Contacts of the helix formed by residues 159 - 172 (chain A) in PDB entry 4NQC
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 GLU 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A ASN* 2.8 39.0 + - - +
158A GLU* 1.3 90.6 - - + +
160A GLU* 1.3 69.1 + - + +
161A CYS 3.5 0.9 - - - -
162A ILE* 3.5 4.2 + - - +
163A ALA* 3.2 22.7 + - - +
29G PHE 5.9 0.2 - - - +
66G ARG* 3.7 16.9 + - - +
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Residues in contact with GLU 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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155A ASN* 3.5 3.7 + - - +
156A TRP* 3.3 30.4 + - + +
159A GLU* 1.3 77.2 - - + +
161A CYS* 1.3 66.0 + - - +
163A ALA* 3.2 10.2 + - - +
164A TRP* 3.0 36.4 + - + -
28G GLY* 3.4 6.5 - - - -
29G PHE* 2.9 45.1 + - - +
30G ASN* 3.6 16.3 + - - +
93G SER* 3.2 31.4 - - - +
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Residues in contact with CYS 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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5A LEU* 3.9 10.4 - - - +
97A GLY* 3.8 5.2 - - - -
98A CYS* 2.1 58.8 - - - -
156A TRP* 2.7 54.6 + - + +
157A LEU 3.5 10.5 - - - +
160A GLU* 1.3 71.3 - - - +
162A ILE* 1.3 62.1 + - - +
164A TRP* 3.3 6.0 + - - +
165A LEU* 3.0 19.2 + - - +
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Residues in contact with ILE 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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98A CYS* 3.8 21.3 - - + -
99A GLU 3.5 29.4 - - - +
100A LEU* 4.3 6.1 - - + +
106A THR* 3.8 26.7 - - + -
107A THR 4.7 0.4 - - - +
157A LEU 4.3 7.4 + - - +
158A GLU* 3.8 22.2 - - - +
159A GLU 3.5 5.4 + - - +
160A GLU 3.3 0.8 - - - -
161A CYS* 1.3 75.6 - - - +
163A ALA* 1.3 56.4 + - - +
165A LEU* 3.3 9.4 + - + +
166A LYS* 2.9 57.1 + - + +
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Residues in contact with ALA 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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159A GLU 3.2 12.3 + - - +
160A GLU* 3.2 15.1 + - - +
162A ILE* 1.3 74.0 - - - +
164A TRP* 1.3 64.9 + - + +
166A LYS* 3.4 11.0 + - - +
167A ARG* 3.1 24.2 + - - +
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Residues in contact with TRP 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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5A LEU* 3.6 18.4 - - + -
7A TYR* 5.3 4.0 - + - -
54A LEU* 4.6 0.2 - - + -
58A HIS* 3.8 31.9 - + - -
62A TYR* 3.6 22.8 + + - -
156A TRP* 4.1 23.3 - + - +
160A GLU* 3.0 42.9 + - - -
161A CYS 3.6 2.2 - - - +
163A ALA* 1.3 76.2 - - + +
165A LEU* 1.3 56.1 + - - +
167A ARG* 3.1 42.8 + - - +
168A PHE* 2.8 64.9 + + + -
93G SER* 3.9 19.2 + - - -
94G ASN* 3.8 14.8 - - - -
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Residues in contact with LEU 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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3A HIS* 3.7 28.5 - - + +
4A SER* 3.6 35.4 - - - +
5A LEU* 3.9 16.5 - - + +
28A VAL* 4.1 16.2 - - + -
98A CYS* 4.2 10.1 - - - +
99A GLU 4.2 1.6 - - - -
100A LEU* 3.8 25.4 - - + +
161A CYS 3.0 13.9 + - - +
162A ILE* 3.5 10.8 - - + +
164A TRP* 1.3 76.1 - - - +
166A LYS* 1.3 56.6 + - - +
168A PHE* 3.4 3.2 + - - -
169A LEU* 2.9 38.7 + - + +
