Contacts of the helix formed by residues 631 - 657 (chain B) in PDB entry 4PE5
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 MET 631 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630B ILE* 1.3 75.3 - - - +
632B VAL* 1.3 62.1 + - - +
633B SER 3.2 3.2 + - - -
634B VAL* 3.8 15.2 + - - +
635B TRP* 4.2 2.8 + - - +
824C ILE* 5.9 5.3 - - - +
827C GLY* 5.9 8.3 - - - +
828C ILE* 6.5 0.4 - - - -
831C ILE* 6.3 2.7 - - + -
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Residues in contact with VAL 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630B ILE* 3.2 2.6 - - - +
631B MET* 1.3 77.9 - - - +
633B SER* 1.3 58.7 + - - +
634B VAL 3.2 0.4 - - - -
635B TRP* 2.9 14.8 + - + +
636B ALA* 2.9 26.2 + - - +
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Residues in contact with SER 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630B ILE* 3.6 19.5 + - - +
631B MET 3.2 0.2 - - - -
632B VAL* 1.3 78.1 - - - +
634B VAL* 1.3 62.3 + - - +
636B ALA* 2.9 11.6 + - - +
637B PHE* 2.9 21.4 + - - +
611C TRP* 4.8 23.6 - - - -
612C GLY* 6.0 1.1 - - - -
615C LEU* 3.9 5.7 - - - +
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Residues in contact with VAL 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631B MET 3.8 11.4 + - - +
632B VAL 3.2 0.2 - - - -
633B SER* 1.3 76.2 - - - +
635B TRP* 1.3 59.9 + - - +
637B PHE* 2.9 24.5 + - - +
638B PHE* 3.0 15.1 + - - +
820C VAL* 5.7 8.1 - - + +
823C GLY 6.0 2.7 - - - -
824C ILE* 5.9 8.3 - - + +
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Residues in contact with TRP 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569B VAL* 6.0 5.6 - - + -
612B LEU* 6.0 1.1 - - - -
631B MET 4.2 2.1 + - - +
632B VAL* 2.9 21.5 + - + +
634B VAL* 1.3 79.8 - - - +
636B ALA* 1.3 55.7 + - - +
638B PHE* 3.9 6.9 + - - +
639B ALA* 3.1 24.9 + - - +
820C VAL* 6.1 2.2 - - - -
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Residues in contact with ALA 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B LEU* 4.8 19.4 - - + +
632B VAL 2.9 11.7 + - - +
633B SER* 2.9 13.0 + - - +
635B TRP* 1.3 75.2 - - - +
637B PHE* 1.3 54.1 + - - +
639B ALA* 2.9 9.3 + - - +
640B VAL* 2.7 34.7 + - - +
615C LEU* 3.6 21.0 - - + +
616C ASN 5.3 3.6 - - - +
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Residues in contact with PHE 637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633B SER 2.9 11.8 + - - +
634B VAL* 2.9 13.2 + - - +
636B ALA* 1.3 75.1 - - - +
638B PHE* 1.3 63.4 + - - +
640B VAL* 2.9 18.2 + - - +
641B ILE* 3.0 12.5 + - - +
615C LEU* 3.8 18.1 - - + +
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Residues in contact with PHE 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B VAL 3.0 14.2 + - - +
635B TRP* 4.0 7.2 - - - +
637B PHE* 1.3 74.8 - - - +
639B ALA* 1.3 51.9 + - - +
641B ILE* 2.9 11.3 + - - +
642B PHE* 2.7 33.9 + - - +
816C VAL* 5.5 4.9 - - + +
820C VAL* 4.3 23.3 - - + -
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Residues in contact with ALA 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B LEU 3.6 23.1 - - - +
613B VAL* 3.7 23.6 - - + +
635B TRP 3.1 14.2 + - - +
636B ALA* 2.9 10.2 + - - +
638B PHE* 1.3 77.8 - - - +
640B VAL* 1.3 57.5 + - - +
642B PHE* 2.9 11.8 + - - +
643B LEU* 2.8 28.1 + - - +
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Residues in contact with VAL 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636B ALA 2.7 15.3 + - - +
637B PHE* 2.9 13.9 + - - +
639B ALA* 1.3 72.7 - - - +
641B ILE* 1.3 63.3 + - - +
