Contacts of the helix formed by residues 654 - 674 (chain B) in PDB entry 1J1C
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 654 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B TYR* 3.9 14.4 - - + +
652B THR* 3.4 9.6 - - + +
653B LEU* 1.3 95.4 - - + +
655B VAL* 1.3 67.5 + - - +
656B ILE* 4.1 10.8 - - + -
657B TYR* 2.9 37.7 + - + +
658B VAL 3.3 6.2 + - - -
851B PRO* 5.7 1.3 - - + -
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Residues in contact with VAL 655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652B THR* 5.8 0.4 - - + -
653B LEU 3.2 3.5 + - - +
654B PRO* 1.3 71.8 - - - +
656B ILE* 1.3 57.8 + - - +
658B VAL* 3.0 10.3 + - + +
659B LYS* 2.8 50.9 + - - +
751B LEU* 4.9 10.5 - - + -
806B ARG* 4.3 17.7 - - - +
810B PRO* 4.1 29.2 - - + -
839B PHE* 3.9 19.3 - - + -
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Residues in contact with ILE 656 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654B PRO* 4.1 9.4 - - + -
655B VAL* 1.3 77.2 - - - +
657B TYR* 1.3 69.8 + - + +
659B LYS* 3.4 6.5 + - + +
660B LEU* 3.0 36.3 + - + +
842B GLU* 3.8 33.2 - - - +
843B LEU* 4.0 20.6 - - + -
848B VAL* 4.2 11.7 - - + -
849B LYS 4.8 10.3 - - - +
851B PRO* 3.9 28.5 - - + -
856B THR* 6.1 0.4 - - + -
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Residues in contact with TYR 657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B TYR* 5.3 3.8 - - - -
653B LEU* 3.8 18.8 - - + -
654B PRO* 2.9 36.6 + - + +
656B ILE* 1.3 78.7 - - + +
658B VAL* 1.3 61.1 + - - +
660B LEU* 3.2 11.4 + - + -
661B TYR* 2.8 67.9 + + + -
691B PRO 5.0 8.0 + - - -
694B ALA* 4.4 15.0 - - + -
850B LEU* 4.8 3.6 - - + +
851B PRO* 3.1 45.9 - - + +
852B ASN* 4.6 7.1 + - - +
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Residues in contact with VAL 658 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B LEU* 3.9 29.4 - - + +
654B PRO 3.8 11.4 - - - +
655B VAL* 3.0 14.3 + - + +
657B TYR* 1.3 77.7 - - - +
659B LYS* 1.3 62.6 + - - +
661B TYR* 4.1 0.2 - - - +
662B MET* 3.0 34.4 + - + +
747B LEU* 3.6 30.5 - - + -
750B LEU* 4.1 28.9 - - + +
751B LEU* 4.3 12.6 - - + -
839B PHE* 4.0 9.9 - - + -
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Residues in contact with LYS 659 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655B VAL* 2.8 24.0 + - - +
656B ILE* 3.5 10.5 - - - +
658B VAL* 1.3 76.5 - - - +
660B LEU* 1.3 62.7 + - - +
663B TYR* 2.9 28.2 + - - +
810B PRO* 5.8 3.4 - - - +
839B PHE* 3.3 57.2 + - + +
840B PHE* 3.1 11.8 - - + -
842B GLU* 2.7 46.1 + - + +
843B LEU* 3.8 17.3 - - + -
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Residues in contact with LEU 660 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656B ILE* 3.0 32.4 + - + +
657B TYR* 3.2 10.5 + - + +
659B LYS* 1.3 77.8 - - - +
661B TYR* 1.3 66.6 + - + +
663B TYR* 3.8 1.4 - - - +
664B GLN* 2.8 37.5 + - - +
694B ALA* 4.1 9.4 - - + +
843B LEU* 3.8 22.9 - - + -
850B LEU* 3.4 31.4 - - + -
856B THR* 4.2 11.7 - - + -
857B PRO* 3.9 24.5 - - + -
859B LEU* 4.2 14.8 - - + -
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Residues in contact with TYR 661 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639B VAL* 4.8 6.5 - - + -
642B VAL* 5.0 5.9 - - + +
653B LEU* 3.8 32.7 - - + +
657B TYR* 2.8 46.2 + + + +
658B VAL* 4.1 3.4 - - - +
660B LEU* 1.3 73.7 - - + +
662B MET* 1.3 61.4 + - - +
664B GLN* 3.3 4.5 + - - +
665B LEU* 2.9 24.0 + - - +
689B LEU* 3.4 46.5 - - + +
