Contacts of the strand formed by residues 85 - 91 (chain A) in PDB entry 1WDR
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 THR 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A TYR* 3.7 14.6 - - - -
48A ASP* 3.3 19.3 + - - +
49A GLY* 3.1 6.2 - - - -
50A VAL* 2.9 28.2 + - - +
79A VAL* 3.9 0.8 - - - +
84A LEU* 1.3 76.9 - - - +
86A LEU* 1.3 63.3 + - - +
172A GLY 4.3 8.5 - - - +
173A LEU* 3.3 14.8 - - + +
175A ILE* 3.6 23.6 - - + +
451A PRO* 6.0 6.1 - - + -
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Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 5.4 0.7 - - + -
50A VAL* 3.2 31.0 - - + +
52A VAL* 3.9 20.2 - - + +
75A LEU* 6.3 0.9 - - + -
76A LEU* 3.6 41.7 - - + -
79A VAL* 4.6 10.3 - - + -
85A THR* 1.3 77.2 - - - +
87A GLN* 1.3 76.0 + - - +
88A ALA* 4.2 16.8 - - + +
161A PHE* 5.7 0.2 - - + -
173A LEU* 2.9 21.0 + - + +
174A ILE* 3.3 15.8 - - + +
175A ILE* 2.8 31.1 + - - -
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Residues in contact with GLN 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TYR* 3.3 35.2 - - + +
50A VAL 2.8 11.0 + - - +
51A MET* 3.3 32.3 - - + +
52A VAL 3.0 25.6 + - - -
86A LEU* 1.3 76.9 - - - +
88A ALA* 1.3 60.0 + - - +
89A ILE 4.0 0.2 - - - -
175A ILE* 3.9 10.5 - - + -
176A ASP* 2.9 39.3 - - - +
178A GLU* 3.6 6.3 - - + +
378A ALA* 5.9 2.8 - - - +
417A THR* 3.1 26.8 + - - -
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A VAL* 3.9 4.0 - - - -
54A VAL* 4.3 6.7 - - + -
86A LEU* 3.9 15.8 - - + -
87A GLN* 1.3 72.1 - - - +
89A ILE* 1.3 61.6 + - - +
90A MET* 3.7 10.2 + - + +
161A PHE* 4.0 27.8 - - + -
174A ILE* 4.4 4.3 - - + -
176A ASP 3.0 8.5 + - - +
177A ILE* 3.4 14.1 - - + -
178A GLU* 2.9 23.0 + - - -
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Residues in contact with ILE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A MET* 3.7 26.2 - - + -
52A VAL 2.9 18.3 + - - +
53A ASP* 3.5 22.0 - - - +
54A VAL* 2.8 34.3 + - - +
88A ALA* 1.3 71.0 - - - +
90A MET* 1.3 67.2 - - - +
91A SER* 3.1 20.4 + - - +
93A HIS* 4.9 4.3 - - + -
178A GLU* 3.3 27.4 - - + +
180A GLY* 4.6 7.2 - - - +
185A GLY* 5.3 2.9 - - - +
295A LYS* 3.6 27.4 - - + +
4B GLC 3.8 10.5 - - - +
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Residues in contact with MET 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A VAL* 4.1 7.9 - - + -
88A ALA* 4.0 17.0 - - + +
89A ILE* 1.3 77.2 - - - +
91A SER* 1.3 58.9 + - - +
92A PHE* 3.3 30.1 + - + -
157A TYR* 4.1 15.0 - - - -
158A MET* 3.9 25.8 - - + -
161A PHE* 4.0 42.2 - - + -
177A ILE* 3.6 25.4 - - + -
178A GLU 2.8 12.5 + - - +
179A VAL* 4.5 2.5 - - - -
180A GLY* 3.0 28.1 + - - +
285A PHE* 4.5 2.9 - - - -
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Residues in contact with SER 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ASP* 2.7 30.6 + - - +
54A VAL 3.1 16.4 + - - -
55A TRP* 3.7 14.8 - - - -
56A TRP* 2.9 26.0 + - - +
89A ILE* 3.1 18.7 + - - +
90A MET* 1.3 67.6 - - - +
92A PHE* 1.3 57.0 + - - +
93A HIS* 3.2 30.8 + - - +
157A TYR* 5.0 0.4 - - - -
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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