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Residues in contact with LYS 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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100A LEU* 3.9 31.2 - - + +
162A ILE* 2.9 43.1 + - + +
163A ALA* 3.8 8.1 - - - +
164A TRP 3.4 0.2 - - - -
165A LEU* 1.3 75.1 - - - +
167A ARG* 1.3 60.6 + - - +
169A LEU* 3.6 10.0 + - + +
170A GLU* 3.3 21.1 + - - +
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Residues in contact with ARG 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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53A ASN 5.3 0.6 + - - -
54A LEU* 3.5 20.9 - - - +
58A HIS* 5.2 1.4 + - - +
163A ALA 3.1 13.5 + - - +
164A TRP* 3.1 50.2 + - - +
166A LYS* 1.3 75.4 - - - +
168A PHE* 1.3 62.1 + - + +
170A GLU* 3.3 7.6 + - - +
171A TYR* 2.8 60.8 + - + +
93G SER* 4.9 6.9 + - - -
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Residues in contact with PHE 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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5A LEU* 3.9 14.4 - - + -
7A TYR* 3.4 25.6 - - - -
28A VAL* 3.9 22.0 - - + -
33A ILE* 3.7 21.5 - - + -
34A THR* 5.8 0.7 - - + -
43A LYS* 6.0 0.4 - - - -
49A TRP* 3.5 11.9 - - + -
50A MET* 3.9 26.9 - - + -
54A LEU* 4.1 11.7 - - + -
58A HIS* 5.3 4.0 - + - -
164A TRP* 2.8 55.0 + + - +
165A LEU* 3.9 2.9 - - - +
167A ARG* 1.3 75.0 - - + +
169A LEU* 1.3 58.6 + - - +
171A TYR* 3.4 20.1 + + - +
172A GLY* 2.9 25.1 + - - -
176A LEU* 3.9 2.9 - - - +
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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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0A MET* 3.9 16.4 - - + -
3A HIS* 3.4 58.3 - - + +
28A VAL* 5.0 0.4 - - + -
100A LEU* 4.8 9.6 - - + -
165A LEU* 2.9 34.2 + - + +
166A LYS* 3.6 11.2 - - + +
167A ARG 3.3 0.2 - - - -
168A PHE* 1.3 74.8 - - - +
170A GLU* 1.3 58.6 + - - +
172A GLY 3.6 0.7 - - - -
173A LYS* 2.9 22.9 + - - -
176A LEU* 3.8 22.0 - - + +
177A GLN* 3.3 24.0 - - - +
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Residues in contact with GLU 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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0A MET* 6.0 1.4 - - - +
166A LYS 3.3 9.6 + - - +
167A ARG* 3.6 10.8 - - - +
168A PHE 3.3 0.4 - - - -
169A LEU* 1.3 76.7 - - - +
171A TYR* 1.4 68.7 + - + +
173A LYS* 2.9 62.5 + - - +
177A GLN* 4.8 3.3 - - - +
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Residues in contact with TYR 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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49A TRP* 3.4 33.7 - - + +
50A MET* 4.5 6.5 - - - -
53A ASN* 3.5 50.4 + - + +
54A LEU* 3.8 19.1 - - + -
167A ARG* 2.8 59.3 + - + +
168A PHE* 3.4 24.5 - + - +
170A GLU* 1.4 82.2 - - + +
172A GLY* 1.3 57.4 + - - +
173A LYS* 3.7 1.4 + - - +
174A ASP 5.2 0.5 + - - -
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Residues in contact with GLY 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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49A TRP* 3.4 31.8 - - - -
168A PHE 2.9 12.8 + - - -
169A LEU 3.6 2.7 - - - -
171A TYR* 1.3 76.5 - - - +
173A LYS* 1.4 50.4 + - - +
174A ASP* 3.3 2.7 - - - -
175A THR* 2.8 29.3 + - - -
176A LEU* 2.9 18.6 + - - +
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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