Contacts of the helix formed by residues 7 - 26 (chain A) in PDB entry 2OFY
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 THR 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A PRO 4.9 3.8 - - - +
6A LEU* 1.3 78.4 - - - +
8A ALA* 1.3 65.2 + - - +
9A GLU* 3.5 16.9 + - - +
10A GLU* 2.9 42.2 + - - +
11A LEU* 3.1 20.0 + - - +
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Residues in contact with ALA 8 (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 THR* 1.3 73.4 - - - +
9A GLU* 1.3 75.6 + - - +
11A LEU* 3.3 6.8 + - - +
12A GLU* 3.0 31.8 + - - +
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Residues in contact with GLU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A THR* 3.1 12.4 + - - +
8A ALA* 1.3 97.1 + - - +
10A GLU* 1.3 57.6 + - - +
12A GLU* 3.9 9.6 - - - +
13A ARG* 2.9 55.0 + - + +
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Residues in contact with GLU 10 (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 PRO 4.5 1.2 - - - +
6A LEU* 3.4 27.9 - - + +
7A THR* 2.9 44.5 + - - +
9A GLU* 1.3 72.8 - - - +
11A LEU* 1.3 65.6 + - - +
13A ARG* 3.3 22.3 + - - +
14A GLY* 3.0 19.8 + - - -
53A ALA 5.5 1.8 - - - +
58B PHE* 5.3 2.1 - - - -
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Residues in contact with LEU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 4.4 26.2 - - + +
7A THR 3.1 10.5 + - - +
8A ALA* 3.8 9.6 - - - +
10A GLU* 1.3 78.2 - - - +
12A GLU* 1.3 58.4 + - - +
14A GLY* 3.2 3.3 + - - -
15A GLN* 2.9 67.0 + - + +
50A GLY 4.2 12.6 - - - +
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Residues in contact with GLU 12 (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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8A ALA 3.0 18.1 + - - +
9A GLU* 3.9 10.3 - - - +
11A LEU* 1.3 78.4 - - - +
13A ARG* 1.3 55.6 + - + +
15A GLN* 3.2 12.5 + - + +
16A ARG* 2.9 68.3 + - + +
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Residues in contact with ARG 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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9A GLU* 2.9 37.6 + - - +
10A GLU* 3.7 31.6 - - - +
12A GLU* 1.3 75.9 - - - +
14A GLY* 1.3 58.4 + - - +
16A ARG* 3.7 9.5 - - - +
17A LEU* 2.9 31.0 + - - +
78A VAL* 3.8 26.7 - - + +
79A THR* 2.8 32.7 + - - +
80A PHE* 4.0 17.8 - - - +
81A GLY 4.8 3.4 + - - +
58B PHE* 3.4 37.0 - - + +
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Residues in contact with GLY 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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10A GLU 3.0 14.3 + - - -
11A LEU* 3.6 3.4 - - - -
13A ARG* 1.3 77.0 - - - +
15A GLN* 1.3 58.6 + - - +
17A LEU* 3.4 4.4 + - - +
18A GLY* 3.0 24.6 + - - -
47A ILE 4.4 1.4 - - - +
50A GLY* 4.1 13.0 - - - -
52A ILE 5.5 3.4 - - - -
55A PRO* 5.1 12.0 - - - +
58B PHE* 3.9 11.8 - - - -
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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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11A LEU* 2.9 53.3 + - + +
12A GLU* 3.6 12.9 - - + +
14A GLY* 1.3 73.3 - - - +
16A ARG* 1.3 65.5 + - - +
18A GLY* 3.2 1.6 + - - -
19A GLU* 3.0 37.9 + - + +
48A GLU 4.9 0.7 - - - +
49A THR 4.8 6.1 + - - +
50A GLY* 4.2 20.3 + - - +
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Residues in contact with ARG 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 GLU* 2.9 60.1 + - + +
13A ARG* 3.7 7.7 - - - +
15A GLN* 1.3 72.5 - - + +
17A LEU* 1.3 63.4 + - - +
19A GLU* 3.3 15.7 + - - +
20A LEU* 3.0 28.4 + - - +
77A VAL* 2.9 43.2 + - + -
78A VAL* 3.5 23.6 - - + +
79A THR* 4.6 4.0 + - - +
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Residues in contact with LEU 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 ARG 2.9 18.2 + - - +
14A GLY 3.6 4.5 - - - +
15A GLN 3.3 0.2 - - - -
16A ARG* 1.3 75.7 - - - +
18A GLY* 1.3 62.8 + - - +
20A LEU* 3.2 8.5 + - - +
