Contacts of the strand formed by residues 192 - 202 (chain A) 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 GLN 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A GLN* 5.1 6.0 + - - +
128A ARG* 3.5 33.9 + - + -
129A PHE 3.1 10.3 - - - +
130A VAL* 4.0 23.3 - - + +
155A SER* 3.1 5.0 - - - -
156A SER* 2.9 44.0 + - - +
190A GLY 3.4 13.7 + - - +
191A ASP* 1.3 72.8 - - - +
193A VAL* 1.3 67.0 + - - +
194A TRP* 4.0 9.6 - - + -
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Residues in contact with VAL 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A GLY 4.0 0.7 - - - +
128A ARG* 3.6 0.3 - - - -
129A PHE* 2.7 47.6 + - + +
139A PHE* 3.8 35.9 - - + -
153A ILE* 4.0 19.1 - - + -
154A VAL 3.4 10.1 - - - +
155A SER* 4.2 5.2 - - - -
185A LEU* 4.1 2.9 - - + -
187A LEU* 3.6 39.5 - - + -
192A GLN* 1.3 81.6 - - - +
194A TRP* 1.3 66.7 + - - +
214A PHE* 4.5 6.2 - - + -
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Residues in contact with TRP 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A VAL* 3.4 24.3 - - + +
127A GLY 3.4 19.1 - - - +
128A ARG* 3.6 46.7 - - + -
153A ILE* 3.6 3.7 - - - +
154A VAL* 2.8 56.2 + - + +
155A SER 3.8 10.5 - - - -
156A SER* 3.8 26.0 - - - -
161A VAL* 4.2 15.3 - - + -
192A GLN* 3.8 17.0 - - + -
193A VAL* 1.3 86.8 - - - +
195A VAL* 1.3 70.9 + - - +
196A GLU* 2.8 31.7 + - + +
214A PHE* 4.3 7.2 - - - -
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Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A VAL* 3.4 5.4 - - - +
109A VAL* 2.7 54.0 + - + -
111A PHE* 3.9 11.7 - - + -
127A GLY 4.5 1.8 + - - -
141A PHE* 4.6 17.0 - - + -
151A LEU* 4.1 27.1 - - + -
152A SER 3.5 9.2 - - - +
153A ILE* 4.8 2.5 - - + -
194A TRP* 1.3 78.6 - - - +
196A GLU* 1.3 57.6 + - - +
214A PHE* 3.7 44.3 - - + -
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Residues in contact with GLU 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ASN* 3.1 30.7 + - + +
108A VAL* 3.8 7.4 - - + +
128A ARG* 5.2 0.3 + - - -
151A LEU* 3.4 6.6 - - - -
152A SER* 2.8 38.3 + - - -
154A VAL* 3.7 15.0 - - + -
163A ARG* 2.9 32.1 + - - -
194A TRP* 2.8 38.8 + - + +
195A VAL* 1.3 71.9 - - - +
197A LYS* 1.3 62.0 + - - +
102F GLN* 3.6 11.3 + - - +
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Residues in contact with LYS 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ARG* 6.2 0.9 - - - +
104A MET* 4.6 23.0 - - - +
106A GLY 3.3 24.8 + - - -
107A ASN* 2.7 46.9 + - - +
108A VAL 5.3 1.8 - - - -
109A VAL* 4.0 6.8 - - + +
150A CYS 3.3 6.7 - - - +
151A LEU* 3.7 16.8 - - + -
196A GLU* 1.3 76.5 - - - +
198A ASP* 1.3 70.4 + - - +
199A PRO* 3.5 8.6 + - - +
202A GLY* 3.8 32.3 + - - +
204A ILE* 4.3 13.2 - - + -
102F GLN* 5.4 4.3 + - - -
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Residues in contact with ASP 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A CYS* 2.9 27.7 + - + +
197A LYS* 1.3 73.1 + - - +
199A PRO* 1.3 75.3 - - - +
200A LYS* 2.8 32.1 + - - +
201A LYS* 3.0 52.7 + - - +
202A GLY* 3.4 5.7 + - - -
101F HIS* 5.1 10.5 - - - -
102F GLN* 6.6 0.2 - - - -
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Residues in contact with PRO 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ASN* 4.0 29.8 - - - +
197A LYS* 3.5 13.2 + - - +
198A ASP* 1.3 89.4 - - - +
200A LYS* 1.3 66.8 + - + +
202A GLY* 5.1 1.4 + - - -
102F GLN* 5.6 7.4 - - - +
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Residues in contact with LYS 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A GLU* 4.5 5.2 - - - +
198A ASP* 2.8 13.1 + - - +
199A PRO* 1.3 85.8 - - + +
201A LYS* 1.3 72.5 + - + +
202A GLY 4.0 1.1 - - - -
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Residues in contact with LYS 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A GLU* 3.6 42.0 + - + +
150A CYS* 2.9 51.7 + - - +
170A THR* 4.1 19.7 - - + -
198A ASP* 3.0 27.6 + - + +
200A LYS* 1.3 89.3 + - - +
202A GLY* 1.3 56.2 + - - +
202C ILE* 4.4 9.2 - - - -
203C GLN 5.9 0.7 - - - -
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Residues in contact with GLY 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A MET* 6.0 0.9 - - - +
148A GLU 3.4 0.6 + - - -
149A ILE* 4.7 4.0 - - - -
197A LYS* 3.8 32.5 + - - +
198A ASP 3.4 8.7 + - - -
199A PRO 5.1 1.5 + - - -
200A LYS 4.0 1.4 - - - -
201A LYS* 1.3 75.1 - - - +
203A HIS* 1.3 63.8 + - - +
204A ILE* 3.5 6.7 + - - +
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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