Contacts of the strand formed by residues 174 - 179 (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 ILE 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A LEU* 4.1 15.7 - - + -
86A LEU* 3.3 21.1 - - + +
88A ALA* 4.4 4.5 - - + -
161A PHE* 4.0 27.6 - - + -
165A MET* 4.9 1.1 - - + -
168A PHE* 4.3 6.5 + - + +
169A LEU* 3.9 29.2 + - + +
172A GLY 3.3 4.8 - - - +
173A LEU* 1.3 87.3 - - + +
175A ILE* 1.3 62.6 + - - +
176A ASP 3.5 24.2 - - - +
177A ILE* 3.9 16.4 - - + -
289A LYS 3.5 9.7 - - - +
290A VAL* 3.4 18.7 - - + +
458A ILE* 4.5 0.5 - - - +
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Residues in contact with ILE 175 (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* 2.9 45.3 - - + +
85A THR* 3.6 30.1 - - + +
86A LEU 2.8 17.8 + - - +
87A GLN* 3.9 8.3 - - + -
172A GLY 4.7 4.3 - - - +
173A LEU 3.7 0.4 + - - -
174A ILE* 1.3 77.6 - - - +
176A ASP* 1.3 82.5 + - + +
290A VAL* 4.5 0.4 - - - -
291A LYS* 3.1 21.5 + - - +
414A PHE* 6.2 3.8 - - + -
451A PRO* 5.9 6.3 - - + -
458A ILE* 3.3 28.0 - - + +
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Residues in contact with ASP 176 (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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87A GLN* 2.9 30.8 - - - +
88A ALA 3.0 25.3 + - - -
174A ILE* 3.5 9.0 - - - +
175A ILE* 1.3 89.8 - - + +
177A ILE* 1.3 64.0 + - - +
178A GLU* 2.5 35.4 + - - +
290A VAL* 4.6 0.4 - - - -
291A LYS* 3.1 16.8 - - + +
293A ALA* 4.1 4.9 - - + +
338A ILE* 4.4 17.6 - - + +
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Residues in contact with ILE 177 (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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88A ALA* 3.4 9.2 - - + +
90A MET* 3.6 29.2 - - + -
161A PHE* 4.0 14.8 - - + -
169A LEU* 4.9 0.7 - - + -
174A ILE* 3.9 21.3 - - + -
176A ASP* 1.3 73.1 - - - +
178A GLU* 1.3 60.7 + - - +
179A VAL* 3.5 13.7 + - + +
285A PHE* 3.6 51.1 - - + -
290A VAL* 4.2 13.5 - - + -
291A LYS 2.8 7.5 + - - -
292A LEU* 3.5 11.0 - - + -
293A ALA 2.9 26.7 + - - +
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Residues in contact with GLU 178 (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 20.4 - - + +
87A GLN* 3.6 14.0 - - + +
88A ALA 2.9 11.8 + - - +
89A ILE* 3.3 25.0 - - + +
90A MET* 2.8 28.4 + - - +
176A ASP* 2.5 31.2 - - - +
177A ILE* 1.3 69.7 - - - +
179A VAL* 1.3 62.4 - - - +
180A GLY 3.3 1.3 + - - -
293A ALA* 3.5 20.2 - - - +
295A LYS* 3.4 19.8 - - + +
338A ILE* 6.0 0.2 - - - +
340A ASN* 2.9 24.6 - - - +
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Residues in contact with VAL 179 (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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90A MET* 4.5 4.7 - - - -
92A PHE* 5.2 2.7 - - + -
158A MET* 4.3 13.0 - - - -
177A ILE* 4.0 18.8 - - + +
178A GLU* 1.3 71.0 - - - +
180A GLY* 1.3 67.1 + - - +
181A LEU* 3.4 17.9 + - + +
185A GLY 4.1 3.5 - - - +
277A ILE* 3.8 29.4 - - + -
278A LEU* 4.0 16.6 - - + -
281A ALA* 3.7 26.7 - - + -
292A LEU* 4.5 3.8 - - + -
293A ALA 2.8 21.3 + - - +
294A ILE* 4.4 7.1 - - + -
295A LYS* 4.9 1.0 + - - +
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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