Contacts of the helix formed by residues 644 - 664 (chain A) in PDB entry 6R4F
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 LEU 644 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482A PHE* 4.3 9.2 - - + -
483A VAL* 5.6 0.2 - - + -
486A VAL* 4.2 23.3 - - + -
506A ILE* 3.6 12.6 - - + +
509A GLY* 3.6 36.1 - - - +
510A LEU* 3.6 27.8 - - + +
513A LEU* 4.7 8.5 - - + +
640A SER* 4.1 10.8 - - - +
641A VAL* 2.9 19.0 + - + +
643A CYS* 1.3 90.1 - - - +
645A GLN* 1.3 65.1 + - - +
646A GLY 3.1 2.9 - - - -
647A ILE* 3.0 30.0 + - + +
648A LEU* 4.0 3.8 + - - +
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Residues in contact with GLN 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548A HIS* 3.6 20.6 - - + +
594A MET* 4.1 4.8 - - + -
596A ASP* 6.1 0.4 - - - +
621A ASP* 3.7 21.2 + - - +
637A VAL* 3.9 17.8 - - - +
638A PRO 3.1 16.6 + - - +
640A SER* 2.4 46.4 + - - +
641A VAL 3.1 16.0 + - - +
642A ASP* 3.4 12.8 + - - +
644A LEU* 1.3 76.9 - - - +
646A GLY* 1.3 63.6 + - - +
648A LEU* 2.9 21.7 + - - +
649A SER* 2.9 23.6 + - - -
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Residues in contact with GLY 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A TYR* 4.9 1.9 - - - -
482A PHE* 4.0 19.9 - - - -
547A TYR* 4.7 8.2 + - - +
548A HIS* 3.8 8.0 - - - -
551A THR* 3.8 19.2 + - - -
642A ASP 4.7 2.2 + - - -
643A CYS 5.2 0.2 - - - -
644A LEU 3.0 2.4 + - - -
645A GLN* 1.3 77.7 - - - +
647A ILE* 1.3 60.2 + - - +
649A SER* 4.5 0.2 - - - -
650A VAL* 3.1 28.1 + - - +
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Residues in contact with ILE 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A VAL* 5.1 0.9 - - + -
479A THR* 4.0 21.3 - - + +
482A PHE* 3.6 40.8 - - + -
483A VAL* 3.5 31.4 - - + -
513A LEU* 3.7 22.0 - - + -
517A ILE* 4.1 26.5 - - + -
644A LEU* 3.0 16.8 + - + +
646A GLY* 1.3 75.4 - - - +
648A LEU* 1.3 62.3 + - - +
650A VAL* 3.4 11.5 - - - +
651A ILE* 3.2 20.2 - - + +
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Residues in contact with LEU 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513A LEU* 4.0 11.7 - - + -
516A LEU* 3.7 36.3 - - + +
517A ILE* 3.8 28.3 - - + +
520A VAL* 4.0 18.2 - - + +
637A VAL* 4.2 6.6 - - + +
638A PRO* 3.5 26.0 - - + +
640A SER* 3.9 15.5 - - - -
644A LEU 4.7 2.2 - - - +
645A GLN* 2.9 24.6 + - - +
647A ILE* 1.3 78.2 - - - +
649A SER* 1.3 57.1 + - - +
651A ILE* 3.4 6.9 + - - +
652A PRO* 3.0 23.9 - - - +
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Residues in contact with SER 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A HIS* 3.0 31.4 - - - -
551A THR* 3.6 14.7 - - - +
592A ILE* 4.1 4.6 - - - +
594A MET* 3.1 22.1 - - - +
619A ILE* 4.4 12.7 - - - +
637A VAL* 4.5 1.5 - - - +
645A GLN* 2.9 18.0 + - - -
646A GLY 4.2 0.4 - - - -
648A LEU* 1.3 75.9 - - - +
650A VAL* 1.3 61.4 + - - +
651A ILE 3.3 0.2 - - - -
652A PRO* 3.4 12.2 - - - +
653A LEU* 4.0 9.7 - - - +
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Residues in contact with VAL 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478A TYR* 3.9 25.8 - - + -
479A THR* 4.4 2.7 - - + -
551A THR* 3.7 18.1 - - + +
554A GLU* 3.7 34.3 - - + -
555A GLY 4.6 3.6 - - - +
