Contacts of the helix formed by residues 159 - 167 (chain A) in PDB entry 1VGO
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 THR 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 TYR* 2.6 59.8 + - + +
156A TYR* 3.8 0.5 + - - -
157A LEU 3.2 1.0 - - - -
158A LEU* 1.3 86.2 - - + +
160A SER* 1.3 66.7 + - - +
161A LEU 3.6 0.2 - - - -
162A ARG* 3.4 7.9 + - - +
163A SER* 2.7 39.0 + - - -
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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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108A VAL* 4.4 5.1 - - - +
112A THR* 4.5 12.7 - - - +
155A TYR* 5.6 1.7 - - - -
156A TYR* 3.2 19.1 + - - -
159A THR* 1.3 82.6 + - - +
161A LEU* 1.3 74.2 + - - +
163A SER* 3.0 7.0 + - - -
164A ALA* 2.9 23.7 + - - +
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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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102A LEU* 3.7 13.0 - - + +
103A ALA* 3.5 38.6 - - + +
106A ALA* 3.2 11.2 - - + +
108A VAL* 3.5 29.8 - - + -
112A THR* 4.0 16.4 - - + -
113A ILE* 6.5 0.2 - - - -
116A LEU* 4.6 12.8 - - + -
156A TYR* 3.0 23.7 + - + +
157A LEU* 4.0 14.4 - - + +
160A SER* 1.3 77.8 - - - +
162A ARG* 1.3 56.5 + - - +
164A ALA 3.4 0.2 + - - -
165A ALA* 2.9 27.2 + - - +
176A PHE* 3.3 16.2 - - + -
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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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157A LEU 3.0 22.6 + - - +
158A LEU* 3.1 30.5 + - + +
159A THR* 4.3 8.7 + - - +
160A SER 3.2 0.6 - - - -
161A LEU* 1.3 73.6 - - - +
163A SER* 1.3 83.2 + - - +
165A ALA* 3.6 1.6 + - - +
166A ALA* 3.2 25.6 + - - +
176A PHE* 3.4 12.1 - - + -
177A ASN* 3.8 24.8 + - - +
180A THR* 6.0 1.3 - - + -
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Residues in contact with SER 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 THR 2.7 20.5 + - - -
160A SER* 3.4 6.1 - - - -
162A ARG* 1.3 92.6 + - - +
164A ALA* 1.3 62.9 + - - +
166A ALA* 3.1 20.0 + - - +
167A LYS* 3.6 16.7 + - - +
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Residues in contact with ALA 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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106A ALA 3.4 20.3 - - - +
107A LYS 4.9 1.3 - - - +
108A VAL* 3.8 21.3 - - + +
160A SER 2.9 14.6 + - - +
161A LEU 3.7 3.4 - - - +
163A SER* 1.3 76.8 - - - +
165A ALA* 1.3 60.6 + - - +
167A LYS* 3.2 34.4 + - + +
168A ARG* 4.0 4.9 + - - +
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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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105A LEU 4.6 1.8 - - - +
106A ALA* 3.8 18.1 + - - +
161A LEU 2.9 18.5 + - - +
162A ARG 4.0 2.9 - - - +
164A ALA* 1.3 79.1 - - - +
166A ALA* 1.3 57.4 + - - +
168A ARG* 3.1 26.1 + - - +
172A VAL* 5.5 1.1 - - + -
173A ARG* 3.7 17.6 - - + +
176A PHE* 3.7 35.0 - - + -
177A ASN* 6.0 0.4 - - - +
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Residues in contact with ALA 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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162A ARG* 3.2 20.8 + - - +
163A SER* 3.1 15.8 + - - +
165A ALA* 1.3 75.7 - - - +
167A LYS* 1.3 59.4 + - + +
168A ARG 3.1 6.2 + - - +
173A ARG* 3.4 35.0 + - - +
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Residues in contact with LYS 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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163A SER* 3.7 16.4 - - - +
164A ALA* 3.3 23.6 - - + +
165A ALA 3.1 0.6 - - - -
166A ALA* 1.3 76.6 - - + +
168A ARG* 1.3 61.2 + - + +
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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