Contacts of the strand formed by residues 164 - 174 (chain A) in PDB entry 1NQF
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 164 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A GLN* 2.7 13.3 - - - +
160A LEU* 2.4 42.7 + - + +
161A GLY* 4.4 3.5 - - - -
163A LYS* 1.3 77.8 - - - +
165A ARG* 1.3 71.4 + - - +
206A LEU* 4.3 20.4 - - + -
207A GLU 3.0 11.0 - - - +
208A HIS* 2.7 31.8 - - + +
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Residues in contact with ARG 165 (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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132A THR* 4.4 5.1 - - - +
133A ARG 3.3 13.9 + - - -
134A ASP* 4.6 12.8 + - - +
157A GLN* 2.7 46.2 + - + +
158A GLN 4.5 1.1 - - - -
159A GLN* 4.0 34.1 - - + +
163A LYS 5.9 0.9 - - - -
164A THR* 1.3 76.8 - - - +
166A VAL* 1.3 65.5 + - - +
167A THR* 4.3 1.0 + - - -
206A LEU* 3.2 5.4 - - - +
207A GLU* 2.6 93.0 + - + +
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Residues in contact with VAL 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A THR* 3.9 0.9 - - - +
157A GLN* 3.2 3.1 - - - +
158A GLN 3.0 30.1 + - - +
160A LEU* 2.4 46.9 - - + -
164A THR* 4.7 0.4 - - + -
165A ARG* 1.3 79.5 - - - +
167A THR* 1.3 68.8 + - - +
168A LEU* 4.2 23.3 + - + +
205A ALA 3.2 6.5 - - - +
206A LEU* 3.3 25.8 - - + -
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Residues in contact with THR 167 (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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133A ARG* 4.1 27.3 - - + +
155A SER* 4.5 1.3 - - - +
156A THR 2.8 20.4 - - - +
157A GLN* 3.6 22.6 + - + +
165A ARG* 4.3 0.3 + - - -
166A VAL* 1.3 75.9 - - - +
168A LEU* 1.3 69.3 + - - +
169A LEU* 5.9 0.7 - - + -
203A TYR* 4.5 13.0 - - + -
204A GLY* 3.1 4.7 - - - -
205A ALA* 2.8 40.1 + - - +
207A GLU* 3.7 18.2 + - - -
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Residues in contact with LEU 168 (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 SER* 3.5 1.0 - - - -
156A THR* 2.9 47.7 + - + +
166A VAL* 4.2 21.1 - - + +
167A THR* 1.3 83.9 - - - +
169A LEU* 1.3 60.8 + - - +
203A TYR* 3.3 5.2 - - - +
204A GLY* 4.0 12.3 - - - -
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Residues in contact with LEU 169 (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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102A ALA* 3.5 28.9 - - + +
103A LEU* 4.4 3.8 - - + -
105A GLN* 5.3 2.7 - - - +
133A ARG* 5.1 6.3 - - - +
153A ASP* 4.2 15.5 - - - +
154A VAL 3.2 12.3 - - - +
155A SER* 3.8 16.4 - - - +
167A THR* 5.9 0.7 - - + -
168A LEU* 1.3 75.2 - - - +
170A GLY* 1.3 71.9 + - - +
171A ASP* 3.6 6.5 - - + +
201A THR* 3.8 11.9 - - + +
202A LEU* 3.6 3.6 - - - +
203A TYR* 2.8 51.0 + - + +
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Residues in contact with GLY 170 (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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152A TYR 4.3 0.2 - - - +
153A ASP* 3.4 1.4 - - - +
154A VAL* 3.1 30.9 + - - +
169A LEU* 1.3 76.3 - - - +
171A ASP* 1.3 60.7 + - - -
201A THR 3.1 9.4 - - - -
202A LEU* 3.8 12.1 - - - -
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Residues in contact with ASP 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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100A PRO* 6.1 0.2 - - - +
101A ILE* 6.1 0.6 - - - +
102A ALA* 3.7 30.5 - - + +
151A ASN* 3.1 19.0 + - - -
152A TYR 3.3 5.4 - - - +
153A ASP* 3.0 27.3 - - - +
169A LEU* 3.6 2.8 - - + +
170A GLY* 1.3 74.8 - - - +
172A TYR* 1.3 77.1 + - - +
173A ALA* 3.8 9.4 + - - +
199A SER* 4.5 2.3 + - - +
200A LYS* 3.5 2.8 - - - +
201A THR* 2.8 44.9 + - - +
202A LEU* 4.9 0.4 - - - +
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Residues in contact with TYR 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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150A GLN* 3.7 18.6 - - + +
151A ASN* 3.4 3.8 - - - +
152A TYR* 2.9 43.5 + + + +
171A ASP* 1.3 79.1 + - - +
173A ALA* 1.3 72.0 + - - +
174A HIS* 3.1 28.0 + + + -
198A LEU* 3.0 44.1 - - + +
199A SER 3.4 8.1 - - - -
200A LYS* 3.7 19.7 - - + +
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Residues in contact with ALA 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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149A TYR* 4.5 11.7 - - + +
150A GLN 3.7 4.5 - - - -
151A ASN* 4.3 15.7 - - + +
171A ASP* 3.8 10.1 + - - +
172A TYR* 1.3 78.5 - - - +
174A HIS* 1.3 57.3 + - - +
197A PHE* 3.8 3.6 - - - +
198A LEU 3.3 0.5 - - - -
199A SER* 2.4 49.1 + - - +
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Residues in contact with HIS 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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148A SER 3.9 2.9 + - - -
149A TYR* 3.7 2.7 - - - -
150A GLN* 3.0 47.6 + - - +
172A TYR* 3.1 26.4 + + - +
173A ALA* 1.3 73.2 - - - +
175A THR* 1.3 96.6 + - - +
176A HIS* 2.2 43.5 + + - -
197A PHE 2.9 13.7 - - - +
198A LEU* 3.3 24.5 - - + +
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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