Contacts of the helix formed by residues 158 - 169 (chain A) in PDB entry 2NQY
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 SER 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A MET 3.9 5.2 - - - -
67A SER* 4.4 6.3 + - - -
117A VAL* 3.9 2.7 - - - +
118A ASP* 2.5 35.5 + - - -
156A THR* 4.4 5.5 - - - +
157A ILE* 1.3 68.6 - - - +
159A VAL* 1.3 66.0 - - - +
160A SER 3.3 2.7 - - - -
161A ASN* 3.1 36.3 + - - +
162A HIS* 3.3 14.7 - - - -
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Residues in contact with VAL 159 (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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66A MET* 3.1 22.6 + - + +
68A ILE* 4.1 17.0 - - + -
84A VAL* 3.9 17.0 - - + -
97A ILE* 4.0 13.5 - - + -
157A ILE* 3.0 30.9 + - + +
158A SER* 1.3 69.6 - - - +
160A SER* 1.3 61.9 + - - +
162A HIS* 3.1 16.6 + - - +
163A PHE* 3.2 43.9 + - + -
179A VAL* 4.1 15.5 - - + -
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Residues in contact with SER 160 (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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60A HIS* 4.8 6.3 + - - -
64A GLY 3.7 5.0 + - - -
65A ASN* 3.5 25.0 - - - -
66A MET* 2.7 36.8 + - - +
158A SER 3.3 1.2 - - - -
159A VAL* 1.3 73.8 - - - +
161A ASN* 1.3 58.6 + - - +
163A PHE* 3.1 12.1 + - - +
164A ARG* 2.9 48.7 + - - +
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Residues in contact with ASN 161 (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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65A ASN* 4.7 3.1 - - - +
115A ILE* 3.4 15.9 - - + +
117A VAL* 3.4 29.7 - - + +
158A SER* 3.1 23.8 + - - +
160A SER* 1.3 75.0 - - - +
162A HIS* 1.3 57.1 + - - +
164A ARG* 2.8 36.0 + - - +
165A ALA* 3.0 22.9 + - - +
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Residues in contact with HIS 162 (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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97A ILE* 3.6 41.1 - - + +
115A ILE* 3.8 11.1 - - + +
117A VAL* 3.4 30.7 - - + +
118A ASP* 4.4 4.6 + - - -
122A TYR* 3.7 17.4 - + - -
146A SER* 2.9 36.7 + - - +
157A ILE* 4.5 2.5 - - + +
158A SER 3.3 25.8 - - - -
159A VAL 3.1 7.7 + - - +
161A ASN* 1.3 73.5 - - - +
163A PHE* 1.3 60.2 + - + +
165A ALA* 3.3 1.6 + - - +
166A TRP* 2.8 43.7 + - + +
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Residues in contact with PHE 163 (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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60A HIS* 3.4 36.6 - + + +
66A MET* 3.9 19.7 - - + -
95A TYR* 3.4 38.8 - + - -
97A ILE* 4.8 1.6 - - + -
159A VAL* 3.2 31.4 + - + -
160A SER* 3.1 17.6 + - - +
162A HIS* 1.3 76.7 - - - +
164A ARG* 1.3 60.1 + - - +
166A TRP* 3.5 33.0 + + - +
167A GLU* 3.1 28.9 + - - +
173A MET* 3.4 22.1 - - + +
176A MET* 4.0 8.7 - - + -
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Residues in contact with ARG 164 (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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60A HIS* 4.2 16.0 + - + -
61A GLN* 5.7 4.4 - - + +
65A ASN* 3.8 16.6 + - - +
160A SER* 2.9 29.7 + - - +
161A ASN* 2.8 38.4 + - - +
163A PHE* 1.3 76.1 - - - +
165A ALA* 1.3 55.6 + - - +
167A GLU* 3.3 9.1 + - - +
168A SER* 3.0 30.0 + - - -
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Residues in contact with ALA 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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114A THR 5.5 0.9 - - - +
115A ILE* 3.7 29.2 - - + -
124A ILE* 4.2 9.9 - - + -
161A ASN 3.0 18.6 + - - +
162A HIS* 3.6 4.9 - - - +
164A ARG* 1.3 71.8 - - - +
166A TRP* 1.3 66.1 + - - +
168A SER* 3.3 10.5 + - - -
169A LEU* 3.2 26.4 + - + +
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Residues in contact with TRP 166 (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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95A TYR* 3.5 38.6 - + + -
96A TYR 3.3 24.9 - - - -
97A ILE* 4.0 11.2 - - + -
124A ILE* 3.6 24.9 - - + +
144A TYR* 3.9 15.9 - + + -
145A TRP 3.8 8.7 + - - -
146A SER* 3.0 28.1 + - - -
162A HIS* 2.8 24.3 + - + +
163A PHE* 3.5 32.8 - + - +
165A ALA* 1.3 73.1 - - + +
167A GLU* 1.3 57.7 + - - +
169A LEU* 3.0 14.9 + - - +
171A MET* 2.9 49.6 + - + +
173A MET* 3.7 20.4 - - + -
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Residues in contact with GLU 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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60A HIS* 2.7 32.9 + - - -
61A GLN* 3.4 15.8 + - - +
163A PHE 3.1 12.5 + - - +
164A ARG* 3.3 6.4 + - - +
166A TRP* 1.3 74.5 - - - +
168A SER* 1.3 56.7 + - - +
170A GLY* 2.9 19.9 + - - -
171A MET 3.5 17.9 - - - +
172A ASN* 4.1 13.1 + - - +
173A MET* 3.3 32.9 + - + +
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Residues in contact with SER 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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164A ARG 3.0 13.6 + - - -
165A ALA* 3.4 13.2 - - - -
167A GLU* 1.3 75.0 - - - +
169A LEU* 1.3 65.3 + - - +
170A GLY 3.2 1.4 + - - -
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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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112A LYS* 4.1 33.3 + - + +
113A GLY* 4.0 18.2 - - - +
114A THR 4.9 1.6 - - - +
124A ILE* 3.7 39.7 - - + -
165A ALA 3.2 10.2 + - - +
166A TRP 3.0 9.5 + - - +
168A SER* 1.3 81.0 - - - +
170A GLY* 1.3 61.9 + - - +
171A MET* 3.3 9.9 + - - -
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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