Contacts of the strand formed by residues 189 - 199 (chain B) in PDB entry 6EZG
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 GLY 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107B LYS 5.2 0.5 - - - +
108B SER* 4.5 4.4 + - - -
109B THR 3.5 8.5 - - - -
111B VAL* 3.7 14.6 - - - -
142B VAL* 4.1 6.7 - - - +
184B ILE* 3.0 15.8 + - - -
185B GLN* 3.1 24.5 + - - +
187B PHE 3.4 1.4 - - - -
188B GLY* 1.3 80.4 - - - +
190B ASP* 1.3 60.5 + - - -
191B PRO* 3.2 4.9 - - - +
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Residues in contact with ASP 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B SER* 3.3 28.0 + - - +
109B THR 2.9 19.1 + - - +
111B VAL* 3.8 2.4 - - - +
184B ILE* 4.3 1.8 - - - -
189B GLY* 1.3 69.1 - - - -
191B PRO* 1.3 65.2 - - - +
192B LYS* 2.6 43.3 + - - +
193B THR* 2.8 49.3 + - - +
194B VAL* 3.7 4.2 - - - +
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Residues in contact with PRO 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B SER* 5.5 0.4 - - - +
181B HIS* 3.6 46.1 + - + +
184B ILE* 3.8 13.4 - - + -
185B GLN* 4.2 22.0 - - + +
189B GLY 3.2 11.7 - - - +
190B ASP* 1.3 86.5 - - - +
192B LYS* 1.3 64.7 + - + +
193B THR 3.4 0.4 - - - -
194B VAL* 3.9 20.3 + - + +
218B LEU 5.7 2.4 - - - +
219B PHE* 5.7 2.8 - - - -
220B ARG 5.9 0.3 + - - -
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Residues in contact with LYS 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B ASP* 2.6 27.7 + - - +
191B PRO* 1.3 79.2 - - + +
193B THR* 1.3 58.3 + - - +
194B VAL 3.7 1.1 - - - -
220B ARG* 3.1 33.4 + - - +
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Residues in contact with THR 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B THR* 3.9 16.0 - - - +
111B VAL 3.0 24.6 + - - +
190B ASP* 2.8 31.9 + - - +
192B LYS* 1.3 81.2 + - - +
194B VAL* 1.3 58.5 + - - +
220B ARG* 3.9 12.5 + - + +
221B ARG* 3.8 15.0 - - - +
477B ALA 3.5 22.9 - - - +
478B LYS 4.2 8.3 - - - +
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Residues in contact with VAL 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B VAL* 3.3 16.8 - - + +
113B VAL* 3.7 29.4 - - + -
177B LEU* 5.4 1.6 - - + -
180B VAL* 4.2 16.2 - - + -
181B HIS* 5.9 1.1 - - - +
190B ASP 3.7 15.7 - - - +
191B PRO* 3.9 19.1 - - + +
192B LYS 3.7 1.8 - - - -
193B THR* 1.3 74.8 - - - +
195B THR* 1.3 67.0 + - - +
196B ILE* 4.6 2.7 - - + +
218B LEU 4.6 6.5 - - - +
219B PHE* 3.7 21.1 - - + +
220B ARG* 2.8 31.6 + - - +
221B ARG 3.3 5.0 + - - -
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Residues in contact with THR 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B VAL 2.7 14.2 + - - -
112B MET* 3.1 8.1 - - + +
113B VAL* 2.7 33.3 + - - +
193B THR* 3.9 0.4 + - - +
194B VAL* 1.3 74.9 - - - +
196B ILE* 1.3 69.7 + - - +
197B PHE* 3.9 2.1 + - + +
220B ARG* 5.6 0.3 - - - +
221B ARG* 3.4 22.3 + - - +
222B ALA 4.4 0.4 - - - +
223B ILE* 3.9 28.3 - - + -
476B PHE* 4.7 2.2 - - + -
477B ALA* 3.3 38.0 + - + +
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Residues in contact with ILE 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B VAL* 3.4 12.3 - - + +
115B ILE* 4.7 5.4 - - + -
177B LEU* 3.6 32.8 - - + -
194B VAL* 4.0 2.8 + - + -
195B THR* 1.3 75.0 - - - +
197B PHE* 1.3 60.2 + - - +
206B VAL* 3.9 29.9 - - + +
209B HIS* 4.1 17.7 - - + -
219B PHE* 3.7 46.4 - - + -
221B ARG 3.1 12.6 + - - +
222B ALA* 3.3 1.0 - - - -
223B ILE 2.9 24.3 + - - +
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Residues in contact with PHE 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B MET* 3.6 34.3 - - + -
113B VAL 2.8 39.8 + - - +
114B TRP* 3.2 42.3 - + + -
115B ILE* 2.9 23.6 + - - +
135B LEU* 4.4 3.8 - - + -
143B LEU* 3.6 21.1 - - + -
195B THR* 4.2 1.6 - - + -
196B ILE* 1.3 75.4 - - - +
198B GLY* 1.3 58.9 + - - +
206B VAL* 3.9 5.6 - - - -
223B ILE* 3.2 31.9 - - + -
225B GLN* 3.8 10.1 - - - -
447B VAL* 4.1 18.4 - - + -
448B PHE* 4.2 8.1 - + - -
473B TRP* 4.1 8.5 - + - -
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Residues in contact with GLY 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B TRP* 3.4 10.6 - - - -
115B ILE* 3.2 17.0 - - - -
197B PHE* 1.3 77.1 - - - +
199B GLU* 1.3 58.5 + - - -
202B GLY 3.7 8.1 - - - -
203B GLY* 3.2 15.4 - - - -
206B VAL* 3.9 2.4 - - - +
223B ILE 3.4 5.1 + - - +
225B GLN* 3.0 26.1 + - - +
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Residues in contact with GLU 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B TRP* 3.5 22.3 - - + -
115B ILE 3.7 3.0 + - - -
117B GLY* 3.1 12.0 + - - -
130B TYR* 5.2 0.2 + - - -
198B GLY* 1.3 73.7 - - - -
200B SER* 1.3 68.9 + - - +
202B GLY 2.8 19.6 + - - -
203B GLY 3.4 2.6 - - - +
225B GLN* 3.1 17.0 - - + +
226B SER* 4.0 2.9 - - - -
440B HIS* 3.5 25.1 + - - -
441B GLY* 3.5 18.0 + - - -
443B GLU* 3.3 22.4 - - - +
444B ILE* 3.7 18.8 - - + +
603B C6K 3.4 16.0 - - - -
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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