Contacts of the strand formed by residues 187 - 193 (chain A) in PDB entry 1NSC
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 TRP 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A ALA* 3.5 45.5 - - + -
122A GLY* 4.2 10.8 - - - -
125A GLU* 4.4 12.8 + - + -
126A CYS 5.1 0.2 - - - -
127A LYS* 3.1 43.0 - - + +
129A PHE* 4.0 18.2 - + - -
180A ALA* 4.6 1.6 - - + -
181A CYS* 3.6 28.9 - - - -
182A HIS* 3.3 28.6 + + + -
186A GLU* 1.3 89.9 + - - +
188A THR* 1.3 59.2 + - - +
189A TYR* 3.4 24.6 - - + +
204A LYS 4.0 0.2 - - - +
205A TYR* 3.5 2.8 - - - -
206A GLY 2.9 28.1 + - - -
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Residues in contact with THR 188 (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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180A ALA* 3.2 7.6 - - - +
181A CYS* 2.9 42.4 + - - -
183A ASP* 4.7 0.7 + - - -
186A GLU 4.9 0.3 + - - -
187A TRP* 1.3 72.6 - - - +
189A TYR* 1.3 64.6 + - - +
190A ILE* 3.7 20.6 - - + -
203A ILE* 3.9 17.9 - - + -
204A LYS 3.4 10.5 - - - +
205A TYR* 3.3 24.4 - - + -
235A CYS* 4.6 12.1 - - + -
255A ILE* 4.5 15.3 - - + +
257A GLU 5.7 0.2 + - - -
258A GLY 4.7 1.9 + - - -
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Residues in contact with TYR 189 (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 LYS* 2.9 24.6 + - - -
129A PHE* 3.6 33.7 - + - -
155A LEU* 4.2 8.5 - - + -
172A HIS* 3.4 38.6 - + + -
173A MET* 3.5 17.8 - - + +
179A SER 3.9 2.7 - - - -
180A ALA* 4.2 0.4 - - + -
186A GLU* 5.2 0.3 + - - -
187A TRP* 3.4 30.0 - - + +
188A THR* 1.3 79.3 - - - +
190A ILE* 1.3 62.7 + - - +
203A ILE* 3.4 4.5 - - - +
204A LYS* 2.9 45.4 + - + -
206A GLY* 3.5 27.5 - - - -
207A GLU* 5.9 0.7 - - - -
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Residues in contact with ILE 190 (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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155A LEU* 3.9 6.7 - - - +
173A MET* 4.1 3.1 - - - -
178A GLY* 3.2 4.5 - - - -
179A SER* 2.9 44.8 + - - +
188A THR* 3.7 19.5 - - + +
189A TYR* 1.3 77.4 - - - +
191A GLY* 1.3 60.5 + - - +
201A ILE* 4.0 18.8 - - + -
202A LYS 3.4 7.6 - - - +
203A ILE* 4.2 14.8 - - + -
223A THR* 4.3 15.9 - - + -
228A CYS* 3.6 30.5 - - - -
237A LEU* 3.9 30.1 - - + -
255A ILE* 4.5 5.4 - - + -
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Residues in contact with GLY 191 (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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155A LEU* 5.3 0.2 - - - -
173A MET* 3.5 17.2 - - - -
175A ALA* 3.6 11.9 - - - -
177A SER 3.3 8.1 - - - -
190A ILE* 1.3 76.5 - - - +
192A VAL* 1.3 64.2 + - - -
200A LEU 3.5 0.5 - - - +
201A ILE* 3.6 1.2 - - - -
202A LYS* 2.8 39.7 + - - +
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Residues in contact with VAL 192 (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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175A ALA* 3.3 2.1 - - - +
176A TRP* 2.8 39.6 + - + -
177A SER* 2.9 26.4 + - - +
191A GLY* 1.3 76.0 - - - -
193A ASP* 1.3 63.5 + - - +
199A ALA* 3.9 0.9 - - + -
200A LEU 3.1 23.1 - - - +
201A ILE* 3.3 31.4 - - + +
221A LEU* 3.2 25.8 - - + +
222A ARG* 4.2 5.4 - - - -
223A THR* 4.1 13.0 - - + -
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Residues in contact with ASP 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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174A ALA* 3.7 19.2 - - + +
175A ALA* 4.3 3.6 - - - +
176A TRP* 3.6 22.4 - - + +
191A GLY 4.2 0.4 + - - -
192A VAL* 1.3 75.1 - - - +
194A GLY* 1.3 64.2 + - - +
199A ALA* 3.4 1.2 - - - +
200A LEU* 2.8 35.2 + - - +
202A LYS* 2.8 39.4 + - - +
93B LYS* 3.8 20.2 + - - +
455B TRP* 4.0 11.8 - - + +
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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