Contacts of the helix formed by residues 579 - 605 (chain T) in PDB entry 6FF7
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 SER 579 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533T TYR 5.3 8.1 - - - -
535T THR 5.7 3.6 - - - -
536T ILE* 4.8 7.7 + - - -
537T HIS* 5.8 1.2 - - - +
575T THR* 4.8 4.9 - - - -
576T THR* 2.7 34.4 + - - -
578T SER* 1.3 72.7 - - - +
580T ARG* 1.3 62.7 + - - -
582T PHE* 3.0 15.8 + - - +
583T VAL* 3.0 15.2 + - - +
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Residues in contact with ARG 580 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5423 GLY 5.1 0.2 - - - -
5433 ASP* 4.7 13.2 - - + -
5443 PRO 5.8 1.1 - - - -
5453 MET* 5.0 14.8 - - + +
575T THR* 4.9 13.7 - - - -
576T THR 4.2 0.2 - - - -
577T SER* 2.3 37.0 + - - +
579T SER* 1.3 72.6 - - - +
581T ILE* 1.3 54.7 + - - +
583T VAL* 3.3 6.2 + - - +
584T LYS* 2.9 25.3 + - - +
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Residues in contact with ILE 581 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5403 ARG* 4.5 5.8 - - + +
5413 GLU 4.4 6.5 - - - +
5423 GLY* 2.8 38.6 - - - +
5433 ASP* 4.2 2.2 - - - +
544T LEU* 6.0 1.7 - - - +
577T SER 2.9 9.0 + - - +
578T SER* 3.8 5.2 - - - +
580T ARG* 1.3 74.9 - - - +
582T PHE* 1.3 63.9 + - - +
584T LYS* 3.8 6.3 - - + -
585T ILE* 3.8 17.0 + - - +
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Residues in contact with PHE 582 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533T TYR* 6.5 0.9 - - + -
536T ILE* 5.0 13.2 - - + -
544T LEU* 5.4 12.5 - - + +
548T ALA* 3.9 15.0 - - + +
578T SER 2.9 16.4 + - - +
579T SER* 3.1 13.0 - - - +
581T ILE* 1.3 80.0 - - - +
583T VAL* 1.3 64.3 + - - +
584T LYS 3.3 0.2 + - - -
585T ILE 3.6 0.2 + - - -
586T PHE* 3.1 20.7 + - - +
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Residues in contact with VAL 583 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579T SER 3.0 10.8 + - - +
580T ARG* 4.0 4.5 - - - +
582T PHE* 1.3 78.7 - - - +
584T LYS* 1.3 69.0 + - - +
586T PHE* 3.1 8.4 - - + +
587T PHE* 3.0 21.3 + - - +
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Residues in contact with LYS 584 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5423 GLY 4.1 10.1 - - - +
5443 PRO* 5.8 5.8 - - + -
580T ARG 2.9 17.1 + - - +
581T ILE* 3.8 11.9 - - + +
582T PHE 3.1 0.4 - - - -
583T VAL* 1.3 79.4 - - - +
585T ILE* 1.3 66.8 + - - +
586T PHE 2.8 1.7 + - - -
587T PHE* 4.1 1.1 - - - +
588T GLN* 2.9 26.2 + - + +
634T ILE* 5.0 18.1 - - + +
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Residues in contact with ILE 585 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545T ARG* 5.6 11.0 - - + -
548T ALA* 4.9 9.5 - - + +
549T LYS 5.6 0.3 + - - -
581T ILE 3.8 11.3 + - - +
582T PHE 3.6 3.5 + - - +
584T LYS* 1.3 79.6 - - - +
586T PHE* 1.3 53.6 + - - +
588T GLN* 4.4 7.0 - - - -
589T GLU* 2.7 40.1 + - + +
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Residues in contact with PHE 586 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548T ALA* 4.5 16.1 - - + +
552T ALA* 3.9 12.7 - - + +
582T PHE 3.1 16.0 + - - +
583T VAL* 3.1 17.7 - - + +
584T LYS 2.8 1.4 + - - -
585T ILE* 1.3 77.9 - - - +
587T PHE* 1.3 58.2 + - - +
589T GLU* 3.7 0.6 - - - -
590T LEU* 2.9 29.0 + - - +
