Contacts of the helix formed by residues 110 - 116 (chain A) in PDB entry 3OMA
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 VAL 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A HEA 3.9 24.9 - - + -
37A GLY* 3.7 17.9 - - - +
40A VAL* 3.7 9.9 - - + +
41A GLY* 3.6 32.3 - - - +
105A LEU* 3.0 21.6 + - + +
106A MET* 3.7 15.6 + - - +
108A PHE 3.7 1.6 - - - -
109A PHE* 1.3 83.0 - - - +
111A VAL* 1.3 72.7 + - + +
112A ILE 3.4 1.8 - - - -
113A PRO* 3.5 4.8 - - - +
114A ALA* 3.2 22.7 + - - +
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Residues in contact with VAL 111 (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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1A HEA 3.6 30.7 - - + -
106A MET 3.5 14.8 + - - +
110A VAL* 1.3 87.7 - - + +
112A ILE* 1.3 62.6 + - + +
114A ALA* 4.0 0.7 - - - +
115A LEU* 3.1 35.7 + - + +
290A ILE* 3.9 37.2 - - + -
428A ALA* 5.3 2.9 - - + -
429A VAL* 4.3 11.4 - - + -
432A ILE* 3.9 23.3 - - + +
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Residues in contact with ILE 112 (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 MET 4.9 0.6 + - - -
107A MET 3.8 9.6 - - - +
108A PHE 5.3 0.7 - - - +
111A VAL* 1.3 73.1 - - + +
113A PRO* 1.3 74.1 - - + +
115A LEU* 4.5 2.0 - - - +
116A PHE* 2.8 53.0 + - + +
201A SER* 4.8 13.5 - - - +
239A ILE* 5.2 2.0 - - + -
286A GLU* 3.6 33.9 - - - +
289A ILE* 3.9 24.0 - - + +
290A ILE* 3.7 33.0 - - + -
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Residues in contact with PRO 113 (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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33A TYR* 3.3 27.2 - - + +
37A GLY* 5.0 0.2 - - - -
108A PHE 3.6 21.3 - - - +
109A PHE 3.8 4.3 - - - -
110A VAL 3.5 16.8 - - - +
112A ILE* 1.3 96.3 - - + +
114A ALA* 1.3 55.5 + - - +
117A GLY* 3.2 8.6 - - - +
118A GLY 2.8 23.6 + - - -
146A TYR* 3.6 39.3 - - + +
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Residues in contact with ALA 114 (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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1A HEA 3.8 30.5 - - + -
33A TYR 4.6 4.5 + - - -
34A LEU* 3.6 16.5 - - + +
37A GLY* 4.8 4.3 - - - -
110A VAL 3.2 15.0 + - - +
111A VAL 4.0 3.8 - - - +
112A ILE 3.1 1.0 - - - -
113A PRO* 1.3 78.9 - - - +
115A LEU* 1.3 60.6 + - - +
118A GLY* 3.2 4.6 - - - -
119A PHE* 3.1 25.4 + - - -
432A ILE* 4.1 13.7 - - + -
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Residues in contact with LEU 115 (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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111A VAL* 3.1 22.0 + - + +
112A ILE* 4.3 1.3 - - - +
114A ALA* 1.3 77.6 - - - +
116A PHE* 1.3 58.6 + - - +
119A PHE* 3.4 12.6 + - + +
120A GLY* 2.9 22.7 + - - -
228A PHE* 4.4 0.2 - - - -
232A ILE* 4.1 4.2 - - - +
290A ILE* 3.3 27.6 - - + +
293A PRO* 3.9 16.0 - - + +
294A ALA* 4.3 15.7 - - + +
297A ILE* 3.7 30.3 - - + -
428A ALA* 4.3 15.5 - - + +
431A GLY 4.6 0.2 - - - -
432A ILE* 3.7 35.0 - - + +
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Residues in contact with PHE 116 (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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112A ILE* 2.8 29.3 + - + +
115A LEU* 1.3 72.5 - - - +
117A GLY* 1.3 67.6 + - - +
120A GLY* 3.1 21.0 - - - -
121A ASN 3.3 3.3 + - - -
201A SER* 4.2 8.3 - - - -
204A GLY* 3.9 19.5 - - - -
205A ALA* 3.9 11.0 - - - -
208A MET* 3.4 35.6 - - + +
232A ILE* 3.6 39.7 - - + -
235A THR* 3.6 25.4 - - + -
236A ALA* 4.0 3.8 - - + -
239A ILE* 3.7 24.9 - - + -
289A ILE 5.7 1.1 - - - +
293A PRO* 4.8 4.7 - - + -
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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