Contacts of the helix formed by residues 643 - 656 (chain A) in PDB entry 3T6A
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 ASP 643 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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556A VAL* 4.2 0.2 - - - +
557A LEU* 3.4 18.8 + - + -
560A ASP* 2.4 34.2 - - - +
637A LEU* 2.9 25.1 + - + +
641A MET* 3.1 8.5 - - + -
642A GLY* 1.3 74.9 - - - +
644A LEU* 1.3 62.0 + - - +
645A TYR* 3.2 9.7 + - - +
646A SER* 2.9 22.8 + - - -
647A PHE* 3.1 21.2 + - - +
707A VAL* 3.6 16.5 - - - +
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Residues in contact with LEU 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A LYS* 5.1 5.4 - - + +
642A GLY* 4.5 5.6 - - - +
643A ASP* 1.3 74.3 - - - +
645A TYR* 1.3 62.0 + - - +
647A PHE* 3.5 7.4 - - + +
648A SER* 3.0 26.0 + - - -
687A PHE* 4.0 29.4 - - + -
691A LEU* 4.2 14.4 - - + -
696A GLU* 3.5 40.2 - - + +
701A PRO* 4.0 17.9 - - + -
705A VAL* 3.9 25.6 - - + -
707A VAL 2.8 15.5 + - - +
709A LEU* 3.7 14.7 - - + +
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Residues in contact with TYR 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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560A ASP* 3.7 38.4 - - + -
563A VAL* 5.6 2.2 - - + +
598A ILE* 2.6 43.3 + - + -
601A ARG* 3.4 20.0 - - + +
602A HIS* 3.3 45.2 + + + -
605A MET* 5.3 1.1 - - + -
643A ASP* 3.2 7.0 + - - +
644A LEU* 1.3 75.9 - - - +
646A SER* 1.3 63.3 + - - +
648A SER* 2.5 23.3 + - - -
649A ALA 3.3 3.5 + - - -
707A VAL* 3.7 11.0 - - + -
708A PRO 3.2 21.5 + - - +
709A LEU 3.7 18.8 - - - -
710A LEU* 4.3 9.4 - - + -
711A MET* 4.5 2.2 - - - -
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Residues in contact with SER 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A VAL* 3.3 23.2 - - - +
560A ASP* 2.4 32.0 + - - -
605A MET* 3.3 19.0 - - - +
637A LEU* 3.9 7.9 - - - -
643A ASP* 2.9 12.7 + - - -
645A TYR* 1.3 72.2 - - - +
647A PHE* 1.3 67.2 + - - +
648A SER 3.1 1.3 - - - -
649A ALA* 3.1 16.4 + - - +
650A LEU* 3.1 20.5 + - - +
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Residues in contact with PHE 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A ALA* 3.3 28.7 - - + -
637A LEU* 3.8 17.2 - - + +
638A LYS* 3.8 17.9 - - + +
643A ASP 3.1 21.5 + - - +
644A LEU* 3.5 10.3 - - - +
646A SER* 1.3 76.8 - - - +
648A SER* 1.3 64.5 + - - +
650A LEU* 3.4 4.2 + - - +
651A MET* 3.1 54.2 + - + +
684A LEU* 4.0 26.5 - - + -
687A PHE* 3.8 33.0 - + - -
688A SER* 4.5 7.6 - - - -
691A LEU* 4.0 16.4 - - + -
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Residues in contact with SER 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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602A HIS* 2.9 17.2 + - - -
644A LEU 3.0 9.3 + - - -
645A TYR* 2.5 20.4 + - - -
647A PHE* 1.3 81.4 - - - +
649A ALA* 1.3 59.4 + - - +
651A MET* 3.3 6.7 + - - +
652A LYS* 2.8 30.8 + - - +
688A SER* 5.9 1.8 - - - -
691A LEU* 5.5 0.7 - - - -
709A LEU* 3.4 33.1 + - - +
711A MET* 5.0 0.9 - - - +
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Residues in contact with ALA 649 (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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602A HIS* 3.6 42.0 - - + +
605A MET* 4.1 24.7 - - + -
606A ALA* 3.6 17.2 - - - +
609A ILE* 5.2 0.2 - - - -
645A TYR 3.3 2.8 + - - +
646A SER* 3.1 8.8 + - - +
648A SER* 1.3 80.3 + - - +
650A LEU* 1.3 62.8 + - - +
652A LYS* 3.4 1.8 + - - +
653A ALA* 3.1 18.0 + - - +
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Residues in contact with LEU 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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556A VAL* 6.2 1.3 - - + -
