Contacts of the strand formed by residues 124 - 129 (chain B) in PDB entry 2WA2
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 LEU 124 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93B ALA* 3.9 13.2 - - + +
98B VAL* 4.0 8.5 - - + +
99B ARG* 3.6 27.8 - - - +
100B GLU* 3.6 10.4 - - - +
101B VAL 2.9 25.0 + - - +
121B GLY 2.8 15.0 + - - +
123B ASN* 1.3 94.6 - - - +
125B ILE* 1.3 57.9 + - - +
126B THR* 3.9 1.4 + - - -
265B ARG* 3.6 48.7 - - + +
266B SER 4.5 10.3 - - - +
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Residues in contact with ILE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B SER* 3.7 30.5 - - - +
90B TYR* 3.4 39.0 - - + +
93B ALA* 3.6 21.3 - - + -
101B VAL* 3.3 13.0 - - + +
103B ALA* 4.1 2.9 - - + -
122B TRP* 3.1 17.4 + - - +
123B ASN 3.2 4.4 - - - +
124B LEU* 1.3 79.9 - - - +
126B THR* 1.3 71.9 + - - +
127B PHE* 3.7 37.9 + - + -
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Residues in contact with THR 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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101B VAL 2.9 7.9 + - - -
102B LYS* 3.8 29.1 - - - +
103B ALA 2.9 27.4 + - - +
104B TYR* 5.9 0.2 - - - -
124B LEU 3.9 1.6 + - - -
125B ILE* 1.3 76.8 + - - +
127B PHE* 1.3 67.2 + - - +
128B LYS* 5.3 3.5 - - + +
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Residues in contact with PHE 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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83B CYS* 3.9 5.2 - - - -
86B GLY* 3.9 21.1 - - - -
89B SER* 4.2 2.2 - - - -
90B TYR* 3.6 41.1 - + - -
103B ALA* 3.5 25.6 - - + -
114B PRO* 3.7 31.0 - - + -
116B LEU* 3.7 23.3 - - + -
125B ILE* 3.7 27.5 + - + -
126B THR* 1.3 80.0 - - - +
128B LYS* 1.3 61.2 + - - +
129B SER 4.3 0.4 - - - +
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Residues in contact with LYS 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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83B CYS* 5.5 0.2 - - - -
103B ALA 2.9 15.1 + - - +
104B TYR* 3.3 24.7 - - + +
105B THR* 3.1 25.1 + - - +
114B PRO* 5.5 0.9 - - - +
126B THR* 5.3 4.3 - - + +
127B PHE* 1.3 74.6 - - - +
129B SER* 1.3 66.6 + - - +
131B VAL* 3.7 25.6 - - + +
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Residues in contact with SER 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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105B THR* 3.2 8.4 - - - +
106B LEU 4.1 6.1 - - - -
107B GLY* 4.6 7.4 - - - -
113B LYS* 5.3 1.5 - - - +
114B PRO* 3.4 30.1 - - - +
127B PHE 4.3 0.6 - - - -
128B LYS* 1.3 82.4 + - - +
130B LYS* 1.3 80.4 + - - +
131B VAL* 3.1 9.8 + - - +
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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