691B PRO* 4.9 10.6 + - - +
694B ALA* 3.8 33.9 - - + -
696B LEU* 3.5 23.4 - - + +
750B LEU* 4.9 10.8 - - + -
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Residues in contact with MET 662 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658B VAL* 3.0 23.8 + - + +
661B TYR* 1.3 74.4 - - - +
663B TYR* 1.3 66.2 + - - +
665B LEU* 3.1 18.8 + - + +
666B PHE* 2.9 50.5 + - + -
687B LEU* 6.0 0.2 - - - -
743B ALA 3.1 28.7 - - - +
746B VAL* 3.9 16.2 - - - -
747B LEU* 3.6 45.3 - - + -
750B LEU* 4.2 8.1 - - + -
839B PHE* 5.1 0.2 - - + -
840B PHE* 3.9 16.4 - - + -
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Residues in contact with TYR 663 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659B LYS 2.9 20.4 + - - +
660B LEU 3.8 1.8 - - - +
662B MET* 1.3 77.1 - - - +
664B GLN* 1.3 66.8 + - + +
666B PHE* 3.2 6.5 + - - +
667B ARG* 3.0 38.6 + - + +
835B CYS* 3.6 36.4 - - + -
840B PHE* 3.4 25.9 - + + -
843B LEU* 3.5 15.7 - - + -
844B ARG* 4.3 9.1 + - - -
859B LEU* 2.7 57.6 + - + -
860B PHE* 4.1 9.9 - + - -
862B PHE* 3.3 19.6 - + - -
877B LEU* 4.5 3.0 + - + +
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Residues in contact with GLN 664 (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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608B ASN* 3.2 40.6 + - - +
660B LEU* 2.8 27.9 + - - +
661B TYR* 3.7 5.5 + - - +
662B MET 3.3 0.2 - - - -
663B TYR* 1.3 82.1 - - + +
665B LEU* 1.3 63.3 + - - +
667B ARG* 3.3 3.4 + - - +
668B SER* 3.1 18.0 + - - -
694B ALA 2.9 18.1 + - - +
695B VAL* 3.2 14.3 - - - +
696B LEU* 2.9 36.5 + - + +
857B PRO* 4.2 15.5 - - - +
858B ALA 5.4 1.9 + - - +
859B LEU* 4.3 19.0 - - + +
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Residues in contact with LEU 665 (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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661B TYR 2.9 14.4 + - - +
662B MET* 3.1 26.2 + - + +
664B GLN* 1.3 75.9 - - - +
666B PHE* 1.3 62.9 + - + +
668B SER* 2.7 30.1 + - - +
669B LEU* 3.0 24.8 + - + +
682B ILE* 4.3 12.6 - - + -
687B LEU* 3.9 38.4 - - + -
696B LEU* 4.0 13.4 - - + +
698B LEU* 4.6 1.6 - - + -
743B ALA* 3.8 31.2 - - + -
746B VAL* 4.9 1.8 - - + -
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Residues in contact with PHE 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662B MET* 2.9 39.4 + - + -
663B TYR 3.2 2.0 + - - +
665B LEU* 1.3 75.8 - - - +
667B ARG* 1.3 57.3 + - - +
669B LEU* 3.4 10.9 + - + -
670B ALA* 2.8 26.3 + - - +
740B VAL* 4.8 7.4 - - + -
743B ALA* 3.6 26.9 - - + -
816B LEU* 4.6 3.4 - - + -
820B LEU* 3.6 39.0 - - + -
831B PRO* 3.3 23.8 - - + +
834B ALA* 3.6 26.5 - - + -
835B CYS* 3.6 20.4 - - - -
840B PHE* 4.0 19.3 - + - -
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Residues in contact with ARG 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606B HIS* 3.9 13.2 + - + -
607B CYS* 4.1 8.3 - - - -
608B ASN* 3.8 13.6 - - - +
663B TYR* 3.0 35.8 + - + +
664B GLN 3.5 8.5 - - - +
665B LEU 3.2 0.2 - - - -
666B PHE* 1.3 74.5 - - - +
668B SER* 1.3 65.6 + - - +
670B ALA* 3.2 6.2 + - - +
671B TYR* 3.0 22.3 + - - +
835B CYS* 3.8 16.2 - - - -
858B ALA 3.7 6.0 + - - -
859B LEU* 3.4 20.7 + - - +
861B ASN* 2.8 47.6 + - - +
862B PHE* 3.6 18.3 - - + +
866B GLU* 2.8 44.1 + - - +
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Residues in contact with SER 668 (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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606B HIS* 4.2 9.3 - - - -