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Residues in contact with PHE 587 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583T VAL 3.0 10.3 + - - +
584T LYS 4.1 0.7 - - - +
586T PHE* 1.3 77.4 - - - +
588T GLN* 1.3 56.1 + - - +
590T LEU* 2.6 10.6 + - - +
591T CYS* 2.5 36.2 + - - -
636T LEU* 6.1 5.4 - - + -
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Residues in contact with GLN 588 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584T LYS* 2.9 19.1 + - + +
585T ILE* 4.4 4.0 - - - -
587T PHE* 1.3 77.2 - - - +
589T GLU* 1.3 57.0 + - - +
591T CYS* 3.2 22.7 - - - +
592T GLU* 4.4 2.6 + - - +
634T ILE* 4.6 19.2 - - + +
636T LEU* 6.1 4.9 - - - +
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Residues in contact with GLU 589 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549T LYS* 5.3 12.6 - - + -
552T ALA* 4.9 7.8 - - + +
585T ILE* 2.7 26.3 + - + +
586T PHE* 3.9 1.6 - - - +
588T GLN* 1.3 74.1 - - - +
590T LEU* 1.3 62.5 + - - +
591T CYS 3.2 0.4 - - - -
592T GLU* 4.2 5.6 + - - +
593T TYR* 4.5 5.9 + - - +
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Residues in contact with LEU 590 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552T ALA* 4.0 21.1 - - + +
555T LEU* 6.5 0.9 - - + -
556T TYR* 6.0 2.9 - - + -
586T PHE 2.9 17.1 + - - +
587T PHE* 2.6 13.7 + - - +
589T GLU* 1.3 72.7 - - - +
591T CYS* 1.3 66.7 + - - +
592T GLU 3.3 0.3 + - - -
593T TYR* 3.4 14.4 + - - +
594T MET* 3.5 12.0 + - - +
599T LEU* 5.4 1.7 - - - +
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Residues in contact with CYS 591 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587T PHE 2.5 14.8 + - - +
588T GLN* 3.2 21.1 - - - +
589T GLU 3.2 0.2 - - - -
590T LEU* 1.3 75.3 - - - +
592T GLU* 1.3 52.7 + - + +
594T MET* 4.2 0.3 - - - +
595T GLY* 2.6 44.2 + - - +
596T LEU* 5.7 4.3 - - + +
599T LEU* 5.5 5.2 - - - -
636T LEU* 5.9 7.2 - - + -
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Residues in contact with GLU 592 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1222A LYS* 3.5 34.0 - - + +
1223A GLU* 4.2 4.7 - - - -
1224A ARG* 4.3 3.8 + - - +
588T GLN 4.4 1.7 + - - +
589T GLU 4.2 4.2 + - - +
590T LEU 3.4 0.8 - - - -
591T CYS* 1.3 77.7 - - + +
593T TYR* 1.3 70.9 + - - +
595T GLY* 2.9 10.3 + - - +
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Residues in contact with TYR 593 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1223A GLU* 5.6 0.3 - - - -
1224A ARG* 5.0 11.4 + - - +
556T TYR* 4.1 24.7 - - + -
589T GLU 4.5 4.6 + - - +
590T LEU* 3.4 13.7 + - - +
591T CYS 3.3 0.6 + - - -
592T GLU* 1.3 79.7 - - - +
594T MET* 1.3 61.3 + - + +
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Residues in contact with MET 594 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1223A GLU* 5.5 1.8 - - - +
556T TYR* 6.0 3.6 - - + -
590T LEU 3.5 4.9 + - - +
591T CYS 3.2 3.5 + - - +
593T TYR* 1.3 80.5 - - + +
595T GLY* 1.3 69.2 + - - +
598T LYS* 3.0 31.3 + - + +
599T LEU* 3.8 24.2 - - + +
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Residues in contact with GLY 595 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1221A THR 5.4 0.9 - - - -
1222A LYS* 4.6 4.0 - - - -
1223A GLU* 4.6 18.1 - - - +
591T CYS 2.6 19.9 + - - +
592T GLU* 2.9 15.6 + - - -
594T MET* 1.3 87.3 - - - +
596T LEU* 1.3 67.9 + - - +
597T PRO 3.5 0.9 - - - -
599T LEU* 3.3 11.4 - - - +
