Contacts of the strand formed by residues 189 - 199 (chain X) in PDB entry 2W6C
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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107X LYS 4.4 3.3 - - - +
108X SER* 4.5 1.5 + - - -
109X THR 3.6 3.1 - - - -
111X VAL* 3.5 19.3 - - - -
142X VAL* 4.0 8.3 - - - +
184X ILE* 3.1 18.6 + - - +
185X GLN* 3.3 22.2 - - - +
187X PHE 3.3 4.2 + - - -
188X GLY* 1.3 80.3 - - - +
190X ASP* 1.3 59.8 + - - -
191X PRO* 3.9 1.7 - - - +
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Residues in contact with ASP 190 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108X SER* 3.5 28.3 + - - +
109X THR 2.9 21.1 + - - +
111X VAL* 3.5 6.6 - - - +
189X GLY* 1.3 69.9 - - - -
191X PRO* 1.3 65.5 - - - +
192X LYS* 2.6 49.9 + - - +
193X THR* 2.9 40.6 + - - -
194X VAL 4.1 0.5 + - - -
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Residues in contact with PRO 191 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108X SER* 5.5 0.7 - - - +
181X HIS* 3.4 43.1 - - + +
184X ILE* 3.9 18.8 - - + -
185X GLN* 4.5 21.3 - - + +
189X GLY 3.9 7.4 - - - +
190X ASP* 1.3 85.8 - - - +
192X LYS* 1.3 67.8 + - + +
193X THR 3.2 1.6 - - - -
194X VAL* 3.4 19.2 - - + +
218X LEU 6.1 0.3 - - - -
219X PHE* 5.8 0.9 - - - -
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Residues in contact with LYS 192 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108X SER* 4.8 4.6 + - - -
190X ASP* 2.6 39.2 + - - +
191X PRO* 1.3 85.1 - - + +
193X THR* 1.3 52.2 + - - +
194X VAL 3.8 1.3 - - - -
220X ARG* 2.6 45.7 + - - +
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Residues in contact with THR 193 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110X THR* 3.8 20.7 - - + +
111X VAL 3.3 19.6 + - - +
190X ASP* 2.9 32.3 + - - -
192X LYS* 1.3 83.8 + - - +
194X VAL* 1.3 61.3 + - - +
195X THR 3.7 0.9 + - - -
220X ARG* 4.0 12.9 + - + +
221X ARG* 4.2 7.0 - - - +
477X ALA 3.6 22.6 - - - +
478X LYS 4.1 11.2 - - - +
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Residues in contact with VAL 194 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111X VAL* 3.3 18.8 - - + +
113X VAL* 4.2 20.4 - - + -
177X LEU* 5.1 2.0 - - + -
180X VAL* 4.6 13.7 - - + -
181X HIS* 5.7 2.5 - - - -
190X ASP 4.2 1.1 - - - +
191X PRO* 3.4 31.6 - - + +
192X LYS 3.8 1.4 - - - -
193X THR* 1.3 74.7 - - - +
195X THR* 1.3 63.6 + - - +
196X ILE* 4.3 3.4 - - + -
218X LEU 4.4 6.5 - - - +
219X PHE* 3.7 25.7 - - + +
220X ARG* 2.7 35.0 + - - +
221X ARG 3.4 2.1 + - - +
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Residues in contact with THR 195 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111X VAL 2.9 9.4 + - - -
112X MET* 3.4 7.2 - - + +
113X VAL* 2.9 24.6 + - - +
193X THR 3.7 0.4 + - - -
194X VAL* 1.3 72.1 - - - +
196X ILE* 1.3 76.9 + - - +
197X PHE* 3.9 2.7 + - + +
221X ARG* 3.3 23.2 + - + +
222X ALA 4.3 0.2 - - - +
223X ILE* 4.0 27.6 - - + -
476X PHE* 4.6 1.3 - - + -
477X ALA* 3.0 42.1 + - + +
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Residues in contact with ILE 196 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113X VAL* 3.5 13.0 - - + +
115X ILE* 4.5 6.1 - - + -
177X LEU* 3.5 31.9 - - + -
194X VAL* 4.0 2.1 + - + -
195X THR* 1.3 76.3 - - - +
197X PHE* 1.3 60.8 + - - +
206X VAL* 3.8 36.1 - - + +
209X HIS* 4.2 13.7 - - + -
219X PHE* 3.8 52.9 - - + -
221X ARG 3.0 6.2 + - - +
222X ALA* 3.3 1.4 - - - +
223X ILE 2.9 24.1 + - - +
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Residues in contact with PHE 197 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112X MET* 3.8 32.1 - - + -
113X VAL 3.0 21.2 + - - -
114X TRP* 3.3 58.2 - + + -
115X ILE* 2.8 24.3 + - - +
135X LEU* 4.4 2.9 - - + -
143X LEU* 4.1 14.4 - - + -
195X THR* 4.4 1.1 - - + -
196X ILE* 1.3 75.3 - - - +
198X GLY* 1.3 59.5 + - - +
206X VAL* 3.9 6.2 - - - +
223X ILE* 3.2 30.7 - - + -
225X GLN* 3.6 14.4 - - - -
447X VAL* 3.9 20.6 - - + -
448X PHE* 4.0 10.5 - + - -
473X TRP* 4.0 12.6 - + - -
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Residues in contact with GLY 198 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114X TRP* 3.5 11.6 - - - -
115X ILE 3.2 16.4 - - - -
197X PHE* 1.3 77.6 - - - +
199X GLU* 1.3 58.7 + - - -
202X GLY 3.8 7.4 - - - -
203X GLY* 3.2 12.7 - - - -
206X VAL* 3.8 2.6 - - - +
223X ILE 3.4 4.9 + - - -
225X GLN* 2.9 27.9 + - - +
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Residues in contact with GLU 199 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114X TRP* 3.7 12.8 - - + -
115X ILE 3.8 2.8 + - - -
117X GLY* 3.0 7.8 - - - -
198X GLY* 1.3 73.9 - - - -
200X SER* 1.3 104.4 + - - +
202X GLY 3.0 8.8 + - - -
203X GLY 3.3 0.6 - - - +
225X GLN* 3.1 14.4 - - - +
226X SER* 4.3 2.6 - - - -
440X HIS* 3.5 17.2 + - - -
441X GLY* 3.5 18.6 + - - -
443X GLU* 3.2 23.1 - - - +
444X ILE* 3.7 25.6 - - + +
601X BM4 3.5 17.3 - - - +
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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