 2.2 + - - +
893B SER* 2.7 40.2 + - - -
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Residues in contact with LEU 861 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B LEU* 5.3 3.4 - - + -
701B VAL* 4.6 13.9 - - + +
799B TRP* 5.4 0.2 - - + -
823B PHE* 3.6 22.2 - - + -
828B PHE* 3.1 50.5 - - + -
830B LEU* 4.6 18.2 - - + -
834B ILE* 6.1 0.4 - - + -
838B ILE* 4.7 9.4 - - + -
857B CYS 4.1 7.7 + - - +
858B LEU* 3.1 23.3 + - - +
860B ARG* 1.3 77.4 - - - +
862B ASP* 1.3 74.1 + - - +
864B MET* 3.4 1.3 + - - +
865B PHE* 3.0 36.4 - - + -
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Residues in contact with ASP 862 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791B TYR* 2.6 37.0 + - - -
795B ASN* 5.8 0.3 - - - +
799B TRP* 4.8 6.3 - - + -
828B PHE* 2.9 32.7 - - + -
858B LEU 2.8 18.9 + - - +
859B VAL* 3.6 7.8 - - - +
860B ARG 3.2 0.8 - - - -
861B LEU* 1.3 85.8 - - - +
863B ALA* 1.3 56.8 + - - +
864B MET 2.4 13.2 + - - -
865B PHE* 2.8 16.6 + - - +
866B ARG* 2.3 33.8 + - - -
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Residues in contact with ALA 863 (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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2B ALA 4.0 15.0 + - - +
775B VAL* 4.0 24.0 - - + +
776B MET* 6.3 1.3 - - - -
859B VAL 3.0 21.7 + - - +
860B ARG* 3.8 10.1 - - - -
862B ASP* 1.3 76.3 + - - +
864B MET* 1.2 79.5 + - + +
865B PHE 3.3 0.7 - - - -
866B ARG* 4.0 7.9 - - - +
867B ALA* 3.5 12.5 + - - +
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Residues in contact with MET 864 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ALA 5.9 2.2 - - - +
4B ILE* 5.6 4.3 - - + -
5B ALA* 5.7 1.1 - - + -
696B TRP* 2.7 54.6 + - + +
697B LEU* 4.9 0.7 - - + -
700B SER* 4.1 23.6 - - - +
701B VAL* 4.4 8.3 - - + -
775B VAL* 5.7 6.1 - - + -
860B ARG* 3.1 30.5 - - - +
861B LEU 3.4 3.3 + - - +
862B ASP 2.4 14.1 + - - +
863B ALA* 1.2 95.2 - - + +
865B PHE* 1.3 69.3 + - + +
867B ALA* 3.6 14.8 - - + -
868B PHE* 2.9 8.5 + - - +
889B LEU* 4.9 14.6 - - + +
893B SER* 5.7 5.6 - - - +
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Residues in contact with PHE 865 (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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693B LEU* 4.1 32.8 - - + -
697B LEU* 4.0 25.4 - - + -
828B PHE* 4.3 29.4 - + + -
830B LEU* 5.8 5.4 - - + -
861B LEU* 3.0 36.6 - - + -
862B ASP 2.8 8.4 + - - +
864B MET* 1.3 79.3 - - + +
866B ARG* 1.3 81.1 + - - +
867B ALA 2.6 2.8 + - - -
868B PHE* 2.9 13.5 + - - -
869B ARG* 2.9 13.1 + - + +
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Residues in contact with ARG 866 (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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2B ALA* 4.2 17.4 - - + +
6B MET* 5.2 0.7 - - - +
791B TYR* 2.8 20.1 + - + +
826B ALA 5.5 1.0 + - - -
827B GLY 5.7 0.4 + - - -
828B PHE* 4.2 13.5 - - - -
862B ASP* 2.3 51.3 + - - -
863B ALA* 3.8 8.3 - - - +
865B PHE* 1.3 85.1 - - - +
867B ALA* 1.3 49.7 + - - +
869B ARG* 3.5 8.5 - - - +
870B SER* 2.8 32.7 + - - -
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Residues in contact with ALA 867 (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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2B ALA 4.8 1.9 - - - +
5B ALA* 3.5 30.3 - - + -
696B TRP* 4.3 9.0 - - + +
863B ALA 3.5 12.5 + - - +
864B MET* 3.3 23.8 - - + +
865B PHE 2.6 2.4 + - - -
866B ARG* 1.3 69.2 - - - +
868B PHE* 1.3 58.5 + - - +
869B ARG 2.4 16.2 + - - -
870B SER* 2.7 10.5 + - - +
871B LEU* 2.8 19.1 + - - +
889B LEU* 4.5 2.2 - - + -
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Residues in contact with PHE 868 (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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691B LEU* 3.8 1.8 - - + -
692B ASP 3.4 22.2 - - - -
693B LEU* 3.3 37.2 - - + -
696B TRP* 3.8 21.4 - + + +
864B MET 2.9 13.2 + - - +
865B PHE 2.9 5.9 + - - +
867B ALA* 1.3 80.6 - - - +
869B ARG* 1.3 61.7 + - + +
871B LEU* 4.1 2.0 - - - -
872B ASP* 3.3 24.0 - - - +
877B GLY* 3.4 10.3 - - - -
878B GLN* 3.3 28.5 - - - -
879B ILE* 3.2 48.6 - - + +
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Residues in contact with ARG 869 (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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865B PHE* 2.9 13.6 + - + +
866B ARG* 4.2 7.4 - - - +
867B ALA 2.4 11.3 + - - -
868B PHE* 1.3 74.7 - - + +
870B SER* 1.3 64.5 + - - +
872B ASP* 3.0 22.8 + - - +
873B LYS* 3.4 3.1 + - - -
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Residues in contact with SER 870 (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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2B ALA* 6.1 0.2 - - - -
5B ALA* 3.4 15.3 + - - -
6B MET* 2.6 47.9 - - - +
9B ALA* 3.5 16.2 - - - +
866B ARG 2.8 18.5 + - - -
867B ALA* 2.7 6.5 + - - -
869B ARG* 1.3 81.1 - - - +
871B LEU* 1.4 56.2 + - - -
872B ASP 3.2 2.5 + - - -
873B LYS* 3.9 8.5 + - - +
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Residues in contact with LEU 871 (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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5B ALA* 3.2 40.4 - - + +
8B LEU* 5.1 7.4 - - + -
9B ALA* 4.8 10.1 - - + +
12B ARG* 3.9 31.1 + - - +
867B ALA 2.8 21.5 + - - +
870B SER* 1.4 73.7 - - - +
872B ASP* 1.3 56.1 + - - +
873B LYS* 3.6 1.8 - - - -
879B ILE* 4.2 22.9 - - + +
880B GLN 5.5 0.2 + - - -
881B VAL* 4.3 13.0 - - + -
889B LEU* 3.9 29.8 - - + -
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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