Contacts of the helix formed by residues 678 - 702 (chain B) in PDB entry 1P48
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 678 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676B ALA* 3.6 3.0 - - - +
677B LYS* 1.3 88.3 - - + +
679B PHE* 1.3 64.9 + - - +
680B ALA* 3.6 6.3 + - - +
681B GLU* 3.1 23.7 + - - +
682B ALA* 3.0 21.8 + - - +
916B GLU* 3.6 13.0 - - - +
925B PHE* 3.8 12.1 - - - -
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Residues in contact with PHE 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B LEU* 4.3 11.4 - - + -
647B PRO* 3.3 26.7 - - + -
649B PRO* 3.9 23.6 - - + -
678B THR* 1.3 72.1 - - - +
680B ALA* 1.3 58.6 + - - +
682B ALA* 3.1 2.5 + - - +
683B LEU* 2.9 44.8 + - + +
909B LEU* 3.4 33.7 - - + -
912B LEU* 3.5 44.0 - - + -
913B LEU* 3.9 15.5 - - + -
916B GLU* 2.8 21.7 + - - +
925B PHE* 3.6 18.1 - - + -
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Residues in contact with ALA 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 4.4 2.1 + - - -
56A TRP* 5.7 1.0 - - - -
678B THR* 3.2 6.9 - - - +
679B PHE* 1.3 76.7 - - - +
681B GLU* 1.3 62.3 + - - +
683B LEU* 3.4 2.8 + - - +
684B ARG* 3.0 22.0 + - - +
913B LEU* 3.8 23.2 - - + +
916B GLU* 3.0 19.3 + - - +
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Residues in contact with GLU 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675B GLY 4.5 1.0 - - - +
676B ALA* 3.4 8.9 - - + -
677B LYS* 3.1 35.1 + - - +
678B THR* 3.1 21.7 + - - +
680B ALA* 1.3 73.9 - - - +
682B ALA* 1.3 61.7 + - - +
684B ARG* 3.1 28.3 + - - +
685B ILE* 2.8 51.2 + - + +
740B LYS* 5.8 3.1 - - - +
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Residues in contact with ALA 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649B PRO* 4.1 15.9 - - + +
651B LEU* 5.1 0.2 - - - +
673B PRO* 3.4 26.2 - - + +
676B ALA* 3.5 18.7 - - + +
678B THR 3.0 13.8 + - - +
679B PHE 3.4 8.7 - - - +
681B GLU* 1.3 77.3 - - - +
683B LEU* 1.3 57.0 + - - +
685B ILE* 3.4 0.6 + - - -
686B GLY* 2.8 23.4 + - - -
925B PHE* 3.8 16.8 - - + -
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Residues in contact with LEU 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 3.4 38.4 - - + +
649B PRO* 4.9 5.5 - - + +
651B LEU* 4.9 8.5 - - + -
679B PHE* 2.9 26.2 + - + +
680B ALA* 3.7 5.6 - - - +
682B ALA* 1.3 74.5 - - - +
684B ARG* 1.3 60.0 + - - +
686B GLY* 3.3 0.8 + - - -
687B SER* 2.9 27.7 + - - -
900B PRO* 4.8 12.6 - - + -
906B LEU* 5.4 0.9 - - + -
909B LEU* 3.9 45.8 - - + -
913B LEU* 3.8 22.9 - - + -
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Residues in contact with ARG 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 3.1 15.8 + - - +
54A SER 4.3 3.6 + - - -
55A LYS* 3.9 34.8 - - - +
56A TRP* 3.4 44.1 - - + +
680B ALA 3.0 13.9 + - - +
681B GLU* 3.6 34.4 + - - +
683B LEU* 1.3 75.2 - - - +
685B ILE* 1.3 69.6 + - - +
687B SER* 2.5 21.0 + - - -
688B GLU* 2.9 49.1 + - - +
737B HIS* 4.6 9.5 - - - -
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Residues in contact with ILE 685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673B PRO* 4.4 6.3 - - + -
676B ALA* 4.2 17.5 - - + +
681B GLU* 2.8 46.3 + - + +
682B ALA* 3.7 3.8 - - - +
684B ARG* 1.3 79.6 - - - +
686B GLY* 1.3 63.1 + - - +
688B GLU* 3.3 4.0 + - - +
689B VAL* 3.0 23.4 + - + +
737B HIS* 3.5 46.9 - - + +
740B LYS* 4.9 15.5 - - + -
741B VAL* 3.6 23.3 - - + -
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Residues in contact with GLY 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651B LEU* 3.8 24.9 - - - -
