Contacts of the helix formed by residues 158 - 168 (chain A) in PDB entry 5V89
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 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A LEU* 3.5 33.0 - - + -
110A PHE* 3.5 25.1 - - + -
111A TYR* 3.7 24.0 - - + +
118A ASP* 3.0 36.0 + - + +
157A THR* 1.3 73.7 - - - +
159A GLN* 1.3 71.4 + - + +
161A TRP* 3.6 1.4 - - + +
162A LEU* 2.8 35.4 + - + +
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Residues in contact with GLN 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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157A THR* 3.3 5.7 + - - +
158A LEU* 1.3 88.2 - - + +
160A GLU* 1.3 66.2 + - + +
162A LEU* 4.3 21.0 - - - +
163A LYS* 3.0 31.5 + - - +
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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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148A LEU* 3.5 33.5 - - + +
149A ASP 4.1 4.0 - - - +
150A ALA* 3.5 17.7 - - - +
151A GLN* 3.0 33.8 + - - +
155A TYR 3.9 2.3 - - - +
156A PHE* 3.5 11.3 - - - -
157A THR* 3.0 48.0 + - - +
159A GLN* 1.3 76.0 - - - +
161A TRP* 1.3 58.3 + - - +
163A LYS* 4.3 1.6 - - - +
164A GLY* 2.9 28.9 + - - -
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Residues in contact with TRP 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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106A CYS* 3.2 34.2 + - - -
107A LEU* 5.5 2.7 - - + -
109A TRP* 3.4 28.4 - + - -
110A PHE* 3.5 43.2 - + + +
113A TYR* 4.0 15.3 - + - -
120A VAL* 4.7 5.6 - - + -
128A PHE* 3.7 34.8 - + - -
148A LEU* 4.0 10.9 - - + +
156A PHE* 3.9 30.0 - + + +
157A THR 3.0 16.3 + - - +
158A LEU 3.6 4.0 - - - +
160A GLU* 1.3 77.0 - - - +
162A LEU* 1.3 60.8 + - - +
165A MET* 2.7 58.0 + - + +
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Residues in contact with LEU 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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103A SER* 3.8 32.1 - - - +
106A CYS* 4.6 7.6 - - - -
107A LEU* 4.0 31.0 - - + -
158A LEU* 2.8 23.9 + - + +
159A GLN* 4.1 22.7 - - - +
161A TRP* 1.3 78.7 - - - +
163A LYS* 1.3 59.0 + - - +
166A THR* 2.6 41.9 + - - +
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Residues in contact with LYS 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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148A LEU 6.1 0.4 - - - +
159A GLN* 3.0 21.4 + - - +
160A GLU* 4.3 1.3 - - - +
162A LEU* 1.3 78.9 - - - +
164A GLY* 1.3 57.9 + - - +
166A THR* 3.8 3.8 - - - -
167A SER* 3.0 29.0 + - - -
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Residues in contact with GLY 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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147A LYS 3.9 10.9 - - - +
148A LEU* 3.7 21.5 + - - -
160A GLU 2.9 17.9 + - - -
163A LYS* 1.3 77.0 - - - +
165A MET* 1.3 57.8 + - - +
167A SER* 2.6 24.8 + - - -
168A LEU* 3.0 17.2 + - - +
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Residues in contact with MET 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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106A CYS* 3.6 10.5 - - - -
109A TRP* 3.8 26.7 - - + -
128A PHE* 4.1 13.9 - - + -
144A LEU* 4.4 6.7 - - + -
148A LEU* 4.1 19.5 - - + +
156A PHE* 5.4 0.2 - - + -
161A TRP* 2.7 67.7 + - + +
164A GLY* 1.3 70.0 - - - -
166A THR* 1.3 63.9 + - - +
168A LEU* 3.3 4.9 + - - +
169A GLN 2.9 17.7 + - - -
170A CYS* 3.0 28.3 + - - +
176A LEU* 3.9 20.0 - - + -
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Residues in contact with THR 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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103A SER* 4.3 8.0 + - - +
106A CYS* 4.8 5.1 - - - +
162A LEU* 2.6 38.0 + - - +
163A LYS* 3.8 5.2 - - - -
165A MET* 1.3 77.4 - - - +
167A SER* 1.3 63.1 + - - +
169A GLN* 3.0 20.2 + - - +
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Residues in contact with SER 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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147A LYS* 4.4 15.6 + - - +
163A LYS* 3.0 15.5 + - - -
164A GLY* 2.6 24.1 + - - -
166A THR* 1.3 76.9 - - - +
168A LEU* 1.3 65.1 + - - +
169A GLN* 3.2 7.2 + - - +
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Residues in contact with LEU 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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144A LEU* 3.9 27.4 - - + -
147A LYS* 4.1 24.2 - - + +
148A LEU* 4.4 7.4 - - + -
164A GLY 3.0 15.9 + - - +
165A MET* 3.8 11.4 - - - +
166A THR 3.2 0.2 - - - -
167A SER* 1.3 82.7 + - - +
169A GLN* 1.3 70.3 + - - +
170A CYS* 3.3 16.9 + - - -
176A LEU* 4.6 6.5 - - + -
179A THR* 4.4 14.9 + - + +
182A TYR* 4.4 13.2 - - + -
183A LEU* 4.0 24.2 - - + -
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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