Contacts of the helix formed by residues 147 - 156 (chain M) in PDB entry 1VQ4
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 LEU 147 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53M GLY* 4.0 23.6 - - - +
55M LYS* 4.2 22.7 - - + -
57M LYS* 5.6 1.3 - - + -
60M VAL* 4.4 20.0 - - + -
115M LEU* 4.6 19.1 - - + -
134M ILE* 4.6 9.9 - - + -
141M ILE* 4.3 19.7 - - + -
144M ASP* 3.2 14.5 + - + +
146M ASP* 1.3 93.6 - - + +
148M SER* 1.3 54.9 + - - +
149M TRP* 2.6 29.2 + - + +
150M ILE* 2.9 26.1 + - + +
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Residues in contact with SER 148 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141M ILE 3.5 16.6 + - - -
142M GLN* 3.6 16.8 - - - -
144M ASP 2.9 22.5 + - - -
145M ASP* 4.3 7.8 + - - -
147M LEU* 1.3 75.8 - - - +
149M TRP* 1.3 62.2 + - - +
150M ILE 3.1 0.7 - - - -
151M CYS* 3.0 24.8 + - - +
152M ALA* 4.2 1.7 + - - +
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Residues in contact with TRP 149 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4320 G 3.4 33.9 + - - -
4330 C 3.5 38.5 - - - +
4340 U 5.6 0.5 + - - -
115M LEU* 3.6 26.0 - - + -
145M ASP 5.6 1.1 - - - -
146M ASP 3.3 28.6 + - - -
147M LEU* 2.6 15.2 + - - +
148M SER* 1.3 77.5 + - - +
150M ILE* 1.3 89.9 + - + -
151M CYS 3.0 4.3 + - - -
152M ALA* 3.4 15.6 + - - +
155M GLN* 3.4 24.6 + - - +
158M ARG* 3.4 38.4 - - - -
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Residues in contact with ILE 150 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113M ARG* 2.7 46.8 + - + +
114M VAL 4.0 8.5 - - - +
115M LEU* 3.9 19.3 - - + -
134M ILE* 3.7 30.3 - - + +
136M PRO* 3.8 5.1 - - + +
141M ILE* 4.6 0.2 - - + -
147M LEU* 2.9 16.6 + - + +
149M TRP* 1.3 114.1 - - + +
151M CYS* 1.3 59.1 + - - +
152M ALA 3.3 0.7 - - - -
155M GLN* 3.7 4.7 - - + +
158M ARG* 4.0 23.6 - - - -
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Residues in contact with CYS 151 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113M ARG* 3.6 8.2 + - - +
136M PRO* 3.3 38.2 - - - +
141M ILE* 4.0 21.8 - - - -
142M GLN* 4.0 19.7 - - + +
148M SER* 3.0 22.1 + - - +
150M ILE* 1.3 79.3 - - - +
152M ALA* 1.3 62.4 + - - +
153M ASP* 3.6 5.4 + - - +
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Residues in contact with ALA 152 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4340 U 5.9 0.4 - - - +
113M ARG* 3.0 11.7 + - - -
148M SER 4.2 1.4 + - - +
149M TRP* 3.4 15.1 + - - +
150M ILE 3.3 1.2 - - - -
151M CYS* 1.3 78.1 - - - +
153M ASP* 1.3 56.1 + - - +
154M ASP* 3.7 21.8 - - - +
155M GLN* 2.7 25.9 + - + +
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Residues in contact with ASP 153 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1830 A 3.9 6.8 - - - +
1840 G 4.1 23.5 + - - +
1850 G 5.1 7.0 + - - +
113M ARG* 4.7 8.1 + - - +
151M CYS 3.6 4.0 + - - +
152M ALA* 1.3 72.4 - - - +
154M ASP* 1.3 57.5 + - - +
155M GLN 3.0 4.7 + - - -
156M ALA* 3.1 23.2 + - - +
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Residues in contact with ASP 154 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1830 A 3.9 12.3 - - - +
1840 G 4.4 10.7 - - - -
1870 A 4.7 19.7 + - - +
1880 C 3.8 15.4 + - - +
4340 U 4.2 8.6 + - - -
152M ALA* 3.7 12.3 - - - +
153M ASP* 1.3 76.5 - - - +
155M GLN* 1.3 80.5 + - - +
156M ALA 3.3 2.2 - - - -
161M ARG* 2.8 21.5 + - - +
163M LEU* 4.6 0.5 - - - +
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Residues in contact with GLN 155 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1880 C 5.8 0.2 + - - -
4330 C 4.3 4.2 + - - -
4340 U 3.3 30.5 + - - -
113M ARG* 3.6 19.7 - - - +
149M TRP* 3.4 32.9 - - - +
150M ILE* 3.7 10.8 - - - +
152M ALA* 2.7 12.5 + - + +
154M ASP* 1.3 92.0 + - - +
156M ALA* 1.3 65.7 + - - +
157M ASP 3.4 0.7 + - - -
158M ARG* 2.5 61.2 + - - +
161M ARG* 4.0 2.9 - - - +
163M LEU* 4.7 9.4 - - - +
168M ARG* 5.8 1.2 - - - +
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Residues in contact with ALA 156 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1830 A 3.8 24.6 - - - +
1840 G 5.0 2.0 - - - +
113M ARG* 3.7 23.3 - - - +
153M ASP* 3.1 17.0 + - - +
154M ASP 3.3 0.8 - - - -
155M GLN* 1.3 76.0 - - - +
157M ASP* 1.3 72.8 + - - +
161M ARG* 2.9 19.4 + - - -
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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