Contacts of the strand formed by residues 90 - 96 (chain B) in PDB entry 1WG8
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 90 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B VAL* 3.7 20.9 - - + +
27B VAL* 3.8 22.2 - - + -
82B LEU* 4.1 9.0 - - + -
87B VAL* 3.6 19.3 - - + -
89B ARG* 1.3 80.1 - - - +
91B ASP* 1.3 64.0 + - - +
92B GLY 3.6 3.3 + - - +
93B ILE* 3.6 37.5 - - + -
222B VAL* 3.0 15.6 + - + +
223B LEU* 3.7 2.8 - - + -
224B ALA* 2.9 27.3 + - - -
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Residues in contact with ASP 91 (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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18B LEU 4.8 2.1 - - - +
21B ARG* 3.4 28.9 + - - +
23B GLY 4.5 0.5 - - - +
24B GLY* 3.1 10.0 - - - -
25B VAL* 2.5 41.3 + - - +
26B TYR* 3.6 23.7 - - + +
90B VAL* 1.3 75.2 - - - +
92B GLY* 1.3 57.4 + - - +
224B ALA* 4.5 11.6 - - - +
227B GLY* 3.3 24.3 - - - -
228B ARG 3.7 1.7 + - - -
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Residues in contact with GLY 92 (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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18B LEU* 4.7 6.7 - - - -
25B VAL 4.1 0.5 - - - +
26B TYR* 3.3 21.7 - - - -
27B VAL 2.9 23.6 + - - -
90B VAL* 3.4 4.1 + - - +
91B ASP* 1.3 80.3 - - - +
93B ILE* 1.3 66.7 + - - +
223B LEU* 4.0 3.1 - - - -
228B ARG 3.4 12.6 - - - -
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Residues in contact with ILE 93 (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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18B LEU* 3.8 5.8 - - - +
27B VAL* 3.4 19.5 - - + +
78B LEU* 4.4 4.3 - - + -
90B VAL* 3.6 24.0 - - + -
92B GLY* 1.3 80.2 - - - +
94B LEU* 1.3 65.7 + - - +
215B PHE* 3.7 34.1 - - + -
219B ALA* 3.5 42.6 - - + +
222B VAL* 3.9 5.8 - - + -
223B LEU* 4.0 8.5 - - + -
228B ARG 3.0 10.1 + - - +
229B LEU* 3.6 7.1 - - + +
230B VAL 2.9 26.7 + - - +
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Residues in contact with LEU 94 (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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14B ALA* 4.3 11.4 - - + -
15B LEU* 5.9 1.3 - - + -
18B LEU* 4.2 23.5 - - + +
27B VAL 2.7 13.8 + - - +
28B ASP* 3.7 13.6 - - - +
29B ALA* 2.9 29.6 + - - +
36B HIS* 3.4 42.4 - - + +
40B ILE* 4.8 5.2 - - + -
93B ILE* 1.3 76.3 - - - +
95B ALA* 1.3 77.7 + - - +
96B ASP* 4.7 2.2 - - + +
230B VAL* 3.2 31.2 - - + +
232B ILE* 4.9 8.3 - - + -
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Residues in contact with ALA 95 (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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29B ALA* 4.4 5.4 - - + -
30B THR* 3.5 8.5 - - + +
75B PHE* 4.9 1.1 - - + -
94B LEU* 1.3 80.2 - - - +
96B ASP* 1.3 55.4 + - - +
97B LEU* 3.7 15.7 + - + -
215B PHE* 3.8 30.5 - - + -
230B VAL 2.9 11.3 + - - +
231B VAL* 3.3 9.9 - - + +
232B ILE* 2.8 31.4 + - - +
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Residues in contact with ASP 96 (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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8B PRO* 5.8 0.2 - - - +
9B VAL* 4.7 8.1 + - - +
30B THR* 2.8 22.6 + - - +
36B HIS* 3.4 19.9 - - + +
94B LEU* 4.4 3.9 - - + +
95B ALA* 1.3 69.4 - - - +
97B LEU* 1.3 61.4 + - - +
232B ILE* 4.0 16.5 - - + +
234B PHE* 3.1 29.5 - - - -
3141B SAM 3.4 56.6 + - - +
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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