Contacts of the helix formed by residues 153 - 168 (chain A) in PDB entry 1NN5
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 ASN 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A TYR* 3.1 10.5 + - - +
152A GLU* 1.3 77.0 - - - +
154A GLY* 1.3 63.3 + - - +
155A ALA* 3.3 11.3 + - - +
156A PHE* 2.9 40.2 + - - +
157A GLN* 3.0 27.3 + - - +
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Residues in contact with GLY 154 (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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137A LEU* 6.5 0.9 - - - -
153A ASN* 1.3 73.2 - - - +
155A ALA* 1.3 61.4 + - - +
157A GLN* 3.3 7.1 + - - +
158A GLU* 3.0 24.1 + - - +
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Residues in contact with ALA 155 (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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153A ASN* 3.3 8.3 + - - +
154A GLY* 1.3 75.8 - - - +
156A PHE* 1.3 63.5 - - - +
158A GLU* 3.4 7.1 + - - +
159A ARG* 3.3 27.7 + - - +
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Residues in contact with PHE 156 (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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105A PHE* 3.2 41.1 - + - -
108A ALA* 3.7 23.6 - - + -
109A LYS* 4.0 17.7 - - + -
151A TYR* 3.4 53.2 - + + +
153A ASN* 2.9 30.2 + - - +
155A ALA* 1.3 76.1 - - - +
157A GLN* 1.3 61.5 + - - +
159A ARG* 3.0 11.5 + - - +
160A ALA* 2.9 25.2 + - + -
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Residues in contact with GLN 157 (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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14A VAL* 3.8 15.7 - - + +
15A ASP* 3.1 56.7 + - + +
105A PHE* 3.8 16.5 - - - -
137A LEU* 5.8 7.9 - - + -
151A TYR 3.0 21.3 + - - +
152A GLU* 4.7 1.3 - - - +
153A ASN 3.0 26.4 + - - +
154A GLY* 3.7 7.4 - - - +
156A PHE* 1.3 77.3 - - - +
158A GLU* 1.3 55.9 + - - +
160A ALA* 3.2 6.5 + - - +
161A LEU* 2.8 30.2 + - - +
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Residues in contact with GLU 158 (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 GLY 3.0 16.4 + - - +
155A ALA* 3.7 6.3 - - - +
157A GLN* 1.3 76.2 - - - +
159A ARG* 1.3 75.6 + - - +
161A LEU* 3.3 9.3 + - + +
162A ARG* 3.0 59.6 + - - +
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Residues in contact with ARG 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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107A GLY 5.0 2.8 + - - -
108A ALA* 2.7 41.1 + - + +
109A LYS 4.4 10.3 + - - -
110A GLU* 4.7 7.2 - - - +
155A ALA* 3.3 16.1 + - - +
156A PHE* 3.0 13.5 + - - +
158A GLU* 1.3 84.5 - - - +
160A ALA* 1.3 65.2 + - - +
162A ARG* 3.2 9.2 + - - +
163A CYS* 3.1 24.3 + - - -
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Residues in contact with ALA 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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14A VAL* 6.1 0.9 - - + -
104A ALA* 3.6 28.0 - - + +
105A PHE* 4.3 24.7 - - + -
108A ALA* 3.7 4.4 - - + +
156A PHE* 2.9 15.7 + - + +
157A GLN* 3.6 10.8 - - - +
159A ARG* 1.3 75.8 - - - +
161A LEU* 1.3 61.1 + - - +
163A CYS* 3.0 4.3 + - - +
164A PHE* 2.9 34.8 + - + -
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Residues in contact with LEU 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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14A VAL* 3.8 25.5 - - + +
132A PHE* 3.9 20.0 - - + -
135A LEU 5.7 4.7 - - - +
