Contacts of the strand formed by residues 49 - 55 (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 GLY 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A VAL 3.4 3.0 + - - -
15A TYR* 3.1 14.7 - - - -
16A VAL 3.0 18.9 + - - -
47A VAL* 3.2 10.2 - - - +
48A ASP* 1.3 81.6 - - - +
50A VAL* 1.3 64.3 + - - +
84A LEU* 3.8 5.2 - - - -
85A THR* 3.1 22.2 - - - -
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Residues in contact with VAL 50 (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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16A VAL 3.0 15.7 - - - +
18A LEU* 3.7 28.5 - - + -
39A LEU* 4.0 14.6 - - + -
42A LEU* 4.0 15.7 - - + -
49A GLY* 1.3 79.7 - - - +
51A MET* 1.3 54.1 + - - +
79A VAL* 3.9 22.0 - - + -
84A LEU* 4.2 8.3 - - + -
85A THR 2.9 14.2 + - - +
86A LEU* 3.2 20.5 - - + +
87A GLN* 2.8 36.7 + - - +
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Residues in contact with MET 51 (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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16A VAL 2.9 6.1 + - - -
17A MET* 3.6 16.9 - - + +
18A LEU* 2.8 28.7 + - - +
50A VAL* 1.3 74.1 - - - +
52A VAL* 1.3 65.6 + - - +
86A LEU* 4.4 0.9 - - - -
87A GLN* 3.3 42.6 - - - +
89A ILE* 3.7 16.8 - - + -
178A GLU* 3.7 30.7 - - + +
295A LYS* 3.4 21.8 - - - +
340A ASN* 4.0 1.3 - - - +
380A GLU* 3.6 18.4 - - - +
417A THR* 3.8 24.0 - - + +
4B GLC 5.6 0.2 - - - -
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Residues in contact with VAL 52 (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* 4.0 16.6 - - + +
19A PRO 5.4 1.1 - - - +
22A VAL* 3.8 29.2 - - + -
51A MET* 1.3 75.1 - - - +
53A ASP* 1.3 75.2 + - + +
54A VAL* 3.6 13.4 + - + -
72A TYR* 4.5 3.1 - - + -
75A LEU* 4.0 18.6 - - + -
76A LEU* 5.3 1.1 - - + -
86A LEU* 3.9 24.0 - - + +
87A GLN 3.0 8.6 + - - +
88A ALA* 3.9 0.2 - - - -
89A ILE* 2.9 31.8 + - - +
4B GLC 6.1 0.2 - - - -
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Residues in contact with ASP 53 (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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20A LEU* 3.7 6.2 - - - +
52A VAL* 1.3 78.5 - - + +
54A VAL* 1.3 53.9 + - - +
55A TRP* 3.3 40.9 + - + +
72A TYR* 2.7 30.3 + - - -
89A ILE* 3.5 8.8 - - - +
91A SER* 2.7 24.1 + - - +
420A ARG* 4.7 0.5 + - - -
4B GLC 2.6 46.5 + - - -
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Residues in contact with VAL 54 (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* 4.2 11.7 - - + +
53A ASP* 1.3 71.7 - - - +
55A TRP* 1.3 59.0 + - - +
56A TRP 3.3 0.2 + - - -
59A ILE* 4.2 4.7 - - + -
69A TRP* 3.8 23.6 - - + -
72A TYR* 3.6 26.5 - - + -
76A LEU* 5.9 2.0 - - + -
88A ALA* 4.3 9.0 - - + -
89A ILE 2.8 20.8 + - - +
90A MET* 4.1 14.4 - - + -
91A SER* 3.1 19.7 + - - -
157A TYR* 2.8 27.3 + - + +
161A PHE* 4.2 17.0 - - + -
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Residues in contact with TRP 55 (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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20A LEU* 4.1 6.6 - - + +
21A GLY* 4.8 8.5 - - - +
23A VAL 4.9 2.2 - - - -
53A ASP* 3.3 34.9 + - + +
54A VAL* 1.3 69.8 - - - +
56A TRP* 1.3 64.7 + - - +
57A GLY 4.4 1.1 - - - +
58A ILE* 3.0 30.8 + - + +
59A ILE* 3.0 16.3 + - - +
72A TYR* 3.4 27.4 + - - -
91A SER* 3.7 13.7 - - - -
93A HIS* 3.3 48.5 - + - -
95A CYS* 3.4 35.0 - - + -
105A ILE* 3.5 37.0 - - + +
157A TYR* 3.3 0.9 - - - -
4B GLC 3.5 18.8 - - - -
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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