21A LEU* 3.0 46.3 + - + +
47A ILE* 5.1 2.5 - - + -
55A PRO* 4.3 12.3 - - + -
60A ILE* 3.8 36.3 - - + -
74A VAL* 3.3 32.5 - - + -
77A VAL* 5.8 1.3 - - - -
78A VAL* 6.1 0.2 - - - +
57B PHE* 4.1 9.4 - - + -
58B PHE* 3.8 25.6 - - + -
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Residues in contact with GLY 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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14A GLY 3.0 12.0 + - - -
15A GLN 3.2 2.9 + - - -
17A LEU* 1.3 76.4 - - - +
19A GLU* 1.3 55.3 + - - +
21A LEU* 3.3 4.8 + - - +
22A ARG* 2.8 28.1 + - - +
47A ILE* 3.1 28.0 + - - -
48A GLU* 3.1 21.4 - - - +
50A GLY 4.9 0.4 - - - -
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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* 3.0 32.7 + - + +
16A ARG* 3.4 16.8 + - - +
18A GLY* 1.3 75.0 - - - +
20A LEU* 1.3 58.7 + - + +
22A ARG* 3.3 6.3 + - - +
23A SER* 2.9 35.1 + - - +
48A GLU 3.7 4.0 + - - +
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Residues in contact with LEU 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 ARG* 3.0 13.0 + - + +
17A LEU* 3.2 9.6 + - - +
19A GLU* 1.3 75.1 - - + +
21A LEU* 1.3 61.9 + - + +
23A SER* 3.4 7.5 + - - -
24A ALA* 2.9 29.9 + - - +
69A LEU* 4.8 4.9 - - + +
74A VAL* 3.9 33.7 - - + +
77A VAL* 3.6 45.3 - - + -
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Residues in contact with LEU 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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17A LEU* 3.0 33.4 + - + +
18A GLY* 3.7 4.9 - - - +
20A LEU* 1.3 73.2 - - - +
22A ARG* 1.3 61.2 + - - +
24A ALA* 3.3 3.3 + - - +
25A ARG* 2.9 29.6 + - - +
44A LEU* 5.7 0.9 - - + -
47A ILE* 3.5 30.1 - - + -
48A GLU* 4.3 11.1 - - + +
60A ILE* 4.0 19.7 - - + -
63A VAL* 4.2 18.6 - - + -
64A ALA* 4.9 7.9 - - + +
67A LEU* 3.8 15.5 - - + +
69A LEU* 3.5 26.7 - - + -
74A VAL* 5.1 2.7 - - + -
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Residues in contact with ARG 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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18A GLY 2.8 17.6 + - - +
19A GLU* 3.6 7.4 - - - +
21A LEU* 1.3 78.6 - - - +
23A SER* 1.3 61.6 + - - +
25A ARG* 3.1 39.7 + - - +
26A GLY* 2.9 38.9 + - - +
48A GLU* 3.4 24.6 + - + +
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Residues in contact with SER 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* 2.9 19.8 + - - +
20A LEU* 3.7 9.6 - - - -
22A ARG* 1.3 77.2 - - - +
24A ALA* 1.3 63.3 + - - +
26A GLY* 3.2 14.7 + - - +
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Residues in contact with ALA 24 (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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20A LEU 2.9 17.3 + - - +
21A LEU 3.7 3.8 - - - +
22A ARG 3.2 0.2 - - - -
23A SER* 1.3 73.3 - - - +
25A ARG* 1.3 65.8 + - - +
26A GLY* 4.3 0.5 - - - -
28A MSE 4.6 4.5 - - - +
67A LEU* 4.0 22.2 - - + +
69A LEU* 3.9 34.3 - - + -
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Residues in contact with ARG 25 (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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21A LEU 2.9 13.1 + - - +
22A ARG* 3.1 42.5 + - - +
24A ALA* 1.3 80.0 - - - +
26A GLY* 1.3 67.4 + - - +
27A ASP 3.1 1.1 + - - -
28A MSE 2.9 63.1 + - + +
29A SER 4.1 3.6 - - - -
30A MSE 3.1 33.8 - - - +
33A VAL* 3.6 32.3 - - + -
44A LEU* 4.4 1.8 - - - -
48A GLU* 2.7 41.3 + - - +
67A LEU* 3.7 16.1 - - + +
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Residues in contact with GLY 26 (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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22A ARG* 2.9 37.2 + - - -
23A SER* 3.2 13.6 + - - -
24A ALA 4.3 0.7 - - - -
25A ARG* 1.3 75.8 + - - +
27A ASP* 1.3 64.0 + - - +
28A MSE 3.4 3.8 + - - +
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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