Contacts of the strand formed by residues 122 - 127 (chain B) in PDB entry 1WYI
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 122 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B THR 2.5 12.8 + - - -
90B TRP* 2.9 29.6 - - - -
91B VAL* 2.8 23.2 + - - +
120B GLY 4.1 0.6 + - - -
121B LEU* 1.3 75.4 - - - +
123B VAL* 1.3 61.8 + - - +
159B LYS* 3.4 19.6 - - - +
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Residues in contact with VAL 123 (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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90B TRP* 3.5 3.3 - - - -
91B VAL* 3.1 30.3 - - + +
93B LEU* 4.0 7.0 - - + -
113B VAL* 4.4 20.4 - - + +
116B ALA* 3.4 22.9 - - + -
117B LEU* 4.2 14.4 - - + +
121B LEU 4.2 5.2 - - - +
122B GLY* 1.3 75.3 - - - -
124B ILE* 1.3 64.4 + - - +
125B ALA* 3.8 9.4 + - + +
159B LYS 3.2 7.5 + - - +
160B VAL* 3.5 20.4 - - + -
161B VAL 3.1 22.0 + - - -
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Residues in contact with ILE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PHE* 3.6 33.9 - - + -
9B GLY* 5.4 1.8 - - - -
40B VAL* 4.8 13.5 - - + -
62B ALA* 5.1 0.9 - - + -
90B TRP* 4.8 12.6 - - + -
91B VAL 2.6 13.8 + - - +
92B VAL* 3.6 18.2 - - + -
93B LEU 3.0 22.4 + - - +
123B VAL* 1.3 74.3 - - - +
125B ALA* 1.3 61.3 + - - +
126B CYS* 3.5 6.9 + - - -
161B VAL* 3.4 10.1 - - + +
163B ALA* 4.0 14.1 - - + -
207B ILE* 4.0 23.1 - - + -
230B LEU* 4.6 15.3 - - + -
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Residues in contact with ALA 125 (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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93B LEU* 3.4 8.3 - - - +
109B ILE* 6.0 1.1 - - + -
113B VAL* 4.5 12.1 - - + -
123B VAL* 3.7 8.2 + - + -
124B ILE* 1.3 72.6 - - - +
126B CYS* 1.3 60.3 + - - +
150B ILE* 3.8 39.0 - - + -
160B VAL* 5.2 3.1 - - + -
161B VAL 3.0 11.1 + - - +
162B LEU* 3.7 10.2 - - + +
163B ALA 2.9 23.9 + - - -
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Residues in contact with CYS 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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92B VAL* 3.7 26.7 - - - -
93B LEU 2.6 15.2 + - - -
94B GLY* 3.4 19.5 - - - +
95B HIS* 3.9 4.7 - - - -
99B ARG* 3.0 24.4 + - - -
124B ILE* 3.8 4.7 - - - -
125B ALA* 1.3 71.8 - - - +
127B ILE* 1.3 69.4 + - - +
150B ILE* 4.2 1.9 - - - +
163B ALA* 3.3 11.4 - - - +
165B GLU* 3.2 25.6 - - - +
230B LEU* 3.8 15.0 - - - -
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Residues in contact with ILE 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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94B GLY 4.9 1.6 - - - -
99B ARG* 4.8 2.5 - - - +
125B ALA 5.0 1.8 - - - +
126B CYS* 1.3 83.4 - - - +
128B GLY* 1.3 59.5 + - - +
143B VAL* 3.4 28.5 - - + -
146B GLN* 3.1 30.5 - - + +
147B THR* 3.5 9.9 - - - +
150B ILE* 3.4 26.5 - - + -
162B LEU* 4.6 9.2 - - + -
163B ALA 2.8 21.0 + - - +
164B TYR* 4.1 4.0 - - + -
165B GLU* 2.9 32.6 + - - +
167B VAL* 6.0 0.2 - - - -
188B LEU* 3.5 23.1 - - + -
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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