Contacts of the strand formed by residues 153 - 161 (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 ASN 153 (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* 3.4 28.8 - - - +
124J GLY 3.0 11.8 + - - +
125J THR* 3.2 26.6 + - - +
126J VAL* 2.8 28.2 + - - +
152J TYR* 1.3 72.4 - - - +
154J VAL* 1.3 68.6 + - - +
155J VAL* 5.5 1.2 - - - +
173J GLU* 4.9 4.3 - - - +
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Residues in contact with VAL 154 (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* 3.5 4.5 - - + +
128J CYS* 3.8 26.0 - - - -
144J THR* 3.8 17.0 - - + +
147J LEU* 3.5 34.5 - - + -
148J ARG* 3.2 52.8 + - + +
152J TYR* 3.6 5.7 + - + +
153J ASN* 1.3 87.0 + - - +
155J VAL* 1.3 67.0 + - - +
156J ASP 3.6 1.5 + - - +
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Residues in contact with VAL 155 (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* 4.0 8.9 - - + +
126J VAL 3.0 9.3 + - - +
127J VAL* 3.4 32.0 - - + -
128J CYS 3.3 19.8 + - - +
153J ASN* 4.1 1.9 + - - +
154J VAL* 1.3 72.6 - - - +
156J ASP* 1.3 62.5 + - - +
157J LEU* 3.4 21.2 + - + +
169J ALA* 5.7 0.7 - - + -
173J GLU* 3.9 31.6 - - + +
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Residues in contact with ASP 156 (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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128J CYS* 4.0 4.3 - - - -
140J LYS* 3.5 25.9 + - - +
141J ASN* 4.0 4.0 - - - +
144J THR* 3.5 26.2 + - - +
148J ARG* 4.2 16.8 + - - +
154J VAL* 3.6 7.6 + - + -
155J VAL* 1.3 70.4 - - - +
157J LEU* 1.3 61.8 + - - +
158J GLY* 2.9 34.1 + - - -
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Residues in contact with LEU 157 (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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133I ARG* 4.0 10.6 + - - -
127J VAL* 3.7 27.4 - - + -
128J CYS 2.9 18.6 + - - +
129J HIS* 3.9 12.8 - - + -
155J VAL* 3.4 24.2 + - + +
156J ASP* 1.3 71.8 - - - +
158J GLY* 1.3 57.3 + - - +
159J ARG 4.0 0.5 + - - -
161J VAL* 3.2 21.5 - - + +
165J GLU* 3.7 47.9 - - + +
166J VAL* 4.9 2.9 - - - -
169J ALA* 3.9 15.0 - - + -
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Residues in contact with GLY 158 (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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133I ARG* 4.7 1.6 - - - -
128J CYS 4.3 1.4 + - - -
130J VAL* 3.4 29.5 + - - +
137J ASP* 4.8 0.2 - - - -
140J LYS* 3.6 14.3 + - - +
156J ASP* 2.9 19.1 + - - -
157J LEU* 1.3 78.7 - - - +
159J ARG* 1.3 60.4 + - - -
161J VAL* 4.0 0.4 - - - -
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Residues in contact with ARG 159 (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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131I GLU* 3.1 27.9 + - - +
132I ASN 3.0 26.9 + - - -
133I ARG* 3.3 32.9 + - + +
134I GLU 4.2 12.2 + - - -
135I PHE* 5.0 1.6 + - - +
136I LEU* 6.1 0.4 - - - +
169I LYS* 5.2 4.0 - - - +
453I VAL* 6.3 0.2 - - - +
130J VAL* 2.8 33.9 - - + +
134J ASP 3.8 4.9 - - - +
135J VAL* 3.9 38.5 - - + +
137J ASP* 3.0 40.3 + - - +
158J GLY* 1.3 69.3 - - - +
160J ASP* 1.3 59.7 + - + +
161J VAL* 2.8 11.5 + - - +
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Residues in contact with ASP 160 (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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133I ARG* 3.4 38.3 + - + +
131J ALA 4.4 2.0 - - - -
132J GLU* 3.2 7.3 - - - +
133J GLY* 2.5 36.9 + - - -
134J ASP 3.8 13.0 + - - +
135J VAL* 5.2 6.7 - - + -
159J ARG* 1.3 74.3 - - + +
161J VAL* 1.3 57.6 + - - +
162J PRO* 3.6 8.2 - - - +
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Residues in contact with VAL 161 (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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133I ARG* 4.4 5.4 - - - +
129J HIS* 4.1 15.0 - - + -
130J VAL 3.5 11.8 + - - +
131J ALA 4.2 0.2 - - - -
132J GLU* 3.1 21.1 + - - +
157J LEU* 3.2 39.3 - - + +
158J GLY 4.0 1.6 - - - -
159J ARG 2.8 22.0 + - - +
160J ASP* 1.3 70.9 + - - +
162J PRO* 1.3 67.2 - - + +
163J ALA* 3.0 7.7 + - - +
165J GLU* 3.9 15.5 - - + -
166J VAL* 3.4 26.2 - - + +
190J ALA* 5.7 0.2 - - - +
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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