Contacts of the helix formed by residues 645 - 656 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509B GLU* 2.6 37.2 + - - -
643B THR 3.7 2.1 + - - -
644B VAL* 1.3 74.7 - - - +
646B GLU* 1.3 66.1 + - - +
647B THR* 4.0 8.0 + - - -
648B ALA* 3.1 23.6 + - - +
649B LYS* 3.3 12.5 + - - +
674B TRP* 3.8 6.1 - - - -
681B LEU* 4.4 2.4 - - - +
682B PRO* 4.3 14.6 - - - +
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Residues in contact with GLU 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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644B VAL 3.6 1.9 + - - +
645B SER* 1.3 73.2 - - - +
647B THR* 1.3 60.8 + - + +
649B LYS* 3.2 32.2 + - - +
650B ASP* 3.0 25.7 + - + +
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Residues in contact with THR 647 (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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645B SER* 3.2 6.8 + - - +
646B GLU* 1.3 78.7 - - + +
648B ALA* 1.3 65.8 + - - +
650B ASP* 3.6 7.6 - - - +
651B LEU* 3.1 6.9 + - - +
672B HIS* 3.0 35.5 - - - -
673B PRO* 4.9 9.5 - - + -
674B TRP* 3.5 24.2 + - - +
681B LEU* 4.8 2.4 - - - +
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Residues in contact with ALA 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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509B GLU* 3.9 3.4 - - - +
604B LEU* 4.9 0.4 - - - +
608B LEU* 3.8 21.5 - - + -
644B VAL* 4.0 5.2 - - + -
645B SER* 3.1 16.0 + - - +
647B THR* 1.3 78.4 + - - +
649B LYS* 1.3 62.1 + - - +
651B LEU* 3.2 4.4 + - - +
652B VAL* 2.9 34.2 + - - +
674B TRP* 3.4 33.0 - - + +
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Residues in contact with LYS 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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636B LEU* 3.6 37.7 + - + +
637B SER* 5.1 3.4 + - - +
641B TRP* 2.8 61.0 + - + -
642B ASN* 4.9 2.4 + - - +
644B VAL 3.8 10.7 + - - -
645B SER 3.3 9.4 + - - +
646B GLU* 3.2 34.6 + - - +
648B ALA* 1.3 77.8 - - - +
650B ASP* 1.3 63.1 + - - +
652B VAL* 3.4 2.1 + - - +
653B SER* 3.0 27.4 + - - -
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Residues in contact with ASP 650 (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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646B GLU* 3.0 12.9 + - + +
647B THR* 3.6 12.8 - - - +
649B LYS* 1.3 77.1 - - - +
651B LEU* 1.3 59.2 + - - +
653B SER* 2.9 20.8 + - - -
654B LYS* 3.1 44.8 + - - +
672B HIS* 2.8 25.1 + - + +
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Residues in contact with LEU 651 (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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516B LEU* 3.7 18.8 - - + -
604B LEU* 3.7 19.1 - - + -
647B THR 3.1 14.5 + - - +
648B ALA* 3.2 5.4 + - - +
650B ASP* 1.3 78.1 + - - +
652B VAL* 1.3 66.3 + - - +
654B LYS* 3.1 3.8 + - - -
655B MET* 3.0 40.9 + - + +
664B LEU* 3.8 24.2 - - + -
669B VAL* 4.4 7.4 - - + -
672B HIS* 3.6 29.2 - - + +
674B TRP* 3.7 22.9 - - + -
675B VAL* 4.5 5.4 - - + -
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Residues in contact with VAL 652 (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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601B GLY 4.5 2.2 - - - +
604B LEU* 3.4 30.1 - - + -
605B TYR* 3.9 31.2 - - + +
608B LEU* 3.5 20.2 - - + -
634B PHE* 4.6 1.3 - - + -
636B LEU* 4.3 9.6 - - + -
641B TRP* 4.1 7.2 - - + -
648B ALA 2.9 20.8 + - - +
649B LYS 3.8 3.8 - - - +
651B LEU* 1.3 74.9 - - - +
653B SER* 1.3 60.3 + - - +
655B MET* 3.1 4.6 + - - +
656B LEU* 3.0 41.4 + - + +
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Residues in contact with SER 653 (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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634B PHE* 4.2 17.6 - - - -
636B LEU* 3.7 17.3 - - - -
649B LYS 3.0 14.0 + - - -
650B ASP* 2.9 19.9 + - - -
652B VAL* 1.3 77.2 - - - +
654B LYS* 1.3 60.9 + - - +
656B LEU 4.0 1.4 - - - -
657B HIS* 3.4 25.5 + - - +
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Residues in contact with LYS 654 (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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650B ASP* 3.1 47.6 + - - +
651B LEU* 3.1 6.0 + - - +
653B SER* 1.3 80.3 + - - +
655B MET* 1.3 63.0 + - - +
656B LEU 3.4 0.4 - - - -
657B HIS* 4.0 9.8 - - + +
662B GLN 4.4 0.6 - - - +
663B ARG* 3.3 26.9 - - - +
664B LEU* 3.3 35.3 + - + -
672B HIS* 4.9 4.9 + - + +
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Residues in contact with MET 655 (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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516B LEU* 4.3 12.1 - - + -
597B ILE* 3.8 15.4 - - + +
598B TRP* 3.8 14.6 + - - -
600B LEU* 3.4 36.6 - - + +
601B GLY* 3.5 18.8 - - - +
604B LEU* 3.6 28.3 - - - -
651B LEU* 3.0 35.9 + - + +
652B VAL 3.1 5.1 + - - +
654B LYS* 1.3 79.8 - - - +
656B LEU* 1.3 57.9 + - - +
657B HIS 3.5 0.4 - - - -
663B ARG* 3.5 20.0 - - - +
664B LEU* 4.8 1.6 - - + +
669B VAL* 4.0 25.6 - - + -
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Residues in contact with LEU 656 (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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598B TRP* 3.5 47.8 + - + +
601B GLY* 3.7 16.8 - - - +
602B ILE* 3.6 14.8 - - + -
605B TYR* 4.2 16.6 - - + -
613B PRO* 4.5 9.9 - - + -
614B PHE* 4.7 4.5 - - + -
632B GLY* 5.5 1.0 - - - +
634B PHE* 3.6 36.1 - - + -
652B VAL* 3.0 34.3 + - + +
653B SER 4.1 0.9 - - - -
655B MET* 1.3 77.5 - - - +
657B HIS* 1.3 69.3 + - - +
658B VAL* 3.3 3.5 + - - -
663B ARG* 4.4 1.3 - - - -
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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