558A LYS* 6.1 0.2 - - + -
646A GLY 3.1 14.8 + - - +
647A ILE* 3.4 16.8 - - - +
649A SER* 1.3 76.5 - - - +
651A ILE* 1.3 73.6 + - + +
652A PRO 3.4 0.2 - - - -
653A LEU* 3.0 8.7 + - + +
654A GLN* 2.9 32.2 + - + +
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Residues in contact with ILE 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A ILE* 4.6 0.7 - - + -
332A GLN* 3.9 16.4 - - - +
479A THR* 5.0 0.7 - - + -
517A ILE* 3.7 41.7 - - + -
520A VAL* 3.9 13.9 - - + -
521A LEU* 3.9 25.6 - - + -
647A ILE* 3.2 22.0 - - + +
648A LEU* 3.7 6.5 - - - +
650A VAL* 1.3 79.7 - - + +
652A PRO* 1.3 68.0 - - + +
654A GLN* 3.0 23.9 + - - +
655A LEU* 2.9 28.6 + - + +
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Residues in contact with PRO 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520A VAL* 3.9 14.4 - - + -
523A MET* 5.5 0.2 - - + -
527A ILE* 3.6 29.1 - - + +
619A ILE* 4.4 15.0 - - + -
635A ILE* 4.4 11.2 - - + -
637A VAL* 4.0 15.5 - - + -
648A LEU 3.0 19.1 - - - +
649A SER 3.4 10.8 - - - +
651A ILE* 1.3 91.4 - - + +
653A LEU* 1.3 56.6 + - - +
655A LEU* 3.6 7.1 + - + +
656A LEU* 2.9 28.4 + - - +
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Residues in contact with LEU 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542A ILE* 4.3 23.1 - - + -
551A THR* 3.6 40.6 - - + +
555A GLY* 3.9 21.8 - - - +
558A LYS* 4.7 1.9 - - - +
559A ILE* 4.6 6.0 - - + +
590A ILE* 4.5 18.2 - - + -
592A ILE* 4.2 12.1 - - + -
619A ILE* 4.1 18.2 - - + -
649A SER 4.0 8.1 - - - +
650A VAL* 3.0 8.6 + - + +
652A PRO* 1.3 73.9 - - - +
654A GLN* 1.3 66.9 + - - +
656A LEU* 3.7 10.7 - - + +
657A ALA* 3.1 23.4 + - - +
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Residues in contact with GLN 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A MET* 3.9 6.7 - - - +
329A ILE* 4.0 18.2 - - + +
332A GLN* 2.9 39.8 + - - -
474A SER 4.7 1.8 + - - -
475A THR* 3.5 33.9 + - + +
478A TYR* 4.9 3.8 - - - +
479A THR* 4.5 0.8 - - - +
554A GLU* 5.5 1.6 + - - +
558A LYS* 4.9 17.7 - - + +
650A VAL* 2.9 34.0 + - + +
651A ILE* 3.3 21.8 - - - +
653A LEU* 1.3 77.0 - - - +
655A LEU* 1.3 62.7 + - - +
657A ALA* 3.4 3.7 + - - +
658A PHE* 3.1 20.8 + - - +
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Residues in contact with LEU 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A ILE* 3.6 21.5 - - + -
330A PHE* 3.5 24.5 - - + -
520A VAL* 5.0 4.5 - - + +
521A LEU* 4.2 14.6 - - + -
524A ASP* 3.5 27.8 - - + +
527A ILE* 3.9 25.4 - - + -
651A ILE* 2.9 33.6 + - + +
652A PRO* 3.9 1.3 - - + +
654A GLN* 1.3 76.5 - - - +
656A LEU* 1.3 57.7 + - - +
658A PHE* 3.2 8.7 + - + +
659A HIS* 2.8 43.3 + - + +
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Residues in contact with LEU 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527A ILE* 3.6 11.1 - - + +
530A LEU* 3.8 16.8 - - + -
531A ALA* 3.8 33.2 - - + +
534A LEU* 3.9 11.7 - - + -
559A ILE* 4.2 14.8 - - + -
590A ILE* 3.8 29.2 - - + -
652A PRO 2.9 20.7 + - - +
653A LEU* 3.7 11.9 - - + +
654A GLN 3.2 0.4 - - - -
655A LEU* 1.3 76.4 - - - +
657A ALA* 1.3 58.0 + - - +
659A HIS* 3.8 1.3 - - - -
660A LEU* 2.8 44.4 + - + +
