Contacts of the strand formed by residues 192 - 202 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123D GLN* 5.7 0.4 - - - +
128D ARG* 3.4 33.8 + - + +
129D PHE 3.0 7.2 - - - +
130D VAL* 3.9 24.6 - - + +
155D SER* 3.1 5.0 - - - -
156D SER* 2.9 44.4 + - - +
190D GLY 3.5 11.1 + - - +
191D ASP* 1.3 76.3 - - - +
193D VAL* 1.3 66.4 + - - +
194D TRP* 4.0 9.4 - - + -
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Residues in contact with VAL 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D GLY 4.1 0.5 - - - +
128D ARG* 3.6 0.2 - - - -
129D PHE* 2.8 42.2 + - + +
139D PHE* 4.0 27.4 - - + -
153D ILE* 3.9 21.3 - - + -
154D VAL 3.3 11.0 - - - +
155D SER* 4.0 5.8 - - - -
185D LEU* 4.0 8.5 - - + -
187D LEU* 3.6 40.8 - - + -
192D GLN* 1.3 82.4 - - - +
194D TRP* 1.3 66.6 + - - +
214D PHE* 4.3 6.0 - - + -
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Residues in contact with TRP 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D VAL* 3.4 23.9 - - + +
127D GLY 3.3 20.9 - - - +
128D ARG* 3.3 49.1 - - + -
153D ILE* 3.6 3.8 - - - +
154D VAL* 2.8 55.7 + - + +
155D SER 3.8 17.0 - - - -
156D SER* 3.8 19.1 - - - -
161D VAL* 4.2 16.6 - - + -
192D GLN* 3.7 16.4 - - + -
193D VAL* 1.3 83.7 - - - +
195D VAL* 1.3 72.9 + - - +
196D GLU* 2.5 33.8 + - + -
214D PHE* 4.3 6.5 - - - -
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Residues in contact with VAL 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D VAL* 3.5 5.5 - - - +
109D VAL* 2.9 49.9 + - + -
111D PHE* 4.2 10.3 - - + -
127D GLY 4.6 1.6 + - - -
141D PHE* 4.3 18.8 - - + -
151D LEU* 4.1 28.3 - - + -
152D SER 3.5 8.1 - - - +
153D ILE* 4.5 4.3 - - + -
194D TRP* 1.3 78.8 - - - +
196D GLU* 1.3 62.9 + - - +
214D PHE* 3.7 40.8 - - + -
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Residues in contact with GLU 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C GLN* 3.6 10.0 + - - +
107D ASN* 3.2 33.0 + - + +
108D VAL* 3.8 7.0 - - + +
109D VAL* 4.2 0.4 - - - -
128D ARG* 5.2 0.2 + - - -
151D LEU* 3.4 7.0 - - - +
152D SER* 2.9 33.9 + - - +
154D VAL* 4.0 13.9 - - + +
163D ARG* 2.7 35.8 + - - -
194D TRP* 2.5 39.9 + - + +
195D VAL* 1.3 73.1 - - - +
197D LYS* 1.3 62.3 + - - +
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Residues in contact with LYS 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C GLN* 5.7 3.2 + - - -
99D ARG* 6.3 1.8 - - - +
104D MET* 6.0 6.3 - - - -
106D GLY 3.4 18.2 + - - -
107D ASN* 2.7 47.4 + - - +
108D VAL 5.4 2.2 - - - -
109D VAL* 4.0 6.6 - - + +
149D ILE* 4.2 7.0 - - + -
150D CYS 3.4 6.3 - - - +
151D LEU* 3.7 17.0 - - + -
196D GLU* 1.3 76.5 - - - +
198D ASP* 1.3 66.0 + - - +
199D PRO* 3.5 12.7 + - - +
202D GLY* 3.7 26.5 - - - +
204D ILE* 4.4 12.3 - - + -
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Residues in contact with ASP 198 (chain D).
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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101C HIS* 4.4 18.2 + - - -
102C GLN* 6.5 1.1 - - - -
150D CYS* 3.0 33.0 + - + +
197D LYS* 1.3 74.2 - - - +
199D PRO* 1.3 68.5 - - - +
200D LYS* 2.5 44.3 + - - +
201D LYS* 2.8 37.5 + - - +
202D GLY* 3.6 4.5 + - - -
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Residues in contact with PRO 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C GLN* 5.9 5.8 - - - +
107D ASN* 3.9 30.1 - - - +
197D LYS* 3.5 12.1 + - - +
198D ASP* 1.3 90.0 - - - +
200D LYS* 1.3 83.1 + - + +
201D LYS 3.7 0.2 + - - -
202D GLY* 5.1 2.5 + - - -
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Residues in contact with LYS 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D GLU* 4.8 3.5 - - - +
198D ASP* 2.5 21.4 + - - +
199D PRO* 1.3 93.8 + - + +
201D LYS* 1.3 72.6 + - + +
202D GLY 4.0 1.1 - - - -
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Residues in contact with LYS 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D GLU* 3.5 41.0 + - + +
149D ILE* 3.4 3.3 - - - +
150D CYS* 2.9 59.0 + - + +
170D THR* 4.1 20.9 - - + -
198D ASP* 2.8 17.6 + - - +
199D PRO 3.3 0.4 - - - -
200D LYS* 1.3 95.8 + - + +
202D GLY* 1.3 59.2 + - - +
202F ILE* 4.3 11.0 - - - -
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Residues in contact with GLY 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D GLU 3.3 1.0 + - - -
149D ILE* 3.8 8.1 - - - -
197D LYS* 3.7 28.7 - - - +
198D ASP 3.8 8.3 - - - -
199D PRO 5.1 2.4 + - - -
200D LYS 4.0 0.6 - - - -
201D LYS* 1.3 77.5 - - - +
203D HIS* 1.3 65.2 + - - +
204D ILE* 3.1 6.8 + - - +
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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