Contacts of the helix formed by residues 12 - 23 (chain A) in PDB entry 1OFV
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 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A THR* 2.7 30.5 + - - +
10A GLN 3.5 1.6 - - - -
11A THR* 1.3 73.0 - - - +
13A VAL* 1.3 65.1 + - - +
14A THR 3.4 0.2 - - - -
15A GLN* 3.2 9.4 + - - +
16A THR* 3.1 25.3 + - - -
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Residues in contact with VAL 13 (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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11A THR* 4.3 8.7 - - - +
12A GLY* 1.3 78.4 - - - +
14A THR* 1.3 63.6 - - - +
16A THR* 3.0 10.4 + - - -
17A ILE* 3.0 26.1 + - + +
88A ALA* 3.9 12.3 - - + -
145A GLU* 3.6 34.1 - - + -
146A ASP* 6.1 0.4 - - - +
170A FMN 2.8 40.6 + - - +
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Residues in contact with THR 14 (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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7A TYR* 4.1 6.3 - - + -
8A GLY 3.4 22.0 - - - +
9A THR* 4.2 0.2 - - - -
13A VAL* 1.3 74.0 - - - +
15A GLN* 1.3 56.9 + - - +
17A ILE* 3.6 8.9 - - + +
18A ALA* 2.8 27.5 + - - +
53A GLY 3.8 19.7 - - - +
54A CYS 3.9 2.7 - - - +
55A PRO* 3.3 18.4 - - - +
86A PHE* 3.7 21.5 - - + -
88A ALA* 3.6 10.4 + - - +
170A FMN 2.8 28.2 + - - -
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Residues in contact with GLN 15 (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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7A TYR* 3.3 43.2 + - + +
9A THR* 3.9 16.4 + - + +
12A GLY* 3.2 12.9 + - - +
13A VAL 3.0 0.6 - - - -
14A THR* 1.3 79.3 - - - +
16A THR* 1.3 61.8 + - - +
18A ALA* 3.1 3.1 + - - +
19A GLU* 2.8 55.6 + - + +
33A LEU* 6.2 0.2 - - + -
35A ASP* 5.2 1.6 - - - +
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Residues in contact with THR 16 (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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12A GLY 3.1 13.1 + - - -
13A VAL* 3.0 12.3 + - - -
15A GLN* 1.3 77.4 - - - +
17A ILE* 1.3 67.3 - - + +
19A GLU* 3.2 15.7 + - - +
20A SER* 3.0 27.0 + - - +
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Residues in contact with ILE 17 (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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13A VAL* 3.0 24.3 + - + +
14A THR* 3.6 9.2 - - - +
15A GLN 3.1 0.2 - - - -
16A THR* 1.3 77.2 - - + +
18A ALA* 1.3 66.8 - - - +
20A SER* 2.9 8.8 + - - -
21A ILE* 2.9 31.2 + - + +
86A PHE* 3.5 27.8 - - + -
87A GLY 4.8 0.4 - - - +
88A ALA* 4.0 20.9 - - + +
141A LEU* 5.1 0.4 - - + -
143A ILE* 3.7 41.1 - - + -
145A GLU* 5.4 1.6 - - + -
152A THR* 5.1 4.0 - - + -
156A ILE* 4.1 20.9 - - + -
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Residues in contact with ALA 18 (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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5A LEU* 3.8 10.3 - - + +
7A TYR* 3.8 15.3 - - + -
14A THR 2.8 17.1 + - - +
15A GLN 3.1 4.7 + - - +
17A ILE* 1.3 78.0 - - - +
19A GLU* 1.3 63.8 + - - +
21A ILE* 3.2 4.2 + - - +
22A GLN* 3.0 22.7 + - - +
33A LEU* 3.6 24.4 - - + +
86A PHE* 3.7 21.1 - - + -
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Residues in contact with GLU 19 (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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15A GLN* 2.8 46.3 + - + +
16A THR* 3.6 16.5 + - - +
18A ALA* 1.3 74.6 - - - +
20A SER* 1.3 59.0 - - - +
22A GLN* 3.4 6.4 + - - +
23A GLN* 3.0 28.7 + - - +
33A LEU* 3.7 25.1 - - + +
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Residues in contact with SER 20 (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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16A THR* 3.0 17.6 + - - +
17A ILE* 2.9 8.6 + - - -
19A GLU* 1.3 76.4 - - - +
21A ILE* 1.3 60.3 + - - +
23A GLN* 3.3 11.9 + - - +
24A GLU* 2.9 31.8 + - - +
156A ILE* 3.8 26.3 - - - +
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Residues in contact with ILE 21 (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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5A LEU* 3.9 14.4 - - + -
17A ILE* 2.9 27.1 + - + +
18A ALA 3.7 5.6 - - - +
20A SER* 1.3 72.2 - - - +
22A GLN* 1.3 67.2 + - - +
24A GLU* 3.1 3.5 + - - +
25A PHE* 3.0 48.4 + - + -
51A ILE* 4.3 6.3 - - + -
86A PHE* 3.7 41.5 - - + -
141A LEU* 4.9 2.0 - - + -
156A ILE* 4.1 20.2 - - + -
159A TRP* 3.7 19.5 - - + -
160A VAL* 4.0 6.5 - - + -
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Residues in contact with GLN 22 (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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5A LEU* 4.7 0.4 - - + +
18A ALA 3.0 13.5 + - - +
19A GLU* 3.7 10.0 - - - +
20A SER 3.2 0.2 - - - -
21A ILE* 1.3 75.4 - - - +
23A GLN* 1.3 63.4 + - - +
25A PHE* 3.2 10.2 + - - +
26A GLY 3.3 0.5 + - - -
27A GLY* 3.0 35.7 + - - +
28A GLU* 3.4 34.3 + - - +
31A VAL* 2.7 43.2 + - + +
32A ASP* 4.5 0.2 - - - +
33A LEU* 3.6 37.8 - - + +
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Residues in contact with GLN 23 (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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19A GLU 3.0 16.8 + - - +
20A SER* 3.7 9.6 + - - +
22A GLN* 1.3 78.4 - - - +
24A GLU* 1.3 62.1 + - - +
26A GLY* 3.1 13.7 + - - -
27A GLY* 3.9 7.5 + - - +
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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