608B ASN* 3.3 27.8 - - - -
609B ILE* 3.9 11.8 - - - +
664B GLN 3.1 9.4 + - - -
665B LEU* 2.7 25.9 + - - +
667B ARG* 1.3 76.4 - - - +
669B LEU* 1.3 57.0 + - - +
671B TYR* 3.2 5.2 + - - +
672B ILE* 3.0 32.7 + - - +
698B LEU* 3.6 21.1 - - - +
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Residues in contact with LEU 669 (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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665B LEU* 3.0 22.9 + - + +
666B PHE* 3.7 15.5 - - + +
668B SER* 1.3 79.7 + - - +
670B ALA* 1.3 66.6 + - - +
672B ILE* 3.9 20.0 - - + -
673B HIS* 3.0 32.0 + - + +
682B ILE* 3.9 24.9 - - + -
698B LEU* 4.3 6.3 - - + -
739B ASP* 3.9 38.8 - - + +
740B VAL* 4.7 1.6 - - - +
743B ALA* 4.2 16.2 - - + -
831B PRO* 3.8 15.9 - - + -
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Residues in contact with ALA 670 (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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666B PHE 2.8 17.6 + - - +
667B ARG* 3.2 8.5 + - - +
669B LEU* 1.3 75.2 - - - +
671B TYR* 1.3 61.6 + - - +
673B HIS* 4.0 2.6 - - - +
674B SER* 3.2 23.7 + - - -
831B PRO* 3.4 16.9 - - + +
832B LEU* 4.0 31.4 - - + +
835B CYS* 5.7 0.2 - - - -
862B PHE* 6.0 0.2 - - + -
866B GLU* 4.4 13.5 - - + +
869B SER* 6.1 0.7 - - - -
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Residues in contact with TYR 671 (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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603B LYS 3.8 4.2 + - - -
604B LEU* 3.7 21.3 - - + -
605B ASP* 2.8 46.9 + - - +
606B HIS* 3.6 28.9 - + + +
609B ILE* 3.5 22.7 - - + -
667B ARG 3.0 12.7 + - - +
668B SER 3.4 7.4 - - - +
670B ALA* 1.3 75.7 - - - +
672B ILE* 1.3 65.9 + - + +
674B SER* 2.7 24.7 + - - -
675B PHE* 3.3 34.3 - + - -
863B THR* 5.2 4.0 - - + -
865B GLN* 4.3 15.0 - - + -
866B GLU* 4.5 15.4 - - + +
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Residues in contact with ILE 672 (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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604B LEU* 4.1 14.4 - - + -
609B ILE* 3.6 28.7 - - + -
668B SER 3.0 13.7 + - - +
669B LEU* 3.6 22.0 - - + +
671B TYR* 1.3 75.2 - - - +
673B HIS* 1.3 68.6 + - + +
675B PHE* 3.0 19.7 + - - +
677B ILE* 3.1 40.0 + - + +
678B CYS 4.6 0.2 - - - -
679B HIS* 3.9 31.9 - - + +
698B LEU* 4.3 7.9 - - + -
701B PHE* 4.0 17.9 - - + -
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Residues in contact with HIS 673 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669B LEU* 3.0 24.4 + - + +
670B ALA* 4.0 4.9 - - - +
672B ILE* 1.3 78.0 - - + +
674B SER* 1.3 54.5 + - - +
675B PHE 2.9 5.8 - - - -
676B GLY* 2.7 24.3 + - - +
677B ILE 3.1 21.5 - - - +
736B SER* 3.2 42.8 + - - -
739B ASP* 2.9 31.1 + - + +
740B VAL* 4.6 3.6 - - + -
831B PRO* 3.5 31.2 - - + +
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Residues in contact with SER 674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670B ALA 3.2 15.7 + - - -
671B TYR* 2.7 20.2 + - - -
673B HIS* 1.3 76.2 - - - +
675B PHE* 1.3 56.1 + - - +
676B GLY 3.3 1.1 + - - -
865B GLN* 2.6 58.7 + - - +
866B GLU 5.2 0.7 - - - -
868B SER* 3.7 9.6 + - - -
869B SER* 5.7 5.2 - - - -
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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
------------------------------------------------------------
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