Contacts of the strand formed by residues 125 - 132 (chain B) in PDB entry 1WYK
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 125 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117B ASP* 3.9 38.4 - - + +
118B VAL 3.4 5.6 - - - +
119B LYS* 4.2 15.7 - - + +
123B GLY 4.8 1.1 - - - +
124B ASP* 1.3 74.1 - - - +
126B ILE* 1.3 62.0 + - - +
127B GLY 3.5 21.8 - - - +
128B HIS* 4.1 11.7 - - + +
213B GLY* 5.0 4.8 - - - +
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Residues in contact with ILE 126 (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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118B VAL 2.8 17.7 + - - +
120B ASN* 3.7 41.1 - - + +
124B ASP* 3.9 5.8 - - + +
125B VAL* 1.3 78.3 - - - +
127B GLY* 1.3 57.7 + - - +
142B VAL* 3.7 28.0 - - + +
143B LYS 3.3 31.2 - - - +
144B GLY* 4.2 2.2 - - - -
212B ARG* 6.0 5.1 - - - +
213B GLY* 3.6 21.3 + - - -
215B SER* 4.6 0.2 + - - -
264B TRP* 4.2 6.1 - - - +
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Residues in contact with GLY 127 (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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118B VAL* 2.9 26.5 + - - -
125B VAL* 3.5 8.3 - - - +
126B ILE* 1.3 82.9 - - - +
128B HIS* 1.3 71.7 + - - -
142B VAL* 4.0 12.8 - - - -
213B GLY 3.5 13.3 + - - -
215B SER 3.7 5.6 - - - -
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Residues in contact with HIS 128 (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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115B LEU* 6.2 3.4 - - + -
116B PHE 3.4 11.0 - - - +
117B ASP* 3.2 26.9 + - - -
118B VAL* 3.9 6.1 - - - +
125B VAL* 4.1 10.7 - - + +
127B GLY* 1.3 79.7 - - - -
129B ALA* 1.3 63.9 + - - +
138B LYS* 3.9 0.7 - - - +
139B PRO* 3.3 15.6 - - - +
213B GLY 3.0 27.3 + - - -
215B SER 2.9 11.5 + - - +
216B GLY* 3.0 33.0 - - - +
217B ARG* 3.2 54.1 + - + +
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Residues in contact with ALA 129 (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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115B LEU* 3.7 4.3 - - - +
116B PHE* 2.8 38.0 + - + +
118B VAL* 4.0 3.8 - - + +
128B HIS* 1.3 76.8 - - - +
130B LEU* 1.3 64.6 + - - +
136B VAL* 4.4 4.5 - - + -
137B MET 3.1 15.5 - - - +
138B LYS* 3.9 12.6 - - + -
146B ILE* 4.0 27.8 - - + -
216B GLY 4.6 2.2 - - - +
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Residues in contact with LEU 130 (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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114B ARG 3.2 12.6 - - - +
115B LEU* 4.0 8.3 - - + -
116B PHE* 4.1 5.4 - - - -
129B ALA* 1.3 75.4 - - - +
131B ALA* 1.3 61.7 + - - +
132B MET* 3.6 35.4 - - + -
135B LYS 3.7 0.5 - - - +
136B VAL* 3.2 4.3 - - - -
137B MET* 2.9 51.0 + - + +
178B PHE* 4.5 5.6 - - + -
216B GLY 3.5 20.6 - - - +
218B PRO* 3.6 31.4 - - + -
226B VAL* 5.3 1.6 - - + -
229B ILE* 4.2 17.7 - - + -
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Residues in contact with ALA 131 (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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113B MET 4.6 0.4 - - - +
114B ARG* 2.8 15.1 + - - +
116B PHE* 3.9 15.2 - - + -
130B LEU* 1.3 70.9 - - - +
132B MET* 1.3 62.9 + - - +
135B LYS 3.3 5.8 - - - -
136B VAL* 4.3 1.1 - - - +
169B LEU* 3.9 22.4 - - + -
173B MET 5.2 0.4 - - - +
176B GLU 3.4 22.7 - - - +
177B ALA* 3.4 3.0 - - - -
178B PHE* 2.8 28.6 + - - -
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Residues in contact with MET 132 (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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2B DIO 3.9 10.3 - - - -
130B LEU* 3.6 13.8 + - + -
131B ALA* 1.3 77.2 - - - +
133B GLU* 1.3 83.1 + - + +
134B GLY 3.3 1.8 - - - -
135B LYS* 2.7 27.4 + - - +
137B MET* 3.8 26.5 - - + +
177B ALA* 3.9 1.7 - - - +
178B PHE* 3.4 20.2 - - + +
180B TYR* 3.7 12.8 - - + -
226B VAL* 3.7 33.9 - - + -
229B ILE* 4.0 9.9 - - + -
247B TRP* 3.8 30.1 - - + -
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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