137A LEU* 5.7 10.5 - - + +
157A GLN 2.8 17.7 + - - +
158A GLU* 3.6 10.8 - - + +
160A ALA* 1.3 76.5 - - - +
162A ARG* 1.3 83.6 + - - +
164A PHE* 3.1 6.5 + - + -
165A HIS* 3.0 53.6 + - + +
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Residues in contact with ARG 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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158A GLU* 3.0 42.4 + - - +
159A ARG* 3.2 9.6 + - - +
161A LEU* 1.3 99.0 - - - +
163A CYS* 1.3 63.3 + - - +
165A HIS* 3.3 39.1 + - - +
166A GLN* 3.1 26.2 + - - +
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Residues in contact with CYS 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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104A ALA* 3.6 22.2 - - - -
107A GLY* 3.6 37.0 - - - -
108A ALA* 4.3 0.4 - - - -
114A LEU* 4.0 18.1 - - + +
159A ARG 3.1 17.1 + - - -
160A ALA 3.0 8.3 + - - +
162A ARG* 1.3 75.4 - - - +
164A PHE* 1.3 66.7 + - - +
166A GLN* 3.0 17.7 + - - +
167A LEU* 3.0 17.9 + - - +
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Residues in contact with PHE 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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12A GLU* 3.7 27.8 - - + -
13A GLY 4.1 21.1 - - - -
14A VAL* 4.7 4.5 - - + -
100A PHE* 3.8 29.2 - - + -
101A SER* 3.8 11.4 - - - -
104A ALA* 3.7 17.2 - - + +
105A PHE* 4.2 12.6 - + - -
132A PHE* 3.5 38.4 - + + -
160A ALA* 2.9 27.1 + - + -
161A LEU* 3.5 10.3 - - + +
163A CYS* 1.3 76.5 - - - +
165A HIS* 1.3 61.0 + - - +
167A LEU* 3.0 18.7 + - + +
168A MET* 3.0 19.4 + - + +
175A TRP* 4.9 4.2 - + - -
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Residues in contact with HIS 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 PHE* 4.8 2.9 - + - -
134A GLN* 4.4 14.7 + - - -
161A LEU* 3.0 48.8 + - + +
162A ARG* 3.5 28.7 + - - +
164A PHE* 1.3 76.7 - - - +
166A GLN* 1.3 64.5 + - - +
168A MET* 3.3 41.2 + - + +
169A LYS* 3.6 13.6 + - - +
177A MET* 5.8 0.4 - - - -
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Residues in contact with GLN 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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114A LEU* 3.4 31.4 - - + -
162A ARG 3.1 16.7 + - - +
163A CYS* 3.0 6.7 + - - +
165A HIS* 1.3 78.6 - - - +
167A LEU* 1.3 60.4 + - - +
169A LYS* 2.6 62.8 + - - +
170A ASP* 4.3 1.6 + - - +
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Residues in contact with LEU 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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100A PHE* 3.7 40.6 - - + +
103A VAL* 3.9 30.1 - - + -
104A ALA 4.4 2.9 - - - +
114A LEU* 4.8 9.6 - - + -
118A LYS* 4.3 13.9 - - + +
163A CYS 3.0 14.6 + - - +
164A PHE* 3.0 14.1 + - - +
166A GLN* 1.3 76.0 - - - +
168A MET* 1.3 61.1 + - - +
170A ASP* 3.2 23.6 + - - +
173A LEU* 5.0 1.0 - - - +
175A TRP* 3.4 21.9 + - + -
211A TRP* 4.2 17.8 + - + +
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Residues in contact with MET 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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132A PHE* 3.4 51.4 - - + -
164A PHE* 3.0 24.7 + - + +
165A HIS* 3.6 34.5 - - + +
166A GLN 3.1 0.6 - - - -
167A LEU* 1.3 73.2 - - - +
169A LYS* 1.3 60.8 + - - +
170A ASP 3.0 8.0 + - - +
171A THR* 5.9 0.2 - - - +
175A TRP* 3.7 41.2 - - + +
177A MET* 3.9 22.7 - - + +
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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