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Residues in contact with LEU 596 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1221A THR 5.4 2.2 + - - -
1222A LYS* 5.4 6.8 - - + +
591T CYS* 4.8 5.7 - - + +
595T GLY* 1.3 74.4 - - - +
597T PRO* 1.3 59.6 - - - +
599T LEU* 3.2 5.3 + - - +
600T ASN* 2.7 31.2 + - - +
638T GLY* 5.7 9.2 - - - -
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Residues in contact with PRO 597 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595T GLY 3.5 0.2 - - - -
596T LEU* 1.3 76.8 - - - +
598T LYS* 1.3 59.4 + - - +
600T ASN* 2.9 8.9 + - + +
601T ALA* 2.9 32.0 + - - +
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Residues in contact with LYS 598 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594T MET* 3.0 27.6 + - + +
595T GLY 4.4 0.2 - - - -
596T LEU 3.4 0.4 - - - -
597T PRO* 1.3 78.8 - - - +
599T LEU* 1.3 59.2 + - - +
601T ALA* 4.4 4.5 - - - +
602T ARG* 3.3 24.5 + - - +
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Residues in contact with LEU 599 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590T LEU 5.4 2.7 - - - +
591T CYS* 4.9 5.2 - - - +
594T MET* 3.8 15.3 - - + +
595T GLY 3.3 19.4 + - - +
596T LEU* 3.2 4.6 + - - +
597T PRO 3.1 0.6 - - - -
598T LYS* 1.3 76.7 - - - +
600T ASN* 1.3 58.0 + - - +
602T ARG* 3.1 3.1 + - - -
603T LEU* 2.6 39.0 + - + +
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Residues in contact with ASN 600 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596T LEU* 2.7 21.0 + - + +
597T PRO* 2.9 9.2 + - + +
599T LEU* 1.3 72.4 - - - +
601T ALA* 1.3 65.8 + - - +
603T LEU* 3.6 6.5 + - - +
604T LYS* 3.3 18.0 + - - +
638T GLY* 4.4 20.0 - - - +
639T LEU* 6.1 3.1 - - + -
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Residues in contact with ALA 601 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597T PRO 2.9 15.4 + - - +
598T LYS* 4.4 4.5 - - - +
600T ASN* 1.3 74.1 - - - +
602T ARG* 1.3 52.9 + - - +
604T LYS* 2.5 13.1 + - - -
605T ASP* 2.4 49.0 + - + +
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Residues in contact with ARG 602 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562T TRP* 6.0 2.4 - - - +
598T LYS 3.3 18.2 + - - +
599T LEU* 3.1 4.2 + - - +
601T ALA* 1.3 78.0 - - - +
603T LEU* 1.3 62.8 + - - +
605T ASP* 4.4 4.5 - - - +
606T GLU* 4.3 15.4 - - - +
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Residues in contact with LEU 603 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599T LEU* 2.6 24.2 + - + +
600T ASN* 3.6 7.4 - - - +
602T ARG* 1.3 76.5 - - - +
604T LYS* 1.3 59.4 + - + +
609T GLN* 4.0 14.9 - - - +
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Residues in contact with LYS 604 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600T ASN 3.3 11.2 + - - +
601T ALA* 2.5 8.4 + - - -
603T LEU* 1.3 74.1 - - + +
605T ASP* 1.3 53.1 + - - +
606T GLU* 2.5 20.0 + - - -
607T THR* 3.4 8.1 + - - -
609T GLN* 3.9 12.6 - - - +
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Residues in contact with ASP 605 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601T ALA* 2.4 45.1 + - + +
602T ARG* 4.5 2.2 - - - +
604T LYS* 1.3 67.4 - - - +
606T GLU* 1.3 55.6 + - - +
607T THR* 2.8 13.2 + - - -
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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