Contacts of the helix formed by residues 54 - 62 (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 LEU 54 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B HIS 3.8 7.2 - - - +
51B PHE* 5.3 8.1 - - + -
53B GLN* 1.3 82.3 + - + +
55B ALA* 1.3 58.3 - - - -
56B ILE 3.5 2.0 - - - -
57B ILE* 3.3 27.4 + - - +
58B PHE* 3.5 27.8 + - + -
149B SER* 3.1 12.5 + - - +
1737B CLA 4.4 8.9 + - - +
1743B CLA 3.4 75.2 - - + +
1744B CLA 4.6 20.6 - - + -
1775B BCR 4.8 10.3 - - + -
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Residues in contact with ALA 55 (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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51B PHE 3.2 20.2 - - - +
52B GLY 3.3 11.4 - - - +
53B GLN 2.3 20.8 + - - -
54B LEU 1.3 66.3 - - - -
56B ILE* 1.3 63.1 + - + +
57B ILE 3.6 0.3 + - - -
58B PHE 3.7 0.7 + - - -
59B LEU* 3.9 8.0 + - - +
146B SER* 3.6 23.2 + - - +
149B SER* 2.9 14.3 + - - +
150B LEU* 3.1 31.5 - - + +
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Residues in contact with ILE 56 (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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52B GLY* 3.1 20.6 - - - +
53B GLN* 3.4 20.7 + - - +
55B ALA* 1.3 78.4 - - + +
57B ILE* 1.3 62.5 + - - +
58B PHE 3.3 1.5 + - - -
59B LEU* 3.8 17.2 + - + +
60B TRP* 3.6 18.0 + - - +
150B LEU* 5.6 5.2 - - + -
1736B CLA 4.7 10.1 - - + -
1738B CLA 4.4 30.7 - - + +
1739B CLA 4.8 10.8 - - + +
1031I CLA 6.1 9.6 - - + -
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Residues in contact with ILE 57 (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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53B GLN* 3.9 12.0 + - + +
54B LEU* 3.3 15.1 + - - +
55B ALA 3.2 0.8 - - - -
56B ILE* 1.3 80.3 - - - +
58B PHE* 1.3 74.5 + - + +
59B LEU 3.6 0.2 - - - -
60B TRP* 3.5 7.7 - - + +
61B THR* 2.6 35.5 + - - +
1737B CLA 4.8 8.7 - - - -
1738B CLA 3.3 42.6 - - + -
1758B CLA 4.0 7.0 - - + -
1775B BCR 3.6 46.7 - - + -
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Residues in contact with PHE 58 (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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54B LEU* 3.5 20.0 + - + +
55B ALA 3.7 0.6 + - - -
56B ILE 3.3 0.2 - - - -
57B ILE* 1.3 100.3 - - + +
59B LEU* 1.3 54.2 + - - +
60B TRP 3.1 4.5 - - - -
61B THR* 4.2 6.0 - - - -
62B SER* 2.9 30.8 + - - -
142B LEU* 3.5 28.3 - - + +
145B LEU* 3.4 31.0 - - + -
146B SER* 2.6 41.7 + - - -
149B SER* 5.0 1.8 - - - -
1744B CLA 5.0 7.9 - - + -
1758B CLA 4.1 15.7 - - + -
1775B BCR 4.2 25.6 - - + -
1776B BCR 5.1 9.4 - - + -
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Residues in contact with LEU 59 (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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55B ALA 3.9 9.2 + - - +
56B ILE* 3.8 18.9 + - + +
57B ILE 3.6 0.2 - - - -
58B PHE* 1.3 73.4 - - - +
60B TRP* 1.3 62.5 + - - +
62B SER* 3.4 9.0 + - - +
143B LEU* 3.8 26.9 - - + -
146B SER* 3.9 9.0 + - - +
1739B CLA 5.8 0.2 - - - -
1031I CLA 3.0 105.9 - - + +
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Residues in contact with TRP 60 (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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56B ILE 3.6 13.0 + - - +
57B ILE* 3.5 12.6 - - + +
59B LEU* 1.3 80.3 - - - +
61B THR* 1.3 71.6 + - - +
63B GLY* 3.1 5.7 + - - -
64B ASN* 2.9 48.2 + - - +
1738B CLA 3.2 42.7 - - + +
1739B CLA 3.5 25.2 - - + +
1757B CLA 3.3 44.4 + + - +
1758B CLA 3.3 67.8 - + + -
1775B BCR 4.5 7.9 - - + -
1031I CLA 4.9 6.7 - - + -
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Residues in contact with THR 61 (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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57B ILE* 2.6 28.2 + - - +
58B PHE* 3.8 4.8 + - - -
60B TRP* 1.3 82.5 - - - +
62B SER* 1.3 65.8 + - - +
64B ASN* 3.2 13.7 + - + +
65B LEU* 2.9 31.1 + - + +
123B TRP* 6.2 0.4 - - + -
142B LEU* 4.3 25.4 - - + -
1758B CLA 4.1 31.7 + - + +
1776B BCR 5.0 5.4 - - + -
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Residues in contact with SER 62 (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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58B PHE 2.9 19.5 + - - -
59B LEU* 3.4 17.1 + - - -
61B THR* 1.3 74.6 - - - +
63B GLY* 1.3 72.4 + - - +
65B LEU* 2.9 21.3 + - - +
66B PHE* 2.9 15.7 + - - +
138B GLY 4.8 0.9 - - - -
139B ALA* 3.8 34.6 + - - +
142B LEU* 4.5 7.0 - - - +
143B LEU* 4.5 9.4 - - - -
1031I CLA 3.4 16.0 - - - +
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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