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Residues in contact with ALA 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A MET* 4.6 2.5 - - + -
558A LYS* 3.9 24.5 - - + +
559A ILE* 3.8 19.7 - - + +
562A ILE* 3.8 9.1 - - + +
563A THR* 3.2 19.5 + - - +
653A LEU 3.1 11.1 + - - +
654A GLN 3.7 7.2 - - - +
656A LEU* 1.3 78.7 - - - +
658A PHE* 1.3 64.5 + - - +
660A LEU* 4.6 0.7 - - - -
661A ALA* 3.0 23.7 + - - +
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Residues in contact with PHE 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A SER* 5.2 4.3 - - - -
323A SER* 3.5 23.8 - - - -
325A MET* 3.9 34.9 - - + +
326A GLN* 3.8 38.8 - - + -
329A ILE* 4.3 6.1 - - + -
330A PHE* 5.6 1.1 - + - -
562A ILE* 4.5 1.3 - - - -
654A GLN 3.1 13.8 + - - +
655A LEU* 3.4 15.3 - - + +
657A ALA* 1.3 77.4 - - - +
659A HIS* 1.3 94.6 + + - +
661A ALA* 3.3 2.6 + - + +
662A VAL* 3.0 46.8 + - + +
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Residues in contact with HIS 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A GLN* 5.9 1.1 - - - -
330A PHE* 6.1 0.4 - + - -
524A ASP* 2.7 35.7 + - - -
527A ILE* 4.3 9.2 - - + -
528A GLN* 3.3 37.4 - - + +
531A ALA* 3.7 20.9 - - + -
655A LEU* 2.8 37.5 + - + +
656A LEU* 4.0 0.9 - - - +
658A PHE* 1.3 95.3 - + - +
660A LEU* 1.3 67.1 + - - +
662A VAL* 3.2 7.9 + - - +
663A LEU* 2.9 28.5 + - + +
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Residues in contact with LEU 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531A ALA* 3.3 26.4 - - + +
534A LEU* 3.8 17.5 - - + +
535A TYR* 3.7 23.7 - - + +
559A ILE* 4.8 5.6 - - + -
563A THR* 3.7 23.2 - - + +
565A MET* 4.0 24.7 - - - -
656A LEU* 2.8 43.4 + - + +
659A HIS* 1.3 75.9 - - - +
661A ALA* 1.3 64.4 + - - +
663A LEU* 3.1 15.4 + - + +
664A ARG* 3.1 10.9 + - - -
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Residues in contact with ALA 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562A ILE* 3.5 34.1 - - + +
563A THR* 4.1 7.0 + - - +
657A ALA 3.0 18.3 + - - +
658A PHE 3.6 4.0 - - - +
660A LEU* 1.3 76.1 - - - +
662A VAL* 1.3 64.5 + - + +
664A ARG* 3.2 18.5 + - - +
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Residues in contact with VAL 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658A PHE* 3.0 46.8 + - + +
659A HIS* 3.6 11.2 - - - +
661A ALA* 1.3 76.7 - - + +
663A LEU* 1.3 67.4 + - + +
664A ARG 3.3 3.6 + - - -
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Residues in contact with LEU 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531A ALA* 3.7 42.4 - - + +
532A THR* 3.8 25.4 - - + +
535A TYR* 3.4 33.6 + - + -
659A HIS* 2.9 15.1 + - + +
660A LEU* 3.1 8.5 + - - +
662A VAL* 1.3 80.2 - - + +
664A ARG* 1.3 59.0 + - - +
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Residues in contact with ARG 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535A TYR* 3.9 14.1 - - - -
660A LEU 3.1 11.9 + - - -
661A ALA* 3.2 14.4 + - - +
662A VAL 4.2 3.4 - - - -
663A LEU* 1.3 80.4 - - - +
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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
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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