Contacts of the strand formed by residues 125 - 131 (chain J) in PDB entry 2I2X
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 THR 125 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122J THR* 4.9 0.9 + - - -
124J GLY* 1.3 75.5 - - - -
126J VAL* 1.3 64.7 + - - +
153J ASN* 3.2 33.6 + - - +
155J VAL* 4.0 23.8 - - + -
173J GLU* 4.3 29.9 + - + +
174J LYS 5.5 0.4 - - - -
175J PRO* 3.0 8.3 - - + +
176J ILE* 2.9 37.0 + - - +
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Residues in contact with VAL 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125J THR* 1.3 78.5 - - - +
127J VAL* 1.3 74.9 + - - +
128J CYS* 4.0 2.5 + - - -
147J LEU* 3.8 37.0 - - + -
152J TYR* 4.2 24.0 - - + -
153J ASN 2.8 12.5 + - - +
154J VAL* 3.5 6.1 - - + +
155J VAL* 3.0 25.8 + - - +
176J ILE* 4.2 12.6 - - + -
177J MET* 3.4 21.3 - - + +
179J THR* 4.0 11.9 - - + -
238J ALA* 4.7 5.4 - - + -
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Residues in contact with VAL 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126J VAL* 1.3 72.5 - - - +
128J CYS* 1.3 58.6 + - - +
129J HIS* 5.7 0.2 - - + -
155J VAL* 3.4 20.4 - - + +
157J LEU* 3.7 30.3 - - + -
166J VAL* 4.8 4.3 - - + -
169J ALA* 4.6 7.6 - - + +
170J VAL* 4.4 10.8 - - + -
173J GLU* 4.6 5.4 - - + -
175J PRO* 3.4 32.1 - - + -
177J MET 3.1 5.8 + - - +
178J LEU* 3.1 25.0 - - + +
179J THR* 2.6 33.8 + - - -
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Residues in contact with CYS 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126J VAL* 4.0 2.7 - - - -
127J VAL* 1.3 78.5 - - - +
129J HIS* 1.3 60.5 + - - +
140J LYS* 4.4 11.7 - - + -
143J VAL* 4.6 4.0 - - - -
144J THR* 4.0 16.2 - - - +
147J LEU* 3.8 24.2 - - - -
154J VAL* 3.8 23.6 - - + -
155J VAL 3.3 8.0 + - - +
156J ASP* 4.0 2.8 - - - +
157J LEU* 2.9 31.5 + - - +
158J GLY 4.3 0.5 + - - -
179J THR* 3.1 22.4 - - - +
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Residues in contact with HIS 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127J VAL* 5.7 0.2 - - + -
128J CYS* 1.3 76.0 - - - +
130J VAL* 1.3 84.9 + - - +
131J ALA* 3.9 14.0 - - - +
140J LYS* 4.4 5.5 - - - +
157J LEU* 3.9 16.6 - - + -
158J GLY 4.3 5.6 - - - -
161J VAL* 4.1 12.3 - - + -
166J VAL* 3.7 27.4 - - + +
178J LEU* 4.3 6.2 - - + +
179J THR* 3.0 26.3 + - - -
180J GLY* 3.6 9.6 - - - -
181J THR* 3.4 21.3 + - - -
190J ALA* 5.3 0.6 + - - +
191J PHE* 4.9 2.6 - + - -
194J VAL* 3.8 20.8 - - + +
207J PHE* 3.9 24.9 - + - -
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Residues in contact with VAL 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129J HIS* 1.3 82.7 - - - +
131J ALA* 1.3 66.3 + - - +
134J ASP* 3.7 31.6 - - + +
135J VAL 5.0 0.2 - - - -
136J HIS 3.6 27.4 - - - +
137J ASP* 4.5 3.8 - - - -
140J LYS* 3.6 28.3 - - + +
158J GLY 3.4 18.4 + - - +
159J ARG* 2.8 30.1 - - + +
161J VAL* 3.5 4.3 + - - +
181J THR* 3.5 15.9 - - + +
183J LEU* 6.0 0.2 - - + -
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Residues in contact with ALA 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129J HIS* 3.9 12.5 + - - +
130J VAL* 1.3 77.3 - - - +
132J GLU* 1.3 64.6 + - - +
134J ASP* 3.1 22.2 + - - +
159J ARG 4.1 0.9 - - - +
181J THR 3.1 10.5 + - - +
187J THR* 3.6 22.2 - - + +
190J ALA* 3.5 21.1 - - + -
191J PHE* 3.8 24.2 - - + -
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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