Contacts of the helix formed by residues 634 - 651 (chain B) in PDB entry 3C4C
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 634 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B ILE* 3.1 22.0 - - - +
632B PRO 2.8 7.0 + - - -
633B TYR* 1.3 73.6 - - - +
635B PHE* 1.3 68.4 + - - +
636B GLN* 2.7 36.5 - - - +
637B SER* 2.9 19.1 + - - -
638B ASP 3.3 4.5 + - - -
701B ARG* 3.2 25.0 + - - -
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Residues in contact with PHE 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B HIS* 3.5 66.8 - + + +
571B SER* 4.1 15.9 - - - -
572B ILE 3.9 17.0 - - - -
573B ILE* 3.8 18.8 - - + +
634B SER* 1.3 70.6 - - - +
636B GLN* 1.3 76.4 + - - +
638B ASP* 3.0 17.3 + - - +
639B VAL* 3.1 12.1 + - + +
706B SER* 5.3 5.8 - - - +
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Residues in contact with GLN 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B SER* 2.7 21.3 - - - +
635B PHE* 1.3 89.1 - - - +
637B SER* 1.3 57.4 + - - +
639B VAL* 3.5 11.1 - - - +
640B TYR 3.4 9.2 + - - -
701B ARG* 3.3 32.8 - - + +
702B ASP* 5.1 1.9 - - - -
704B ARG* 2.8 51.4 + - - +
705B PRO 5.0 1.7 - - - +
706B SER* 4.4 12.8 + - - -
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Residues in contact with SER 637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B ARG* 5.6 1.0 - - - -
619B TRP 5.1 1.6 - - - +
621B ALA* 4.2 5.6 + - - +
623B GLU* 3.6 19.1 - - - -
624B VAL* 3.8 22.3 - - - +
632B PRO 4.2 0.9 - - - -
633B TYR* 4.2 14.9 - - - -
634B SER* 2.9 24.9 + - - -
636B GLN* 1.3 72.4 - - - +
638B ASP* 1.3 64.3 + - - +
639B VAL 3.2 0.4 - - - -
640B TYR* 3.0 5.9 + - - +
641B ALA* 2.9 25.5 + - - +
704B ARG* 4.1 5.2 - - - +
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Residues in contact with ASP 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B MET* 3.1 27.0 - - + +
568B HIS* 3.2 15.3 + - - +
573B ILE* 3.6 13.0 - - + +
574B HIS* 3.2 19.3 + - - +
575B ARG* 3.0 26.9 + - - -
576B ASP 4.1 3.1 + - - -
577B LEU* 4.2 9.7 + - - +
634B SER 3.3 3.4 + - - +
635B PHE 3.0 10.7 + - - +
637B SER* 1.3 79.2 + - - +
639B VAL* 1.3 64.3 + - - +
641B ALA* 3.3 9.3 + - - +
642B PHE* 3.2 19.2 + - - +
707B PHE* 4.3 2.6 - - - -
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Residues in contact with VAL 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B HIS* 4.5 1.8 - - + -
635B PHE* 3.1 11.1 + - + +
636B GLN* 3.5 13.7 - - - +
638B ASP* 1.3 75.5 - - - +
640B TYR* 1.3 66.7 + - - +
642B PHE* 2.9 17.4 + - - +
643B GLY 3.1 5.2 + - - -
696B CYS* 3.9 35.7 - - + +
704B ARG* 4.0 9.2 - - + -
705B PRO* 3.2 27.6 - - + +
706B SER* 4.5 4.7 - - - +
707B PHE* 3.7 30.5 - - + -
710B ILE* 4.0 4.5 - - + -
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Residues in contact with TYR 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618B LEU 4.3 4.6 + - - -
619B TRP 4.2 1.3 - - - -
620B MET 3.7 21.5 + - - -
621B ALA* 3.5 30.3 - - + -
