Contacts of the strand formed by residues 109 - 115 (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 THR 109 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106X PRO* 3.6 33.2 - - + -
108X SER* 1.3 76.2 - - - +
110X THR* 1.3 72.9 + - - +
140X GLU* 3.0 25.3 + - - +
141X VAL* 4.5 0.2 - - - -
142X VAL* 3.6 22.4 - - + +
188X GLY 2.8 9.1 + - - +
189X GLY* 3.6 1.6 - - - -
190X ASP* 2.9 26.6 + - - +
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Residues in contact with THR 110 (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 4.3 0.2 + - - -
109X THR* 1.3 78.0 + - - +
111X VAL* 1.3 65.3 + - - +
112X MET* 4.7 0.4 - - + -
141X VAL* 3.3 23.8 - - + +
142X VAL 3.0 22.7 + - - -
193X THR* 3.8 21.9 - - + +
477X ALA* 3.8 37.2 - - + +
478X LYS* 3.0 33.7 - - + +
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Residues in contact with VAL 111 (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* 1.3 76.9 - - - +
112X MET* 1.3 67.1 + - - +
113X VAL* 4.1 12.6 - - + -
142X VAL* 3.3 13.5 - - + +
144X VAL* 4.1 22.2 - - + -
180X VAL* 4.4 3.6 - - + -
184X ILE* 4.0 17.3 - - + -
189X GLY* 3.5 14.1 - - - -
190X ASP 3.5 35.7 - - - +
193X THR 3.3 6.8 + - - +
194X VAL* 4.1 13.9 - - + -
195X THR 2.9 24.8 + - - -
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Residues in contact with MET 112 (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* 4.7 0.4 - - + -
111X VAL* 1.3 79.7 - - - +
113X VAL* 1.3 61.5 + - - +
114X TRP 4.1 0.2 - - - -
135X LEU* 4.6 11.4 - - + -
141X VAL* 4.1 29.8 - - + -
142X VAL 3.0 7.9 + - - +
143X LEU* 3.6 10.9 - - + +
144X VAL* 2.8 28.6 + - - +
195X THR* 3.4 7.9 - - + +
197X PHE* 3.8 34.3 - - + -
223X ILE* 4.4 8.5 - - + -
473X TRP* 4.1 32.5 - - + +
474X ALA* 4.4 8.3 - - - -
477X ALA* 4.0 21.5 - - + -
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Residues in contact with VAL 113 (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* 4.1 10.5 - - + -
112X MET* 1.3 76.1 - - - +
114X TRP* 1.3 60.5 + - - +
115X ILE* 3.8 1.5 + - + +
144X VAL* 3.2 32.1 - - + +
146X LEU* 3.5 35.0 - - + -
177X LEU* 3.8 11.9 - - + -
180X VAL* 4.3 13.5 - - + -
194X VAL* 4.2 14.8 - - + -
195X THR 2.9 9.9 + - - -
196X ILE* 3.5 14.1 - - + +
197X PHE* 3.0 28.0 + - - +
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Residues in contact with TRP 114 (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* 1.3 70.8 - - - +
115X ILE* 1.3 66.8 + - - +
116X TYR* 3.7 17.2 + + + +
117X GLY 5.1 0.2 - - - -
125X SER* 5.7 0.7 - - - -
130X TYR* 3.5 50.1 - + + -
143X LEU* 5.0 1.8 - - + -
144X VAL 2.7 15.8 + - - +
145X SER* 3.5 18.0 - - - -
146X LEU* 3.2 28.3 + - - +
197X PHE* 3.3 62.5 - + + -
198X GLY* 3.5 12.3 - - - -
199X GLU* 3.7 29.8 - - + -
225X GLN* 3.9 14.6 - - - -
444X ILE* 4.2 9.0 - - + -
448X PHE* 3.5 27.1 - + + -
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Residues in contact with ILE 115 (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 4.2 6.1 - - - +
114X TRP* 1.3 77.7 - - - +
116X TYR* 1.3 67.5 + - - +
117X GLY 3.7 0.2 + - - -
146X LEU* 3.9 26.7 - - + -
148X TYR* 3.8 9.4 - - + -
173X GLN* 3.6 40.8 - - + +
177X LEU* 5.3 1.6 - - + -
196X ILE* 4.5 13.2 - - + -
197X PHE 2.8 14.2 + - - +
198X GLY* 3.2 20.8 - - - -
199X GLU 3.8 0.7 + - - -
202X GLY* 3.3 9.5 - - - +
205X SER* 4.2 8.7 - - - -
206X VAL* 4.2 18.2 - - + -
209X HIS* 4.4 14.4 - - + +
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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