Contacts of the helix formed by residues 670 - 679 (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 TYR 670 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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554A LEU* 4.4 0.5 - - - +
555A ILE* 3.0 28.3 - - + +
558A LYS* 3.7 34.2 + - + +
591A GLN* 3.5 29.6 - - + +
592A VAL* 3.6 7.6 - - - +
597A HIS* 4.2 15.9 - + - +
600A LEU* 4.2 14.6 - - + -
666B SER 4.7 2.5 - - - +
667B TRP 3.6 0.4 + - - -
668B ARG 3.4 0.6 - - - -
669B GLY* 1.3 73.1 - - - +
671B TRP* 1.3 110.1 + + + +
673B GLU* 4.1 2.9 - - - +
674B LEU* 3.7 21.2 + - + +
1787B CLA 2.5 40.4 + + + -
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Residues in contact with TRP 671 (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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600A LEU* 5.3 0.2 - - - +
662B MET* 3.2 36.1 - - + -
666B SER* 3.0 34.8 - - - -
667B TRP 4.8 0.9 - - - -
668B ARG 3.0 5.0 + - - +
670B TYR* 1.3 109.5 - + - +
672B GLN* 1.3 65.6 + - - +
673B GLU 3.2 0.5 + - - -
674B LEU* 3.5 13.9 + - + +
675B ILE* 3.2 27.2 + - + +
699B ALA* 3.7 19.1 - - + -
1773B PQN 3.5 49.3 - + + -
1780B BCR 3.9 18.8 - - + -
1787B CLA 3.3 44.2 - + - -
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Residues in contact with GLN 672 (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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568A LEU* 4.3 10.3 - - + -
586A ARG 4.3 0.7 - - - +
668B ARG* 2.6 59.2 + - - +
669B GLY* 4.0 3.6 - - - +
671B TRP* 1.3 77.1 - - - +
673B GLU* 1.3 53.6 + - - +
675B ILE* 3.1 5.5 + - - +
676B GLU* 2.4 51.6 + - - +
697B PRO 4.4 0.2 + - - -
698B VAL* 3.4 12.2 - - - +
699B ALA* 2.8 27.7 - - + +
77C MET 4.8 0.3 - - - +
79C LEU* 3.5 25.1 - - - +
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Residues in contact with GLU 673 (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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558A LYS* 5.2 6.9 - - + +
562A PHE* 4.3 21.0 - - + +
566A SER* 2.7 37.0 + - - +
568A LEU* 3.6 19.4 - - + +
569A ILE* 4.4 5.0 + - - +
572A LYS* 5.1 4.1 - - - +
592A VAL* 4.2 23.3 - - - +
593A SER 5.7 0.2 - - - +
597A HIS* 4.7 10.6 + - - -
669B GLY 3.5 13.8 + - - +
670B TYR* 4.3 4.9 - - - +
671B TRP 3.2 1.6 - - - -
672B GLN* 1.3 76.8 - - - +
674B LEU* 1.3 63.9 + - - +
675B ILE 3.1 1.1 - - - -
676B GLU* 2.9 32.3 - - + +
677B THR* 3.3 7.6 + - + +
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Residues in contact with LEU 674 (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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443A ILE* 5.1 3.6 - - + -
447A ASN* 3.4 28.3 - - - +
554A LEU* 3.4 17.7 - - + -
558A LYS* 2.8 35.6 - - + +
670B TYR* 3.7 19.6 + - + +
671B TRP* 3.5 13.7 + - + +
673B GLU* 1.3 80.1 - - - +
675B ILE* 1.3 62.7 + - + +
676B GLU 3.2 0.2 - - - -
677B THR* 3.2 15.2 + - + +
678B LEU* 2.7 45.4 + - + +
1780B BCR 5.6 3.4 - - + -
1787B CLA 5.0 4.7 - - - +
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Residues in contact with ILE 675 (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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671B TRP* 3.2 19.7 + - + +
672B GLN* 3.1 13.6 + - - +
673B GLU 3.1 0.8 - - - -
674B LEU* 1.3 84.7 - - + +
676B GLU* 1.3 56.2 + - - +
678B LEU* 3.6 8.1 - - + -
679B ALA* 2.7 31.9 + - - +
697B PRO* 3.9 23.8 - - + +
698B VAL 4.3 13.5 - - - +
699B ALA* 4.8 2.9 - - + -
1770B CLA 3.7 42.4 - - + -
1773B PQN 5.0 10.5 - - + -
1780B BCR 4.5 20.2 - - + -
79C LEU* 4.6 2.1 - - + +
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Residues in contact with GLU 676 (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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440A ASP* 5.2 2.1 - - - +
562A PHE* 6.2 1.6 - - + -
566A SER* 5.9 0.9 - - - +
567A ARG* 3.0 51.9 - - + +
568A LEU* 3.5 18.3 - - + +
672B GLN* 2.4 52.9 + - - +
673B GLU* 2.9 20.0 - - + +
675B ILE* 1.3 77.2 - - - +
677B THR* 1.3 56.3 + - + -
679B ALA* 4.0 4.6 - - - +
680B TRP* 3.9 14.0 + - - +
78C GLY 4.6 1.4 - - - -
79C LEU* 3.9 33.6 + - + +
81C TYR* 5.7 2.8 - - + -
37D LEU* 5.9 1.0 - - - +
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Residues in contact with THR 677 (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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439A ARG 4.8 1.1 - - - +
440A ASP* 3.7 32.2 - - + +
443A ILE* 4.3 10.9 - - + +
444A SER* 4.2 18.2 + - - -
558A LYS* 5.5 1.8 - - + -
562A PHE* 3.6 34.5 - - + -
673B GLU* 3.5 13.5 - - + +
674B LEU* 3.2 14.7 + - + +
676B GLU* 1.3 73.6 - - + +
678B LEU* 1.3 66.4 + - - +
679B ALA 3.3 0.7 - - - -
680B TRP* 3.1 22.8 + - - +
681B ALA 3.8 3.5 + - - -
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Residues in contact with LEU 678 (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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443A ILE 4.5 0.4 - - - +
444A SER* 3.6 29.8 - - - +
447A ASN* 2.7 38.8 - - + +
1800A CLA 3.1 48.5 - - + +
674B LEU* 2.7 29.6 + - + +
675B ILE* 3.6 9.2 - - + -
677B THR* 1.3 77.5 + - - +
679B ALA* 1.3 56.1 + - - +
680B TRP 3.3 1.6 - - - -
681B ALA* 3.5 11.5 - - - +
682B HIS* 2.9 22.2 - - - -
1770B CLA 4.7 6.2 - - + +
1780B BCR 4.8 6.1 - - + -
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Residues in contact with ALA 679 (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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675B ILE 2.7 18.4 + - - +
676B GLU* 4.0 7.6 - - - +
678B LEU* 1.3 75.7 - - - +
680B TRP* 1.3 51.4 + - - +
682B HIS* 3.9 2.9 - - - -
683B GLU* 2.3 38.7 - - - +
693B TRP* 4.1 16.2 - - + -
697B PRO* 4.1 15.0 - - + -
1770B CLA 4.2 3.4 - - + -
79C LEU* 5.3 0.9 - - + -
81C TYR 4.5 11.7 - - - +
37D LEU* 4.5 9.0 - - - +
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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