Contacts of the helix formed by residues 15 - 28 (chain A) in PDB entry 4OG6
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 SER 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ARG* 1.3 82.4 - - - +
16A ILE* 1.3 65.7 - - - +
17A ASP* 3.3 9.5 + - - +
18A ASP* 3.0 34.1 + - - +
19A VAL* 3.2 16.6 + - - +
21A ARG* 4.5 0.7 + - - -
77A TYR* 4.2 18.8 - - - -
78A PHE* 3.4 18.1 - - - -
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Residues in contact with ILE 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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15A SER* 1.3 73.3 - - - +
17A ASP* 1.3 66.0 + - - +
19A VAL* 3.1 6.7 + - - +
20A VAL* 3.0 20.8 + - + +
48A LEU* 5.9 0.2 - - + -
77A TYR* 5.2 7.9 + - + +
78A PHE* 3.7 23.8 - - + -
255A GLU* 3.6 39.7 - - + +
258A GLN* 3.7 35.7 - - - +
259A LEU* 3.9 32.5 - - + +
262A LYS* 4.0 15.3 - - + -
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Residues in contact with ASP 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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15A SER* 3.2 7.6 + - - +
16A ILE* 1.3 80.7 - - - +
18A ASP* 1.3 56.5 + - - +
20A VAL* 3.3 10.1 + - + +
21A ARG* 2.9 52.6 + - - +
262A LYS* 2.8 38.8 + - - +
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Residues in contact with ASP 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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10A LEU* 5.0 3.0 - - + +
12A PRO 3.8 6.7 - - - +
13A LEU* 3.7 22.8 - - + +
14A ARG* 2.7 38.7 + - - +
15A SER* 3.0 23.2 + - - +
17A ASP* 1.3 73.9 - - - +
19A VAL* 1.3 64.1 + - - +
21A ARG* 2.8 39.3 + - - +
22A LEU 3.0 17.8 + - - -
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Residues in contact with VAL 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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13A LEU* 4.3 16.8 - - + -
15A SER 3.2 13.4 + - - +
16A ILE* 3.1 8.0 + - - +
18A ASP* 1.3 76.1 - - - +
20A VAL* 1.3 61.9 + - - +
22A LEU* 3.1 8.3 + - + +
23A PHE* 3.0 44.9 + - + -
40A VAL* 4.1 13.0 - - + -
41A LEU* 4.4 2.2 - - + -
44A VAL* 4.4 9.2 - - + -
78A PHE* 3.6 24.5 - - + -
259A LEU* 3.8 25.4 - - + -
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Residues in contact with VAL 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 ILE 3.0 20.5 + - - +
17A ASP* 3.6 12.1 - - - +
18A ASP 3.3 0.2 - - - -
19A VAL* 1.3 72.8 - - - +
21A ARG* 1.3 63.4 + - - +
23A PHE* 3.2 3.3 + - - +
24A ALA* 2.9 22.6 + - + +
259A LEU* 4.2 7.6 - - + -
262A LYS* 3.9 33.9 - - + +
263A LEU* 3.9 19.3 - - + -
266A LEU* 4.2 24.0 - - + -
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Residues in contact with ARG 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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10A LEU* 3.8 25.0 - - + +
15A SER* 4.5 0.8 + - - -
17A ASP* 2.9 40.1 + - - +
18A ASP* 2.8 44.3 + - - +
20A VAL* 1.3 76.7 - - - +
22A LEU* 1.3 62.6 + - - +
24A ALA* 3.2 8.4 + - - +
25A ALA* 2.9 23.6 + - - +
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Residues in contact with LEU 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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7A GLN* 4.3 19.3 - - - +
10A LEU* 3.7 20.3 - - + +
11A PHE* 4.0 11.0 - - + -
13A LEU* 3.9 26.9 - - + -
18A ASP 3.0 11.8 + - - +
19A VAL* 3.1 8.9 + - - +
21A ARG* 1.3 76.2 - - - +
23A PHE* 1.3 59.0 + - + +
25A ALA* 3.2 4.1 + - + +
26A GLU* 2.9 33.8 + - + +
36A LEU* 4.3 15.0 - - + -
37A LEU* 4.1 17.7 - - + -
40A VAL* 3.9 23.3 - - + -
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Residues in contact with PHE 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 VAL* 3.0 30.9 + - + -
20A VAL 3.2 3.1 + - - +
22A LEU* 1.3 78.5 - - + +
24A ALA* 1.3 55.9 + - - +
26A GLU* 3.4 0.7 + - - +
27A LEU* 2.9 37.6 + - + +
37A LEU* 3.8 41.3 - - + -
40A VAL* 4.9 4.3 - - + -
41A LEU* 3.6 41.1 - - + -
236A VAL* 3.7 32.5 - - + -
239A MET* 4.2 2.9 - - - -
240A VAL* 4.0 14.1 - - + -
263A LEU* 3.6 29.8 - - + -
266A LEU* 3.9 8.5 - - + -
267A LEU* 6.1 0.4 - - + -
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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 VAL* 2.9 13.4 + - + +
21A ARG* 3.2 12.3 + - - +
23A PHE* 1.3 76.1 - - - +
25A ALA* 1.3 61.1 + - - +
27A LEU* 3.4 4.4 + - - +
28A GLY* 3.1 18.9 + - - -
266A LEU* 3.6 25.5 - - + +
270A LEU* 5.5 1.9 - - - +
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Residues in contact with ALA 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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6A ALA 6.0 1.8 - - - +
10A LEU* 4.2 15.5 - - + -
21A ARG 2.9 15.6 + - - +
22A LEU* 3.2 7.4 + - + +
24A ALA* 1.3 76.0 - - - +
26A GLU* 1.3 64.4 + - + +
28A GLY* 3.1 12.4 + - - -
29A ARG* 3.3 19.4 + - - +
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Residues in contact with GLU 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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7A GLN* 3.1 38.1 + - - +
22A LEU* 2.9 26.8 + - + +
23A PHE 3.9 2.9 - - - +
25A ALA* 1.3 78.9 - - + +
27A LEU* 1.3 57.5 + - - +
29A ARG* 3.0 32.2 + - - +
31A GLU 4.1 1.2 - - - +
32A PRO* 3.4 23.0 - - + +
33A ASP* 2.8 32.1 + - - +
36A LEU* 3.7 9.1 - - + +
37A LEU* 3.9 34.5 - - + -
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Residues in contact with LEU 27 (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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23A PHE* 2.9 25.2 + - + +
24A ALA 3.9 3.8 - - - +
25A ALA 3.3 0.2 - - - -
26A GLU* 1.3 76.1 - - + +
28A GLY* 1.3 58.3 + - - +
29A ARG 3.3 1.7 + - - +
32A PRO* 4.3 3.6 - - + -
37A LEU* 5.8 0.4 - - + -
233A LYS* 3.5 46.9 - - + +
236A VAL* 4.0 35.0 - - + -
266A LEU* 4.0 21.3 - - + -
267A LEU* 3.9 27.1 - - + -
270A LEU* 4.1 21.6 - - + +
272A HIS* 4.3 6.0 + - + +
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Residues in contact with GLY 28 (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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24A ALA 3.1 9.6 + - - -
25A ALA* 3.1 9.5 + - - -
27A LEU* 1.3 76.2 - - - +
29A ARG* 1.3 60.6 + - - +
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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