Contacts of the helix formed by residues 84 - 90 (chain B) in PDB entry 1W4R
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 VAL 84 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B LEU* 4.9 1.1 - - + -
53B ILE* 3.6 41.1 - - + -
76B LEU* 3.9 25.8 - - + -
77B PRO 4.1 18.4 - - - +
78B ALA* 4.2 7.9 - - + -
81B LEU 3.0 12.3 + - - +
83B ASP* 1.3 83.4 - - + +
85B ALA* 1.3 63.5 + - - +
86B GLN 3.1 3.3 + - - -
87B GLU* 3.2 16.2 + - + +
88B ALA* 3.0 18.9 + - - +
108B PHE* 5.3 0.2 - - + -
170H LYS* 6.2 1.8 - - - +
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Residues in contact with ALA 85 (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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81B LEU 3.5 3.7 + - - -
82B ARG* 3.1 25.3 + - - +
84B VAL* 1.3 78.5 - - - +
86B GLN* 1.3 57.8 + - - +
88B ALA* 3.6 8.8 - - - +
89B LEU* 2.8 40.8 + - + +
108B PHE* 4.3 10.1 - - + -
112B MET* 4.5 7.4 - - + -
1193E DTU 5.1 7.6 - - + -
190H PHE* 4.1 20.9 - - + -
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Residues in contact with GLN 86 (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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82B ARG 3.8 2.4 + - - +
83B ASP 3.6 14.2 - - - +
84B VAL* 3.9 1.0 - - - -
85B ALA* 1.3 87.9 + - - +
87B GLU* 1.3 67.1 + - - +
89B LEU* 3.6 5.7 + - - -
90B GLY* 3.8 1.6 + - - -
189H TYR* 3.1 52.7 + - - +
190H PHE* 3.7 16.5 - - - -
191H LYS* 3.5 46.4 - - + +
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Residues in contact with GLU 87 (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 LEU* 4.1 7.4 - - + -
74B GLU* 4.3 16.0 - - + +
76B LEU* 3.7 33.0 - - + +
83B ASP 4.3 1.6 - - - +
84B VAL* 3.3 26.4 - - - +
86B GLN* 1.3 84.1 + - - +
88B ALA* 1.3 65.6 + - - +
90B GLY* 3.1 11.6 + - - -
91B VAL* 3.7 16.5 - - - +
170H LYS* 5.6 4.2 + - - -
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Residues in contact with ALA 88 (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 LEU* 3.6 17.2 - - + +
53B ILE* 5.1 0.2 - - + -
84B VAL 3.0 16.1 + - - +
85B ALA* 3.2 5.6 + - - +
87B GLU* 1.3 74.8 - - - +
89B LEU* 1.3 64.0 + - - +
90B GLY 3.1 1.4 + - - -
91B VAL* 3.2 19.0 + - - +
94B ILE* 3.7 15.8 - - + +
108B PHE* 3.7 28.5 - - + -
112B MET* 4.1 4.3 - - + -
117B LYS* 3.5 11.2 - - - -
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Residues in contact with LEU 89 (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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85B ALA* 2.8 25.1 + - + +
86B GLN 3.9 0.2 - - - +
87B GLU 3.3 0.6 - - - -
88B ALA* 1.3 78.5 - - - +
90B GLY* 1.3 56.4 + - - +
112B MET* 3.9 23.6 - - + -
115B ALA* 5.4 7.0 - - + -
117B LYS* 3.0 26.7 + - - +
1193E DTU 5.9 2.5 - - - -
190H PHE* 3.3 31.9 - - + +
191H LYS* 3.7 24.9 + - + +
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Residues in contact with GLY 90 (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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49B LYS* 3.7 23.6 + - - +
86B GLN 3.8 4.7 + - - -
87B GLU 3.1 7.7 + - - -
88B ALA 3.1 1.6 - - - -
89B LEU* 1.3 77.4 - - - +
91B VAL* 1.3 66.1 + - - +
191H LYS* 4.2 12.7 - - - +
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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