643B LEU* 2.9 11.1 + - - +
644B ALA* 2.9 21.0 + - - +
614C LEU 5.8 1.3 - - - +
615C LEU* 4.9 11.9 - - - +
616C ASN* 5.5 4.7 - - + -
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Residues in contact with ILE 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B PHE 3.0 10.3 + - - +
638B PHE* 2.9 13.5 + - - +
640B VAL* 1.3 75.3 - - - +
642B PHE* 1.3 63.5 + - - +
644B ALA* 2.9 19.6 + - - +
645B SER* 3.0 16.3 + - - -
554C PHE* 6.2 4.9 - - + -
647C TYR* 4.2 23.7 - - + +
816C VAL* 6.3 3.4 - - + -
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Residues in contact with PHE 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B VAL 5.7 1.3 - - - +
638B PHE 2.7 16.1 + - - +
639B ALA* 3.2 15.7 - - - +
641B ILE* 1.3 72.6 - - - +
643B LEU* 1.3 57.6 + - - +
645B SER* 4.3 5.0 - - - -
646B TYR* 3.2 23.0 + - - +
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Residues in contact with LEU 643 (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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613B VAL 5.0 7.6 + - - +
614B PHE* 6.1 2.0 - - - +
639B ALA 2.8 12.0 + - - +
640B VAL* 2.9 13.4 + - - +
642B PHE* 1.3 76.3 - - - +
644B ALA* 1.3 65.5 + - - +
646B TYR* 2.9 17.8 + - - +
647B THR* 3.0 17.5 + - - +
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Residues in contact with ALA 644 (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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640B VAL 2.9 11.3 + - - +
641B ILE 2.9 7.8 + - - +
643B LEU* 1.3 74.5 - - - +
645B SER* 1.3 52.9 + - - +
647B THR* 2.9 9.8 + - - -
648B ALA* 2.7 35.5 + - - +
644C VAL 5.6 0.4 - - - +
647C TYR* 3.6 33.4 - - + -
648C THR* 4.4 20.2 - - - -
651C LEU* 5.4 2.2 - - + -
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Residues in contact with SER 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B ILE 3.0 14.0 + - - -
642B PHE* 4.3 5.6 - - - -
644B ALA* 1.3 75.9 - - - +
646B TYR* 1.3 58.2 + - - +
647B THR 2.9 3.1 + - - -
648B ALA* 2.9 7.6 + - - -
649B ASN* 2.8 36.6 + - - +
647C TYR* 5.4 0.6 - - - -
651C LEU* 5.5 3.5 - - - +
808C LEU* 5.9 4.9 - - - -
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Residues in contact with TYR 646 (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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645A ALA* 4.1 13.9 - - + +
553B PRO* 5.2 5.0 - - - +
642B PHE 3.2 19.2 + - - +
643B LEU* 2.9 11.3 + - - +
645B SER* 1.3 78.3 - - - +
647B THR* 1.3 56.6 + - - +
649B ASN* 5.2 2.2 - - - -
650B LEU* 3.5 19.3 + - - +
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Residues in contact with THR 647 (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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645A ALA* 4.3 19.6 - - - +
648A THR* 3.9 27.4 - - - -
649A ALA* 4.5 4.8 - - - +
643B LEU 3.0 10.0 + - - -
644B ALA* 2.9 9.5 + - - -
646B TYR* 1.3 78.4 - - - +
648B ALA* 1.3 67.5 + - - +
649B ASN 3.4 0.2 - - - -
650B LEU* 3.0 15.4 + - - +
651B ALA* 3.0 14.0 + - + +
648C THR* 5.7 7.6 - - - -
647D THR* 6.1 3.8 - - - -
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Residues in contact with ALA 648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644B ALA 2.7 19.0 + - - +
645B SER* 3.7 5.8 - - - +
647B THR* 1.3 73.0 - - - +
649B ASN* 1.3 64.4 + - - +
651B ALA* 2.9 17.0 + - - +
652B ALA* 3.0 11.2 + - - +
648C THR* 4.2 3.4 - - - +
651C LEU* 3.7 19.1 - - + +
652C ALA* 3.7 40.0 - - + +
655C LEU* 5.3 2.6 - - + +
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Residues in contact with ASN 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B PRO* 3.7 22.1 - - + +
