Contacts of the helix formed by residues 144 - 153 (chain N) in PDB entry 1VQM
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 GLY 144 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79N PRO* 3.3 18.4 - - - -
141N ARG 2.8 13.0 + - - -
142N THR 3.0 0.2 - - - -
143N ARG* 1.3 80.5 - - - +
145N ALA* 1.3 62.5 + - - +
146N HIS* 3.4 10.3 - - - -
147N ILE* 2.8 34.0 + - - +
148N ALA 3.5 1.2 + - - -
169N PRO* 4.0 8.2 - - - +
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Residues in contact with ALA 145 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140N GLN* 3.1 39.8 + - + +
141N ARG* 4.8 0.2 - - - -
143N ARG* 3.6 2.0 - - + -
144N GLY* 1.3 75.6 - - - +
146N HIS* 1.3 56.0 + - - +
148N ALA* 2.7 26.5 + - - +
149N GLU* 3.1 22.8 + - + +
169N PRO* 4.1 12.8 - - + +
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Residues in contact with HIS 146 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30349 A 3.7 8.4 - + - +
30359 C 3.3 28.6 + - + +
30489 C 3.9 1.6 + - - -
30499 G 2.8 41.4 + - - -
77N ASN* 5.8 0.4 - - + -
78N MET* 3.9 10.1 - - + -
79N PRO* 4.6 2.2 - - + -
141N ARG* 3.2 67.1 + - + +
144N GLY* 3.7 11.7 - - - -
145N ALA* 1.3 78.0 - - - +
147N ILE* 1.3 65.1 + - + +
149N GLU* 4.0 10.9 + - - +
150N TYR* 3.4 19.9 + - - +
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Residues in contact with ILE 147 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30349 A 4.9 0.9 - - - -
30499 G 3.0 20.9 - - - +
30509 G 2.9 16.2 - - - +
77N ASN* 5.1 2.9 - - + +
79N PRO* 6.0 1.3 - - + -
144N GLY* 2.8 28.6 + - - +
145N ALA 2.7 4.9 + - - -
146N HIS* 1.3 89.4 - - + +
148N ALA* 1.3 66.8 + - + +
150N TYR* 3.1 8.5 + - + +
151N ASP* 3.0 17.2 + - - +
158N LEU* 3.3 22.8 - - + +
159N TYR* 2.9 38.6 - - + +
167N ASP* 3.9 10.3 - - + +
169N PRO* 5.6 1.3 - - + -
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Residues in contact with ALA 148 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144N GLY 4.3 0.2 - - - +
145N ALA* 2.7 15.9 + - - +
147N ILE* 1.3 77.5 - - + +
149N GLU* 1.3 56.9 + - + +
151N ASP* 2.7 27.2 + - - +
152N GLU* 3.0 10.0 + - - +
166N ALA* 4.1 20.7 - - - +
167N ASP* 4.4 2.7 - - + -
169N PRO* 4.2 25.1 - - + -
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Residues in contact with GLU 149 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145N ALA* 3.1 19.4 + - + +
146N HIS* 4.2 10.6 + - - +
148N ALA* 1.3 77.3 - - + +
150N TYR* 1.3 58.2 + - - +
152N GLU* 3.0 28.3 - - + +
153N GLN* 3.7 13.3 + - - +
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Residues in contact with TYR 150 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30329 G 4.6 11.1 + - - -
30339 U 5.2 2.6 + - - -
30349 A 3.3 72.8 + + + +
30499 G 4.0 10.1 - - - -
146N HIS 3.4 15.1 + - - +
147N ILE* 3.1 13.2 + - + +
148N ALA 2.9 1.0 - - - -
149N GLU* 1.3 78.1 - - - +
151N ASP* 1.3 59.1 + - - +
152N GLU 3.1 2.5 + - - -
153N GLN* 3.5 26.8 + - + +
158N LEU* 3.9 34.3 - - + +
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Residues in contact with ASP 151 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147N ILE 3.0 4.8 + - - +
148N ALA* 2.7 11.8 + - - +
150N TYR* 1.3 75.0 - - - +
152N GLU* 1.3 65.0 + - - +
153N GLN 3.2 0.7 - - - -
154N LEU* 3.1 33.8 + - - +
158N LEU* 3.2 34.6 + - + +
165N ALA 2.5 31.7 - - - +
166N ALA* 3.2 15.8 - - - +
167N ASP* 3.2 18.3 - - - +
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Residues in contact with GLU 152 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148N ALA 3.0 5.7 + - - -
149N GLU* 3.0 26.4 - - + +
151N ASP* 1.3 74.2 - - - +
153N GLN* 1.3 51.7 + - + +
154N LEU* 2.5 22.1 + - - +
166N ALA* 5.6 5.5 - - - +
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Residues in contact with GLN 153 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30349 A 3.1 54.4 + - - +
149N GLU 3.9 15.3 + - - +
150N TYR* 3.5 22.1 + - + +
151N ASP 3.2 1.3 - - - -
152N GLU* 1.3 72.7 - - + +
154N LEU* 1.3 67.2 + - - +
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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