605A MET* 4.6 12.8 - - - -
609A ILE* 4.2 28.3 - - + +
630A ILE* 3.6 34.5 - - + +
633A VAL* 3.8 18.4 - - + -
634A ALA* 3.8 24.7 - - + +
637A LEU* 3.9 9.6 - - + -
646A SER* 3.1 15.6 + - - +
647A PHE 3.7 7.2 - - - +
649A ALA* 1.3 74.4 - - - +
651A MET* 1.3 64.2 - - - +
653A ALA* 3.2 9.0 + - - +
654A LEU* 3.1 26.7 + - - +
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Residues in contact with MET 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A ALA* 4.8 4.9 - - + -
647A PHE* 3.1 46.7 + - + +
648A SER* 3.3 8.5 + - - +
650A LEU* 1.3 75.4 - - - +
652A LYS* 1.3 62.2 + - - +
654A LEU* 3.2 10.9 + - - +
655A GLU* 3.2 35.7 + - - +
680A TYR* 3.6 32.0 + - + -
684A LEU* 3.6 41.7 - - + +
685A LYS* 3.9 7.2 - - + +
688A SER* 4.0 18.8 - - - +
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Residues in contact with LYS 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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602A HIS* 4.5 15.4 + - + -
603A ASN* 3.6 13.9 + - - +
606A ALA* 4.0 16.6 - - + +
648A SER 2.8 16.9 + - - +
649A ALA* 3.6 6.3 - - - +
650A LEU 3.2 0.2 - - - -
651A MET* 1.3 73.9 - - - +
653A ALA* 1.3 66.0 + - - +
655A GLU* 3.3 11.6 + - - +
656A MET* 3.1 27.9 + - + +
723A THR* 4.6 0.2 - - - -
724A PHE* 2.7 54.4 + - - +
725A GLU* 5.2 1.3 - - - -
727A THR* 3.1 34.7 + - + +
728A ASP* 5.9 0.4 - - - +
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Residues in contact with ALA 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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606A ALA 3.6 11.4 - - - +
609A ILE* 3.5 36.6 - - + -
610A ALA* 4.0 6.5 - - - +
613A ILE* 5.7 0.9 - - + -
649A ALA 3.1 10.1 + - - +
650A LEU 3.2 9.2 + - - +
652A LYS* 1.3 76.8 - - - +
654A LEU* 1.3 64.7 + - + +
656A MET* 3.1 31.5 + - + +
659A ILE* 3.5 13.2 - - - +
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Residues in contact with LEU 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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613A ILE* 4.1 9.6 - - + -
627A LEU* 3.7 31.4 - - + +
630A ILE* 3.8 24.5 - - + -
631A ILE* 3.9 23.6 - - + +
634A ALA* 5.5 1.3 - - + -
650A LEU* 3.1 18.7 + - + +
651A MET* 3.2 11.2 + - - +
653A ALA* 1.3 77.6 - - + +
655A GLU* 1.3 58.0 + - - +
659A ILE* 3.8 16.5 - - + +
660A THR* 4.0 7.4 + - - -
666A TRP* 3.9 12.0 - - + -
680A TYR* 3.5 42.6 + - + +
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Residues in contact with GLU 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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651A MET* 3.2 28.6 + - - +
652A LYS* 3.7 9.4 - - - +
653A ALA 3.1 0.4 - - - -
654A LEU* 1.3 78.3 - - - +
656A MET* 1.3 66.3 + - - +
657A PRO* 3.3 5.7 - - - +
660A THR* 3.9 11.8 + - - -
680A TYR* 4.1 11.0 - - - +
685A LYS* 4.8 16.2 - - - +
688A SER* 4.1 16.6 + - - -
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Residues in contact with MET 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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606A ALA* 3.5 37.9 - - + +
607A ILE* 4.2 1.8 - - - +
610A ALA* 3.7 23.6 - - + -
652A LYS* 3.1 19.7 + - + +
653A ALA* 3.1 21.9 + - - +
655A GLU* 1.3 77.6 - - - +
657A PRO* 1.3 65.3 - - - +
658A GLN* 3.7 12.1 - - - +
659A ILE* 2.8 11.6 + - + -
660A THR* 2.8 26.3 + - - -
724A PHE* 3.6 33.7 - - + -
725A GLU* 3.6 12.6 - - - +
808A LEU* 4.3 6.5 - - - -
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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
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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