671B ILE* 4.1 11.3 - - - +
673B PRO* 4.4 5.2 - - - -
682B ALA 2.8 17.6 + - - -
683B LEU 3.7 1.6 - - - -
685B ILE* 1.3 77.4 - - - +
687B SER* 1.3 61.8 + - - +
689B VAL* 3.3 2.6 + - - +
690B TYR* 2.9 25.2 + - - +
900B PRO* 4.3 1.6 - - - +
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Residues in contact with SER 687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 3.7 10.3 - - - -
15A GLY 3.7 22.7 - - - -
56A TRP* 3.7 15.6 - - - -
683B LEU 2.9 14.3 + - - -
684B ARG* 2.5 25.1 + - - -
686B GLY* 1.3 74.8 - - - +
688B GLU* 1.3 58.0 + - - +
690B TYR* 3.4 2.4 - - - +
691B HIS* 2.9 37.9 + - - -
900B PRO* 4.1 18.4 - - - +
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Residues in contact with GLU 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A SER 4.6 4.7 - - - +
55A LYS* 3.5 5.2 - - - -
56A TRP* 2.8 37.7 + - - +
57A MET* 4.3 17.5 - - + +
684B ARG* 2.9 40.1 + - - +
685B ILE* 3.6 6.5 - - - +
687B SER* 1.3 80.1 + - - +
689B VAL* 1.3 64.0 + - - +
691B HIS* 3.4 2.2 + - + +
692B ASN* 2.9 31.6 + - - +
735B ALA* 4.2 5.9 - - + +
737B HIS* 2.8 32.5 + - + +
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Residues in contact with VAL 689 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B VAL* 5.8 1.8 - - + -
671B ILE* 3.9 23.1 - - + -
685B ILE 3.0 21.4 + - - +
686B GLY 3.8 3.8 - - - +
688B GLU* 1.3 74.8 - - - +
690B TYR* 1.3 64.5 + - - +
692B ASN* 3.2 3.1 + - - +
693B LEU* 2.9 23.8 + - + +
728B ILE* 4.7 1.6 - - + +
731B ALA* 3.7 7.0 - - + +
732B ILE* 3.8 37.2 - - + +
735B ALA* 4.0 11.4 - - + -
737B HIS* 3.9 18.8 - - + -
741B VAL* 4.4 16.2 - - + -
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Residues in contact with TYR 690 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG 4.4 9.6 - - - -
653B VAL* 3.8 36.8 - - + -
671B ILE* 4.8 0.2 - - - +
686B GLY 2.9 17.5 + - - +
687B SER 3.4 4.3 - - - +
689B VAL* 1.3 79.4 - - - +
691B HIS* 1.3 73.3 + + - +
693B LEU* 3.2 9.2 + - + +
694B LYS* 3.0 51.5 + - + +
708B VAL* 3.4 14.7 - - - +
712B GLY 2.7 28.6 + - - -
713B GLY* 4.3 1.1 - - - -
714B VAL* 4.7 3.1 - - + -
899B ALA* 4.1 7.0 - - + -
900B PRO* 3.5 23.6 - - + -
901B ALA* 3.3 23.2 - - + +
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Residues in contact with HIS 691 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG* 3.0 28.0 - - + -
15A GLY* 3.2 14.8 + - - -
16A ASN* 3.1 26.4 + - - -
56A TRP* 5.7 1.3 - - - -
57A MET* 3.8 39.1 - - + +
59A LYS* 6.1 0.9 + - - -
687B SER* 2.9 31.0 + - - +
688B GLU* 3.4 1.8 + - + +
690B TYR* 1.3 86.3 - + - +
692B ASN* 1.3 65.5 + - - +
694B LYS* 3.2 12.5 + - - +
695B SER* 3.2 22.3 + - - -
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Residues in contact with ASN 692 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A MET* 3.5 25.0 - - - +
688B GLU* 2.9 27.3 + - - +
689B VAL 3.7 3.8 - - - +
691B HIS* 1.3 76.7 - - - +
693B LEU* 1.3 60.3 + - - +
695B SER* 3.0 19.7 + - - -
696B LEU* 3.1 21.2 + - - +
731B ALA* 3.9 16.8 - - - +
734B ALA* 3.8 20.7 - - + +
735B ALA* 3.5 24.4 - - - +
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Residues in contact with LEU 693 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B VAL* 3.5 50.0 - - + +
654B LEU* 4.6 5.2 - - + -
689B VAL* 2.9 14.6 + - + +
690B TYR* 3.2 12.3 - - + +
692B ASN* 1.3 76.2 - - - +
694B LYS* 1.3 59.1 + - - +
696B LEU* 3.3 2.1 + - - +
697B THR* 2.8 48.3 + - - +
714B VAL* 4.0 10.8 - - + -
727B LEU* 3.9 37.9 - - + +
728B ILE* 4.5 6.5 - - + -
731B ALA* 3.7 12.5 - - + +
