Contacts of the helix formed by residues 106 - 118 (chain A) in PDB entry 1OVY
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 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A VAL* 3.3 35.6 - - + +
34A PHE* 4.5 1.8 - - - +
35A ARG* 3.7 23.1 - - + +
40A ILE* 3.5 24.7 - - + -
98A GLY* 2.9 29.6 - - - +
99A GLY 4.8 0.4 - - - -
100A TYR* 2.9 15.0 + - + +
105A ARG* 1.3 72.3 - - + +
107A LYS* 1.3 61.8 + - - +
108A ALA 3.2 0.2 - - - -
109A LEU* 3.1 26.0 + - + +
110A ALA* 3.6 3.6 + - - +
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Residues in contact with LYS 107 (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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71A ILE* 5.0 5.4 - - - +
99A GLY 4.0 1.8 - - - -
100A TYR* 3.6 7.6 + - + -
102A TYR* 3.2 42.0 - - + -
103A HIS* 3.2 21.8 + - - +
104A GLY 2.5 42.0 + - - +
105A ARG* 2.8 12.7 + - - +
106A VAL* 1.3 79.8 - - - +
108A ALA* 1.3 74.2 + - - +
109A LEU 3.1 0.3 + - - -
110A ALA 3.2 1.0 + - - -
111A ASP* 2.4 50.7 + - + +
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Residues in contact with ALA 108 (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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71A ILE* 3.0 46.7 - - + -
75A LYS* 4.1 19.3 + - + +
105A ARG 3.0 3.6 + - - +
107A LYS* 1.3 89.2 - - - +
109A LEU* 1.3 52.5 + - + +
111A ASP* 3.2 8.0 - - - +
112A ALA* 2.7 36.7 + - - +
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Residues in contact with LEU 109 (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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31A LEU* 4.6 3.1 - - + +
33A VAL* 3.8 15.3 - - + -
34A PHE 4.5 0.2 - - - +
40A ILE* 3.7 15.3 - - + +
41A TYR 3.1 38.8 - - - +
42A ALA* 3.1 24.7 - - + -
44A ILE* 5.4 2.4 - - - +
71A ILE* 4.0 13.5 - - + -
74A ALA* 3.7 28.9 - - + -
75A LYS* 4.6 2.0 - - - +
78A GLY 5.1 5.0 - - - +
106A VAL* 3.4 18.4 - - + +
108A ALA* 1.3 79.1 - - + +
110A ALA* 1.3 64.4 + - - +
111A ASP 3.1 0.3 + - - -
112A ALA* 3.2 12.6 + - - +
113A ALA* 3.5 10.2 + - - +
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Residues in contact with ALA 110 (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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31A LEU* 3.7 14.1 - - + +
33A VAL* 3.7 9.3 - - + +
93A VAL 5.5 0.2 - - - +
95A PHE* 3.4 20.9 - - + -
99A GLY* 4.4 4.3 - - - -
102A TYR* 3.0 40.0 + - + +
106A VAL 3.6 1.4 + - - +
107A LYS 3.2 1.6 + - - +
109A LEU* 1.3 79.4 - - - +
111A ASP* 1.3 51.5 + - - +
113A ALA* 3.7 3.4 - - - +
114A ARG* 2.7 31.8 + - - +
118A LEU* 5.3 0.3 - - - +
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Residues in contact with ASP 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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75A LYS* 3.4 16.6 + - - -
102A TYR* 4.2 16.5 - - + +
107A LYS* 2.4 43.8 + - + +
108A ALA* 3.2 7.6 - - - +
110A ALA* 1.3 67.7 - - - +
112A ALA* 1.3 58.8 + - - +
113A ALA 3.0 1.6 - - - -
114A ARG* 2.5 29.1 + - - +
115A GLU* 2.6 33.2 + - - +
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Residues in contact with ALA 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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75A LYS* 4.1 15.3 - - + +
79A GLU* 3.5 51.5 - - + +
82A ALA* 4.6 3.1 - - + +
108A ALA 2.7 19.4 + - - +
109A LEU* 3.6 7.2 - - - +
111A ASP* 1.3 74.6 + - - +
113A ALA* 1.3 59.7 + - - +
115A GLU* 4.4 3.2 - - - +
116A ALA* 3.2 21.8 + - - +
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Residues in contact with ALA 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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31A LEU* 3.7 25.4 - - + -
82A ALA* 4.0 11.1 - - + +
92A GLN* 2.9 50.2 - - + +
93A VAL 4.4 0.9 - - - +
109A LEU 3.5 3.6 + - - +
110A ALA 3.9 1.3 - - - +
111A ASP 3.0 0.4 - - - -
112A ALA* 1.3 77.0 - - - +
114A ARG* 1.3 65.9 + - - +
116A ALA* 3.3 4.2 + - - +
117A GLY 3.0 16.3 + - - -
118A LEU* 3.4 2.6 + - - -
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Residues in contact with ARG 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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95A PHE* 5.8 1.4 - - - -
101A LEU* 4.1 10.5 + - - +
102A TYR* 3.2 38.2 - - + -
110A ALA 2.7 20.5 + - - +
111A ASP* 2.5 17.5 + - - +
113A ALA* 1.3 71.1 - - - +
115A GLU* 1.3 57.3 + - - +
117A GLY* 2.7 22.5 + - - -
118A LEU* 3.2 45.2 + - - +
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Residues in contact with GLU 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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75A LYS* 5.7 2.7 + - - -
79A GLU* 5.5 2.6 - - - +
111A ASP* 2.6 29.4 + - - +
112A ALA* 4.4 3.8 - - - +
114A ARG* 1.3 76.3 - - - +
116A ALA* 1.3 60.6 + - - +
117A GLY* 3.3 1.4 + - - -
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Residues in contact with ALA 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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79A GLU* 6.3 0.7 - - + -
82A ALA* 6.0 0.2 - - + -
83A LYS* 5.5 4.9 - - + +
86A LEU* 3.5 30.3 - - + +
92A GLN* 4.9 0.7 - - - +
112A ALA 3.2 19.6 + - - +
113A ALA* 3.5 8.5 - - - +
114A ARG 3.0 0.6 - - - -
115A GLU* 1.3 80.1 - - - +
117A GLY* 1.3 58.7 + - - +
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Residues in contact with GLY 117 (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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86A LEU* 4.8 0.9 - - - +
91A LYS* 4.6 0.9 - - - +
92A GLN* 2.7 27.7 + - - +
113A ALA 3.0 5.7 + - - -
114A ARG 2.7 8.7 + - - -
115A GLU 3.1 1.3 - - - -
116A ALA* 1.3 80.5 - - - +
118A LEU* 1.3 54.8 + - - -
119A GLU* 3.1 14.1 + - - +
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Residues in contact with LEU 118 (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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31A LEU* 5.6 0.2 - - + -
92A GLN* 3.9 4.7 - - - -
93A VAL 2.6 39.9 - - - +
94A VAL* 3.3 29.6 - - + +
95A PHE* 4.4 4.3 - - + -
102A TYR* 3.5 23.6 - - + +
110A ALA 5.8 0.2 - - - +
113A ALA 3.4 0.9 + - - -
114A ARG* 3.2 49.3 + - - +
117A GLY* 1.3 69.4 - - - +
119A GLU* 1.3 78.5 + - - +
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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