Contacts of the strand formed by residues 188 - 197 (chain F) in PDB entry 2JG8
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 GLU 188 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129F LYS* 3.2 36.8 + - + +
130F PHE 3.2 6.1 - - - +
131F THR* 4.0 17.1 + - + +
156F ARG* 3.4 1.0 - - - +
157F SER* 2.8 36.8 + - - +
186F GLY 4.0 9.2 - - - +
187F GLU* 1.3 76.4 - - - +
189F VAL* 1.3 66.6 + - - +
190F TRP* 3.8 19.2 - - + -
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Residues in contact with VAL 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F GLY 4.5 0.2 - - - +
129F LYS* 3.8 0.9 - - - -
130F PHE* 2.9 46.1 + - + +
140F PHE* 4.0 33.9 - - + -
154F LEU* 4.1 25.8 - - + -
155F TYR 3.2 13.0 - - - +
156F ARG* 4.2 14.6 - - + -
181F LEU* 4.6 1.6 - - + -
183F LEU* 4.1 15.9 - - + -
187F GLU 5.4 0.2 - - - -
188F GLU* 1.3 79.7 - - - +
190F TRP* 1.3 68.1 + - - +
209F PHE* 4.4 7.3 - - + -
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Residues in contact with TRP 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F LEU* 3.6 32.1 - - + +
128F GLY 3.7 20.4 - - - +
129F LYS* 4.1 18.4 - - + -
154F LEU* 3.5 3.5 - - - +
155F TYR* 2.7 75.4 + + + +
157F SER* 4.3 0.9 - - - -
158F GLY* 3.5 28.9 - - - -
188F GLU* 3.8 41.1 - - + -
189F VAL* 1.3 83.9 - - - +
191F LEU* 1.3 75.6 + - - +
192F ALA* 4.3 3.7 - - + +
209F PHE* 4.8 5.6 - - - -
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Residues in contact with LEU 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F LEU* 3.6 5.7 - - - +
110F ILE* 2.7 39.7 + - + +
112F PHE* 4.1 18.8 - - + -
128F GLY 5.1 0.4 + - - -
142F TYR* 3.6 39.9 - - + -
152F VAL* 4.0 16.8 - - + -
153F LEU 3.1 4.7 - - - +
154F LEU* 3.6 42.0 - - + -
190F TRP* 1.3 79.8 - - - +
192F ALA* 1.3 55.6 + - - +
209F PHE* 3.7 31.0 - - + -
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Residues in contact with ALA 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F ASN 5.9 0.4 - - - -
108F SER 3.3 18.4 - - - +
109F LEU* 4.2 2.9 - - - -
110F ILE* 3.7 8.0 - - - +
152F VAL* 3.4 6.1 - - - -
153F LEU* 2.7 32.6 + - + +
155F TYR* 3.8 30.3 - - + -
190F TRP* 4.3 4.0 - - + +
191F LEU* 1.3 75.9 - - - +
193F VAL* 1.3 63.9 + - - +
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Residues in contact with VAL 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F PRO* 3.8 15.3 - - + -
105F ALA 3.3 27.1 - - - +
107F ASN* 3.1 20.5 - - - +
108F SER 2.9 16.5 + - - +
110F ILE* 3.5 23.5 - - + +
150F LEU* 3.5 19.5 - - + -
151F CYS 3.4 18.4 - - - +
153F LEU* 4.1 6.4 - - - +
192F ALA* 1.3 75.7 - - - +
194F ASN* 1.3 59.8 + - - +
197F TYR* 3.7 24.2 - - + -
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Residues in contact with ASN 194 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210E GLY* 6.2 0.6 - - - -
106F PRO* 3.5 5.7 - - - +
107F ASN* 2.8 36.7 + - - +
151F CYS* 3.3 36.4 + - - +
153F LEU* 4.0 17.7 - - + +
163F THR* 4.9 3.2 - - - +
165F CYS* 4.8 1.4 - - - -
193F VAL* 1.3 75.0 - - - +
195F ASP* 1.3 67.0 + - - +
196F TYR* 2.8 32.4 + - - +
197F TYR* 4.1 3.8 - - - +
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Residues in contact with ASP 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F PRO* 4.7 5.3 - - - +
107F ASN* 2.7 31.3 + - - +
194F ASN* 1.3 81.9 + - - +
196F TYR* 1.3 70.1 + - + +
197F TYR* 3.2 21.7 - - - -
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Residues in contact with TYR 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F ASN* 3.6 43.9 + - + +
150F LEU* 3.6 0.2 - - - -
151F CYS* 3.0 49.8 + - - +
167F HIS* 3.4 34.9 - + - -
193F VAL* 3.9 2.3 - - - +
194F ASN* 2.8 15.6 + - - +
195F ASP* 1.3 87.0 - - + +
197F TYR* 1.3 58.3 + - - +
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Residues in contact with TYR 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F PRO* 4.1 18.8 - - + -
104F PRO* 3.2 44.2 - - - +
106F PRO* 3.6 33.4 - - + -
149F ASN 3.5 1.2 + - - -
150F LEU* 4.0 4.0 - - - -
193F VAL* 3.7 27.4 - - + -
194F ASN 4.1 0.2 - - - +
195F ASP 3.2 17.9 - - - -
196F TYR* 1.3 73.4 - - - +
198F ASP* 1.3 70.4 + - + +
199F MET* 3.9 0.3 - - - +
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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