Contacts of the helix formed by residues 644 - 652 (chain B) in PDB entry 2WSC
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 644 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469A ALA* 3.1 38.3 + - - +
104B PHE* 3.4 14.8 - - - -
634B GLY 4.7 7.2 - - - -
635B ILE* 5.8 2.5 - - - +
640B CYS* 3.6 16.8 - - - -
642B SER 4.0 1.0 + - - -
643B LEU* 1.3 74.1 - - - +
645B VAL* 1.3 72.0 - - - +
646B TRP 3.1 2.1 + - - -
647B ALA* 3.7 5.6 + - - +
648B TRP* 3.5 22.2 + - - +
1740B CLA 3.2 14.0 - - - +
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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
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104B PHE* 3.5 26.0 - - + -
106B ARG* 6.2 0.2 - - - +
114B ASN* 4.4 6.5 - - - +
643B LEU* 5.5 0.7 - - - -
644B SER* 1.3 76.6 + - - +
646B TRP* 1.3 75.2 + - + +
648B TRP* 3.5 4.9 + - - +
649B MET* 2.9 28.6 + - - +
1739B CLA 3.6 42.6 - - + -
1740B CLA 3.5 37.2 - - + +
1780B BCR 3.9 9.4 - - + -
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Residues in contact with TRP 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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106B ARG* 5.9 0.8 - - - +
114B ASN* 4.3 11.2 - - - +
117B TYR* 4.2 17.8 + + - -
631B LEU* 4.9 0.7 - - - -
643B LEU* 3.7 37.5 - - + +
644B SER 3.1 1.2 - - - -
645B VAL* 1.3 87.5 - - + +
647B ALA* 1.3 51.5 + - - +
649B MET* 2.8 42.6 - - + +
650B PHE* 2.7 30.4 + - - -
722B ALA 3.9 0.7 - - - -
723B ALA* 3.4 16.5 - - - +
726B ILE* 3.0 55.6 - - + +
727B ALA* 3.8 21.8 - - + -
1739B CLA 3.6 28.3 - - + -
1757B CLA 3.9 11.0 - - - -
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Residues in contact with ALA 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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650A ASN* 4.3 16.8 - - - +
631B LEU* 3.8 37.3 - - + +
632B ILE* 4.5 0.7 - - + -
634B GLY 5.8 0.2 - - - -
635B ILE* 4.4 11.9 - - + -
643B LEU* 5.5 2.6 - - + +
644B SER* 3.7 8.2 + - - +
645B VAL 3.6 0.4 - - - -
646B TRP* 1.3 73.8 - - - +
648B TRP* 1.3 60.6 + - - +
650B PHE* 3.1 11.7 + - - +
651B LEU* 2.9 36.3 + - - +
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Residues in contact with TRP 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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465A ASP* 3.6 32.8 - - + +
466A THR* 3.5 40.5 + - + +
469A ALA* 4.5 8.5 - - + -
635B ILE* 4.9 5.3 - - + +
644B SER 3.5 16.8 + - - +
645B VAL 3.7 2.0 - - - +
646B TRP 3.3 0.2 - - - -
647B ALA* 1.3 76.0 - - - +
649B MET* 1.3 61.1 + - - +
651B LEU* 4.8 2.5 - - - -
652B PHE* 2.8 41.9 + + + +
1740B CLA 4.3 10.3 - + + -
1780B BCR 2.9 58.1 - - + -
1786B CLA 3.2 68.2 - - + +
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Residues in contact with MET 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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645B VAL 2.9 15.8 + - - +
646B TRP* 2.8 41.4 + - + +
648B TRP* 1.3 78.6 - - + +
650B PHE* 1.3 49.0 + - - +
652B PHE* 3.1 11.5 + - - +
653B GLY* 2.3 35.9 + - - -
719B PHE* 3.5 35.6 - - - +
722B ALA* 4.7 5.6 - - + -
723B ALA* 3.3 29.6 - - + +
1739B CLA 3.9 12.8 - - + -
1757B CLA 4.9 3.8 - - + -
1780B BCR 3.4 36.3 - - + -
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Residues in contact with PHE 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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653A LEU* 5.1 2.0 - - + -
628B SER* 5.4 1.6 - - - -
631B LEU* 3.7 22.2 - - + -
632B ILE* 4.6 7.9 - - + -
646B TRP 2.7 11.5 + - - +
647B ALA* 3.1 15.0 + - - +
649B MET* 1.3 78.6 - - - +
651B LEU* 1.3 68.3 + - + +
653B GLY* 3.4 3.3 + - - +
654B HIS* 3.1 39.8 + + - -
720B THR* 3.2 43.5 - - + +
723B ALA* 4.4 6.7 - - + -
724B PHE* 4.0 17.5 - + + -
1785B CLA 3.5 59.9 - + + -
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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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465A ASP* 5.0 4.0 - - - +
649A ILE 5.2 2.2 - - - +
650A ASN* 3.3 38.6 - - + +
653A LEU* 4.5 18.8 - - + -
635B ILE* 5.1 0.4 - - + -
647B ALA 2.9 27.9 + - - +
648B TRP* 4.7 1.3 - - - -
650B PHE* 1.3 93.0 - - + +
652B PHE* 1.3 68.1 + - - +
653B GLY 2.9 0.7 - - - -
654B HIS* 3.2 20.6 + - + +
655B LEU* 2.9 22.3 + - - +
1786B CLA 3.0 46.5 - - + +
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Residues in contact with PHE 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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648B TRP* 2.8 26.3 + + + +
649B MET* 3.2 9.4 - - - +
651B LEU* 1.3 75.1 - - - +
653B GLY* 1.3 63.3 + - - +
655B LEU* 4.6 0.4 - - - +
656B VAL* 2.9 61.9 + - + +
715B VAL* 4.2 10.1 - - + -
719B PHE* 4.0 28.3 - + + -
1771B CLA 3.6 23.1 - + + -
1780B BCR 3.6 58.1 - - + -
1786B CLA 3.4 27.6 - - + +
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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
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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