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Residues in contact with LYS 694 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ASP* 4.8 11.3 + - - -
690B TYR* 3.0 47.1 + - + +
691B HIS* 3.2 16.3 + - - +
693B LEU* 1.3 76.5 - - - +
695B SER* 1.3 63.1 + - - +
697B THR* 3.7 1.2 - - - -
698B LYS* 3.1 38.0 + - + +
706B GLY* 2.8 28.2 + - - +
708B VAL* 4.4 8.7 - - - +
714B VAL* 3.7 26.9 - - + -
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Residues in contact with SER 695 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A MET* 5.7 1.6 - - - +
691B HIS 3.2 9.8 + - - -
692B ASN* 3.0 22.0 + - - -
694B LYS* 1.3 77.2 - - - +
696B LEU* 1.3 59.0 + - - +
698B LYS* 3.5 9.7 + - - +
699B LYS* 3.0 29.0 + - - +
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Residues in contact with LEU 696 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692B ASN* 3.1 23.5 + - + +
693B LEU 3.8 3.4 - - - +
695B SER* 1.3 75.8 + - - +
697B THR* 1.3 66.6 + - - +
699B LYS* 3.2 15.2 + - + +
700B ARG* 3.1 48.1 + - - +
727B LEU* 4.3 11.9 - - + +
730B ASP* 4.0 15.9 - - + +
731B ALA* 3.9 31.9 - - + +
734B ALA* 4.5 10.5 - - + -
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Residues in contact with THR 697 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693B LEU* 2.8 38.3 + - - +
694B LYS 3.7 4.5 - - - -
696B LEU* 1.3 78.0 - - - +
698B LYS* 1.3 56.5 + - - +
701B TYR* 2.9 44.6 + - + +
705B ALA* 3.4 25.4 - - + +
714B VAL* 3.9 13.4 - - + +
716B PRO* 3.8 32.5 - - + -
727B LEU* 4.0 8.0 - - - +
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Residues in contact with LYS 698 (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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159A HIS 6.0 2.2 + - - -
161A GLY 5.4 4.0 - - - +
694B LYS* 3.1 32.4 + - + +
695B SER* 3.9 6.7 - - - +
697B THR* 1.3 75.6 - - - +
699B LYS* 1.3 59.1 + - - +
702B GLY* 2.9 37.7 + - - +
703B ALA* 2.8 45.0 + - - +
706B GLY* 3.5 27.1 - - - +
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Residues in contact with LYS 699 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695B SER 3.0 18.4 + - - +
696B LEU* 3.2 18.6 + - + +
698B LYS* 1.3 78.4 - - - +
700B ARG* 1.3 62.7 + - + +
702B GLY 4.8 0.5 + - - -
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Residues in contact with ARG 700 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696B LEU* 3.1 30.9 + - - +
699B LYS* 1.3 87.6 - - + +
701B TYR* 1.3 87.5 + - + +
702B GLY 3.5 0.7 - - - -
726B ASP* 5.2 1.4 - - - +
727B LEU* 3.7 29.9 - - - +
730B ASP* 2.8 36.1 + - - +
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Residues in contact with TYR 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B THR* 2.9 31.1 + - + +
700B ARG* 1.3 94.9 + - + +
702B GLY* 1.3 62.1 + - - +
704B SER* 6.0 0.3 - - - -
705B ALA* 3.6 19.4 + - + +
716B PRO* 4.0 9.9 - - + -
717B ASN* 4.4 18.6 - - + +
718B ILE* 4.4 6.5 - - + +
723B GLU* 2.8 39.3 + - - +
727B LEU* 3.4 34.8 - - + +
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Residues in contact with GLY 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698B LYS* 2.9 22.9 + - - -
699B LYS 4.6 0.6 + - - -
700B ARG 3.5 1.4 - - - -
701B TYR* 1.3 80.0 - - - +
703B ALA* 1.3 68.2 + - - -
704B SER* 3.2 4.0 - - - -
705B ALA* 2.9 18.4 + - - +
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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
------------------------------------------------------------
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