Contacts of the helix formed by residues 645 - 656 (chain A) in PDB entry 2WNT
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 645 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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509A GLU* 2.5 38.1 + - - -
643A THR 3.8 1.2 + - - -
644A VAL* 1.3 76.4 - - - +
646A GLU* 1.3 67.3 + - - +
647A THR* 4.0 7.5 + - - -
648A ALA* 3.1 21.8 + - - +
649A LYS* 3.2 10.0 + - - +
674A TRP* 3.8 5.7 - - - -
681A LEU* 4.9 0.9 - - - +
682A PRO* 4.3 15.5 - - - +
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Residues in contact with GLU 646 (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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644A VAL 3.6 2.0 + - - -
645A SER* 1.3 71.5 - - - +
647A THR* 1.3 62.9 + - + +
649A LYS* 2.9 17.7 + - + +
650A ASP* 2.8 28.1 + - - +
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Residues in contact with THR 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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645A SER* 3.2 7.0 + - - +
646A GLU* 1.3 80.4 - - + +
648A ALA* 1.3 63.0 + - - +
650A ASP* 3.6 8.5 - - - +
651A LEU* 3.1 7.3 + - - +
672A HIS* 3.0 34.5 - - - -
673A PRO* 4.8 10.6 - - + -
674A TRP* 3.5 24.7 + - - +
681A LEU* 5.2 1.6 - - - +
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Residues in contact with ALA 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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509A GLU* 3.8 4.3 - - - +
604A LEU* 4.8 0.4 - - - +
608A LEU* 3.9 21.3 - - + -
644A VAL* 4.0 5.8 - - + -
645A SER* 3.1 14.9 + - - +
647A THR* 1.3 78.5 + - - +
649A LYS* 1.3 61.0 + - - +
651A LEU* 3.3 3.6 + - - +
652A VAL* 2.9 34.9 + - - +
674A TRP* 3.3 33.9 - - + +
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Residues in contact with LYS 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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636A LEU* 3.6 39.4 + - + +
637A SER* 4.9 4.2 + - - +
641A TRP* 2.8 55.7 + - + -
642A ASN* 4.6 4.9 + - - +
644A VAL* 3.8 12.9 + - + -
645A SER 3.2 8.5 + - - +
646A GLU* 2.9 14.4 + - - +
648A ALA* 1.3 79.3 - - - +
650A ASP* 1.3 62.0 + - - +
652A VAL* 3.4 5.8 + - - +
653A SER* 3.0 26.7 + - - -
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Residues in contact with ASP 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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646A GLU 2.8 12.6 + - - +
647A THR* 3.6 13.2 - - - +
649A LYS* 1.3 76.9 - - - +
651A LEU* 1.3 59.0 + - - +
653A SER* 3.0 20.2 + - - -
654A LYS* 3.2 44.3 + - - +
672A HIS* 2.7 25.2 + - - +
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Residues in contact with LEU 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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516A LEU* 3.8 12.3 - - + -
604A LEU* 3.7 18.6 - - + -
647A THR 3.1 14.9 + - - +
648A ALA* 3.7 4.0 - - - +
649A LYS 3.2 0.4 - - - -
650A ASP* 1.3 78.6 + - - +
652A VAL* 1.3 66.3 + - - +
654A LYS* 3.1 4.6 + - - +
655A MET* 3.0 41.5 + - - +
664A LEU* 3.8 21.3 - - + -
669A VAL* 4.4 7.0 - - + -
672A HIS* 3.6 31.0 - - + +
674A TRP* 3.7 30.3 - - + -
675A VAL* 4.5 4.9 - - + -
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Residues in contact with VAL 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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601A GLY 4.5 2.0 - - - +
604A LEU* 3.5 28.5 - - + -
605A TYR* 3.9 24.0 - - + +
608A LEU* 3.6 19.7 - - + -
634A PHE* 4.4 7.2 - - + -
636A LEU* 4.4 5.8 - - + -
641A TRP* 5.1 2.5 - - + -
648A ALA 2.9 21.6 + - - +
649A LYS* 3.8 6.1 - - - +
651A LEU* 1.3 75.1 - - - +
653A SER* 1.3 59.0 + - - +
655A MET* 3.2 4.4 + - - +
656A LEU* 3.0 49.9 + - + +
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Residues in contact with SER 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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634A PHE* 4.2 15.0 - - - -
636A LEU* 3.9 15.7 - - - -
649A LYS 3.0 15.0 + - - -
650A ASP* 3.0 20.3 + - - -
652A VAL* 1.3 77.7 - - - +
654A LYS* 1.3 62.2 + - - +
656A LEU 4.0 0.6 - - - -
657A HIS* 3.4 25.8 + - - +
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Residues in contact with LYS 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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650A ASP* 3.2 46.9 + - - +
651A LEU* 3.1 5.8 + - - +
653A SER* 1.3 80.9 + - - +
655A MET* 1.3 64.8 + - - +
656A LEU 3.4 0.7 - - - -
657A HIS* 3.9 9.8 - - + +
662A GLN 4.4 2.1 - - - +
663A ARG* 3.3 25.6 - - - +
664A LEU* 3.4 36.0 + - + -
672A HIS* 4.9 4.8 + - + +
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Residues in contact with MET 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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516A LEU* 4.3 11.0 - - + -
597A ILE* 3.7 14.9 - - + +
598A TRP* 3.8 13.7 + - - -
600A LEU* 3.4 37.5 - - + +
601A GLY* 3.5 18.4 - - - +
604A LEU* 3.8 27.4 - - - -
651A LEU* 3.0 37.3 + - + +
652A VAL 3.7 4.5 - - - +
654A LYS* 1.3 78.6 - - - +
656A LEU* 1.3 59.2 + - - +
657A HIS 3.4 0.4 - - - -
663A ARG* 3.4 21.6 - - - +
664A LEU* 4.8 1.8 - - + +
669A VAL* 4.0 26.9 - - + -
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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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598A TRP* 3.6 49.0 + - + +
601A GLY* 3.8 17.9 - - - +
602A ILE* 3.7 12.6 - - + -
605A TYR* 4.3 13.9 - - + -
613A PRO* 4.5 9.2 - - + -
614A PHE* 4.7 4.8 - - + -
632A GLY* 5.3 3.6 - - - +
634A PHE* 3.6 35.9 - - + -
652A VAL* 3.0 35.4 + - + +
653A SER 4.1 1.3 - - - -
654A LYS 3.4 0.2 - - - -
655A MET* 1.3 77.1 - - - +
657A HIS* 1.3 70.0 + - - +
658A VAL* 3.3 3.3 + - - -
663A ARG* 4.4 1.1 + - - -
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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