622B PRO* 3.9 16.4 - - + -
636B GLN 3.4 3.4 + - - -
637B SER 3.0 10.4 + - - +
639B VAL* 1.3 76.9 - - - +
641B ALA* 1.3 70.9 + - - +
643B GLY* 2.8 13.9 + - - -
644B ILE* 3.3 29.3 + - + +
656B TYR* 3.5 20.6 + - - -
669B VAL* 4.3 8.0 - - - +
676B PRO* 4.7 3.9 - - + +
696B CYS 3.4 11.6 + - - +
697B LEU* 3.8 45.0 - - + +
698B LYS 4.5 0.2 - - - -
699B LYS* 6.3 1.1 - - + -
704B ARG* 3.9 13.2 - - - +
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Residues in contact with ALA 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B ASP* 5.9 0.4 - - - +
577B LEU* 3.6 37.0 - - + +
619B TRP* 3.7 23.6 - - + +
637B SER 2.9 11.4 + - - +
638B ASP* 3.5 13.2 - - - +
639B VAL 3.2 0.2 - - - -
640B TYR* 1.3 77.8 - - - +
642B PHE* 1.3 62.2 + - - +
644B ILE* 3.2 7.0 + - - +
645B VAL* 3.1 23.0 + - - +
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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
----------------------------------------------------------
557B ALA* 3.8 17.5 - - - -
560B THR* 4.0 15.9 - - + -
561B ALA* 3.8 26.7 - - + -
564B MET* 4.6 0.7 - - + -
577B LEU* 3.9 17.7 - - + +
638B ASP 3.2 4.4 + - - +
639B VAL 2.9 10.6 + - - +
641B ALA* 1.3 76.3 - - - +
643B GLY* 1.3 59.9 + - - +
645B VAL* 3.3 9.4 + - + +
646B LEU* 2.9 53.8 + - + +
696B CYS* 4.2 12.3 - - - -
707B PHE* 3.6 31.6 - + + -
710B ILE* 3.3 27.8 - - + -
714B ILE* 3.9 6.3 - - + -
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Residues in contact with GLY 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639B VAL 3.1 6.7 + - - -
640B TYR 2.8 8.8 + - - -
642B PHE* 1.3 76.1 - - - +
644B ILE* 1.3 57.6 + - - -
646B LEU* 3.0 10.8 + - - +
647B TYR* 2.8 27.3 + - - +
693B MET* 3.9 6.5 - - - +
696B CYS* 3.9 16.9 - - - +
697B LEU* 3.7 20.0 - - - -
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Residues in contact with ILE 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618B LEU 3.5 20.9 - - - +
619B TRP* 3.5 32.8 - - + +
640B TYR* 3.3 26.3 + - + +
641B ALA 3.2 9.2 + - - +
643B GLY* 1.3 74.4 - - - +
645B VAL* 1.3 51.4 + - - +
647B TYR* 3.1 7.7 + - + +
648B GLU* 2.7 33.7 + - + +
655B PRO* 3.9 31.2 - - + -
656B TYR* 4.5 1.1 - - - +
676B PRO* 3.8 21.5 - - + -
697B LEU* 3.7 15.5 - - + +
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Residues in contact with VAL 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B LEU* 4.3 12.3 - - + -
557B ALA* 6.4 0.2 - - - -
560B THR* 4.9 9.0 - - + +
577B LEU* 4.0 23.8 - - + -
578B LYS* 4.0 8.1 - - - -
579B SER 4.1 0.2 - - - +
582B ILE* 3.6 25.1 - - + -
619B TRP* 3.9 14.8 - - - +
641B ALA 3.1 16.9 + - - +
642B PHE* 3.5 15.9 - - + +
643B GLY 3.2 0.2 - - - -
644B ILE* 1.3 75.4 - - - +
646B LEU* 1.3 61.3 + - + +
648B GLU* 2.9 32.2 + - - +
649B LEU* 3.1 16.5 + - + +
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Residues in contact with LEU 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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557B ALA* 3.8 22.0 - - + -
