Contacts of the helix formed by residues 157 - 165 (chain B) in PDB entry 3EOV
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 157 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B ARG 3.5 19.5 - - - -
43B ILE* 4.1 3.1 - - - +
154B VAL* 4.1 2.0 - - - -
156B ASP* 1.3 87.3 + - - +
158B MET* 1.3 57.5 + - - +
159B ASP* 2.9 11.7 + - - -
160B VAL* 3.0 25.7 + - - +
161B VAL* 3.1 15.1 + - - +
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Residues in contact with MET 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B VAL* 4.1 20.2 - - + -
118B GLY* 4.1 16.8 - - - +
136B ILE* 5.0 0.2 - - - -
137B THR 3.8 22.0 - - - +
138B THR* 4.1 17.0 - - + -
154B VAL* 3.9 20.4 - - + +
156B ASP* 3.4 2.3 - - - -
157B GLY* 1.3 78.4 - - - +
159B ASP* 1.3 59.6 + - - +
161B VAL* 3.4 15.9 + - + +
162B LEU* 3.1 44.2 + - + +
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Residues in contact with ASP 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B GLY* 4.8 3.6 + - - -
158B MET* 1.3 81.9 + - - +
160B VAL* 1.3 59.6 + - + +
162B LEU* 3.5 8.9 + - - +
163B ARG* 3.0 27.0 + - - +
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Residues in contact with VAL 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B VAL* 4.3 12.1 - - + -
40B LEU* 3.8 38.1 - - + +
41B GLY* 4.1 8.5 - - - +
42B ARG 3.8 17.5 - - - +
43B ILE* 3.7 24.0 - - + -
157B GLY* 3.0 13.8 + - - +
159B ASP* 1.3 79.3 - - + +
161B VAL* 1.3 63.4 + - - +
163B ARG* 3.3 8.2 + - - +
164B ILE* 3.2 25.1 + - + +
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Residues in contact with VAL 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ILE* 3.9 27.6 - - + -
85B ILE* 4.0 16.8 - - + +
136B ILE* 4.1 24.9 - - + -
138B THR* 3.6 25.1 - - + -
154B VAL* 4.4 1.8 - - + -
157B GLY 3.1 13.5 + - - +
158B MET* 3.6 23.6 - - + +
159B ASP 3.3 0.2 - - - -
160B VAL* 1.3 78.3 - - - +
162B LEU* 1.3 56.7 + - - +
163B ARG 3.1 0.2 - - - -
164B ILE* 3.3 12.0 + - - +
165B GLU* 3.1 23.6 + - - +
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Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B VAL* 6.3 0.2 - - + -
138B THR* 3.4 37.9 - - + +
158B MET* 3.1 33.8 + - + +
159B ASP* 3.5 8.9 + - - +
161B VAL* 1.3 73.7 - - - +
163B ARG* 1.3 62.5 + - - +
165B GLU* 3.8 15.5 + - - +
166B LYS* 3.2 36.4 - - - +
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Residues in contact with ARG 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ILE* 4.9 5.2 - - + +
38B GLU* 3.4 26.9 + - - -
40B LEU* 3.7 37.8 + - + +
159B ASP 3.0 17.5 + - - +
160B VAL* 3.3 10.3 - - - +
161B VAL 3.1 0.4 - - - -
162B LEU* 1.3 79.4 - - - +
164B ILE* 1.3 61.3 + - - +
166B LYS* 3.5 14.5 + - - +
167B THR* 3.7 8.0 + - - -
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Residues in contact with ILE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B VAL* 3.8 28.3 - - + -
35B ILE* 5.1 1.8 - - + -
40B LEU* 3.7 17.3 - - + -
43B ILE* 4.6 3.6 - - + -
76B PHE* 4.5 7.9 - - + -
79B VAL* 3.6 18.6 - - + +
85B ILE* 4.3 24.9 - - + -
160B VAL* 3.2 22.9 + - + +
161B VAL 3.3 6.0 + - - +
163B ARG* 1.3 74.0 - - - +
165B GLU* 1.3 63.6 + - - +
166B LYS 3.0 6.6 + - - -
167B THR* 3.0 23.6 + - - +
179B VAL* 3.8 29.4 - - + -
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Residues in contact with GLU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B VAL* 3.4 21.1 - - + +
80B ILE 4.4 2.5 - - - +
81B GLN* 3.6 27.7 + - + +
82B ASN* 2.6 32.2 + - - +
84B MET 5.4 0.7 - - - +
85B ILE* 4.2 7.2 - - + +
138B THR* 2.9 29.8 + - + +
161B VAL 3.1 15.0 + - - +
162B LEU* 4.0 14.0 - - - +
163B ARG 3.4 0.4 - - - -
164B ILE* 1.3 74.8 - - - +
166B LYS* 1.3 86.7 + - - +
167B THR 3.5 2.1 - - - +
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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