645B SER* 2.8 21.6 + - - +
646B TYR* 5.2 0.9 - - - -
648B ALA* 1.3 73.3 - - - +
650B LEU* 1.3 49.3 + - - +
652B ALA* 2.9 11.4 + - - +
653B PHE* 2.6 35.7 + - - +
655C LEU* 5.5 4.0 - - - +
807C THR 5.6 0.4 - - - -
808C LEU* 4.1 24.9 - - + +
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Residues in contact with LEU 650 (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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645A ALA* 4.7 6.1 - - + +
646A SER* 5.9 0.7 - - - -
649A ALA* 3.9 17.5 - - + -
553B PRO* 3.5 20.4 - - + +
646B TYR 3.5 16.4 + - - +
647B THR* 3.0 13.0 + - - +
649B ASN* 1.3 75.8 - - - +
651B ALA* 1.3 58.2 + - - +
653B PHE* 2.9 4.9 + - - +
654B MET* 2.8 28.1 + - - +
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Residues in contact with ALA 651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A ALA* 3.9 20.3 - - + +
652A ALA* 4.7 14.4 - - + -
653A ALA* 5.8 1.2 - - + +
647B THR* 3.0 11.0 + - + +
648B ALA* 2.9 13.3 + - - +
650B LEU* 1.3 74.7 - - - +
652B ALA* 1.3 62.6 + - - +
654B MET* 2.9 16.6 + - - +
655B ILE* 2.9 14.8 + - - +
652C ALA* 5.0 10.8 - - + +
656C VAL* 5.4 5.6 - - + -
651D ALA* 6.4 0.2 - - + -
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Residues in contact with ALA 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B ALA 3.0 9.5 + - - +
649B ASN* 2.9 14.7 + - - +
651B ALA* 1.3 75.8 - - - +
653B PHE* 1.3 58.8 + - - +
655B ILE* 2.9 7.4 + - - +
656B GLN* 2.9 30.3 + - - +
655C LEU* 4.2 17.0 - - + +
656C VAL* 4.2 11.8 - - + +
805C PRO* 3.5 29.9 - - + +
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Residues in contact with PHE 653 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552B GLU* 5.3 5.2 - - + -
553B PRO* 3.9 23.1 - - + -
649B ASN 2.6 15.9 + - - +
650B LEU 3.4 8.5 - - - +
652B ALA* 1.3 72.4 - - - +
654B MET* 1.3 58.0 + - - +
656B GLN* 4.1 2.2 - - - -
657B GLU* 3.8 22.0 + - - +
805C PRO 4.1 8.9 + - - -
806C ALA 4.4 13.0 - - - +
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Residues in contact with MET 654 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A ALA* 4.9 7.2 - - + +
650A ASN* 6.1 0.4 - - - -
653A ALA* 4.5 22.8 - - + +
650B LEU 2.8 11.2 + - - +
651B ALA* 2.9 14.3 + - - +
653B PHE* 1.3 78.9 - - - +
655B ILE* 1.3 58.1 + - - +
656B GLN 3.4 0.7 - - - -
657B GLU 4.2 10.5 - - - +
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Residues in contact with ILE 655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651B ALA 2.9 13.3 + - - +
652B ALA* 2.9 8.2 + - - +
654B MET* 1.3 77.2 - - - +
656B GLN* 1.3 64.6 + - - +
657B GLU 4.9 0.7 - - - -
656C VAL* 4.9 17.0 - - + +
805C PRO* 5.2 2.0 - - + -
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Residues in contact with GLN 656 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652B ALA 2.9 9.1 + - - +
653B PHE* 4.5 3.1 - - - +
654B MET 3.4 0.2 - - - -
655B ILE* 1.3 81.1 - - - +
657B GLU* 1.3 68.2 + - + +
658B GLU* 3.4 6.1 + - - +
803C ASN* 3.4 30.0 - - + +
805C PRO* 3.5 43.5 - - + +
806C ALA* 5.3 0.7 - - - -
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Residues in contact with GLU 657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B PHE 3.8 14.3 + - - +
654B MET* 4.2 12.0 - - - +
655B ILE 4.9 0.3 - - - -
656B GLN* 1.3 80.0 - - + +
658B GLU* 1.3 59.8 + - - +
659B TYR* 3.7 8.4 + - + +
803C ASN* 3.8 8.5 - - + +
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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