642B PHE* 2.9 46.0 + - + +
643B GLY* 3.0 10.3 + - - +
645B VAL* 1.3 78.0 - - + +
647B TYR* 1.3 51.3 + - - +
649B LEU* 3.0 12.4 + - + +
650B MET* 2.8 38.3 + - + +
689B MET* 3.6 33.7 - - + -
692B LEU* 4.4 8.7 - - + -
693B MET* 3.8 32.3 - - + -
696B CYS* 4.8 2.5 - - - -
714B ILE* 4.9 0.7 - - + -
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Residues in contact with TYR 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643B GLY 2.8 12.5 + - - +
644B ILE* 3.3 13.7 - - + +
646B LEU* 1.3 75.8 - - - +
648B GLU* 1.3 57.5 + - - +
649B LEU 3.1 0.9 + - - -
651B THR* 2.7 60.7 + - + +
653B GLN* 3.6 18.9 - - + +
654B LEU 4.0 3.1 + - - -
655B PRO* 3.7 36.5 - - + +
656B TYR 5.5 0.7 + - - -
657B SER* 5.7 0.3 + - - -
676B PRO* 4.1 15.7 - - + -
677B ASP* 3.3 41.4 + - - +
678B LEU* 4.2 7.6 - - + -
680B LYS* 3.8 19.4 - - - +
681B VAL* 5.8 0.2 - - + -
693B MET* 3.8 21.7 - - - -
697B LEU* 5.6 1.6 - - + -
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Residues in contact with GLU 648 (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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537B LEU* 5.7 0.4 - - + -
541B LEU* 3.1 25.9 - - + +
542B HIS* 3.2 19.0 - - + -
579B SER* 2.9 35.5 + - - -
619B TRP* 2.8 33.3 + - + -
644B ILE* 2.7 19.8 + - + +
645B VAL* 3.0 18.9 - - + +
647B TYR* 1.3 72.9 - - - +
649B LEU* 1.3 55.9 + - - +
652B GLY* 3.3 17.9 - - - -
653B GLN 3.5 13.6 + - - +
654B LEU* 3.0 23.5 - - + +
655B PRO* 4.9 0.2 - - + -
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Residues in contact with LEU 649 (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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537B LEU* 4.0 34.1 - - + -
541B LEU* 4.2 4.7 - - + -
553B LEU* 3.6 44.3 - - + +
556B ILE* 4.4 9.9 - - + -
557B ALA* 3.7 40.4 - - + +
560B THR* 6.1 0.2 - - - +
645B VAL* 3.1 22.3 + - + +
646B LEU* 3.0 16.4 + - + +
648B GLU* 1.3 76.8 - - - +
650B MET* 1.3 79.3 + - + +
651B THR 3.3 2.3 + - - -
652B GLY* 3.4 8.5 + - - -
682B ARG* 5.4 1.7 + - - +
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Residues in contact with MET 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550B MET* 3.7 22.2 - - - +
553B LEU* 3.4 39.0 - - + -
554B ILE* 4.3 8.7 - - + +
646B LEU* 2.8 18.8 + - + +
649B LEU* 1.3 94.4 - - + +
651B THR* 1.3 58.7 + - + +
681B VAL* 3.3 21.1 - - + -
682B ARG* 2.9 36.2 + - - +
685B CYS* 3.6 25.8 - - + -
689B MET* 3.8 19.3 - - + -
693B MET* 3.6 15.3 - - + -
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Residues in contact with THR 651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647B TYR* 2.7 58.5 + - + +
649B LEU 4.1 0.4 - - - -
650B MET* 1.3 80.7 - - - +
652B GLY* 1.3 57.9 + - - +
653B GLN* 2.9 39.5 + - - +
680B LYS* 4.1 14.3 - - - +
681B VAL* 3.9 19.7 - - + +
682B ARG* 4.7 8.6 + - - +
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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