Contacts of the strand formed by residues 170 - 174 (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 ILE 170 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LYS* 6.3 3.1 - - - -
156A ILE* 3.1 24.5 - - - -
157A SER* 3.0 16.0 + - - +
168A ASN 4.8 2.0 - - - +
169A SER* 1.3 72.7 - - - +
171A PHE* 1.3 68.8 + - - +
172A HIS* 3.7 29.1 + - + +
159B LYS* 5.2 16.8 - - + +
160B LEU 5.0 3.1 - - - +
161B GLY* 3.6 12.6 - - - +
162B LYS* 3.6 26.2 - - + +
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Residues in contact with PHE 171 (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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112A LEU* 4.3 11.7 - - + -
132A THR* 3.9 11.7 - - + -
134A TYR* 3.7 39.5 - + - -
154A HIS* 4.0 9.9 - + + -
155A LEU 3.9 3.6 - - - -
156A ILE* 3.7 21.5 - - + -
166A VAL* 4.4 10.5 - - - -
169A SER* 4.5 8.1 - - - -
170A ILE* 1.3 78.8 - - - +
172A HIS* 1.3 62.0 + - - +
173A MET 3.7 0.4 - - - -
204A LYS* 4.9 1.6 + - - -
95B LEU* 3.6 20.3 - - + +
97B ILE* 4.5 4.5 - - + -
102B PHE* 4.2 16.8 - + - -
161B GLY* 2.8 38.5 + - - +
163B ILE* 3.8 30.5 - - + -
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Residues in contact with HIS 172 (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* 4.8 2.2 - - - -
129A PHE* 4.2 5.4 - + - -
155A LEU* 2.9 34.7 + - + +
156A ILE 3.9 2.7 - - - -
157A SER* 2.8 35.0 + - - -
170A ILE* 3.8 28.8 + - + +
171A PHE* 1.3 74.2 - - - +
173A MET* 1.3 65.4 + - + +
189A TYR* 3.4 53.3 - + + -
204A LYS* 3.0 31.9 + - + +
209A TYR* 3.0 9.4 + - - -
95B LEU* 4.1 2.7 - - - +
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Residues in contact with MET 173 (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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154A HIS* 3.4 7.9 - - - +
155A LEU* 2.9 34.0 + - + -
171A PHE 3.7 1.0 - - - -
172A HIS* 1.3 83.5 - - - +
174A ALA* 1.4 67.4 + - - +
175A ALA* 4.3 2.2 - - + -
189A TYR* 3.5 45.1 - - + +
190A ILE 4.1 0.2 - - - -
191A GLY* 3.5 29.2 - - - +
202A LYS* 3.8 29.2 - - - +
203A ILE 4.8 0.2 - - - -
204A LYS* 3.8 17.7 - - + +
209A TYR* 4.1 9.4 - - + -
94B ALA 3.3 13.5 - - - +
95B LEU* 4.0 5.0 - - - +
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Residues in contact with ALA 174 (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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151A LYS 5.3 1.3 - - - +
153A ARG 3.6 8.3 - - - +
154A HIS* 3.5 23.8 - - + +
173A MET* 1.4 70.9 - - - +
175A ALA* 1.3 61.5 + - - +
193A ASP* 3.7 18.3 - - + +
202A LYS* 2.8 31.7 + - - +
93B LYS* 4.1 20.0 - - + +
94B ALA 2.9 18.1 + - - +
95B LEU* 4.7 0.7 - - - +
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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