Contacts of the helix formed by residues 15 - 26 (chain G) in PDB entry 2OV2
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 15 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13G ALA 3.5 0.6 - - - -
14G VAL* 1.3 79.5 - - - +
16G LYS* 1.3 60.9 + - - +
18G CYS* 3.9 1.0 - - - +
19G LEU* 3.0 31.6 + - - +
115G THR* 4.8 7.3 - - - +
159G ALA* 4.9 0.3 - - - +
200G GCP 3.0 44.7 + - - -
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Residues in contact with LYS 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G VAL* 4.0 19.7 - - + +
9G VAL* 3.5 11.4 - - - +
10G GLY* 2.9 32.3 + - - +
11G ASP 2.8 21.6 + - - -
14G VAL* 3.8 11.0 - - + -
15G GLY* 1.3 76.3 - - - +
17G THR* 1.3 63.6 + - - +
19G LEU* 3.4 11.7 + - - +
20G LEU* 3.1 28.4 + - - +
57G ASP* 3.9 10.5 - - - +
58G THR* 3.4 20.4 - - - +
59G ALA 4.5 0.2 - - - -
60G GLY 4.0 2.0 - - - +
81G CYS* 4.2 7.9 - - + -
115G THR* 5.4 0.2 - - - +
200G GCP 2.6 50.0 + - - +
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Residues in contact with THR 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G LYS* 1.3 73.5 - - - +
18G CYS* 1.3 63.0 + - - +
20G LEU* 3.2 2.5 + - - +
21G ILE* 2.8 44.1 + - + +
29G PRO* 5.0 7.4 - - + -
33G ILE 5.5 4.7 - - - +
35G THR* 2.9 3.3 + - - +
40G TYR* 4.2 4.9 - - - +
57G ASP* 2.6 26.2 + - - +
200G GCP 3.2 12.7 + - - +
202G MG 2.1 30.5 - - - -
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Residues in contact with CYS 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G GLY 3.9 0.2 - - - +
16G LYS 3.3 0.2 - - - -
17G THR* 1.3 77.2 - - - +
19G LEU* 1.3 53.6 + - - +
21G ILE* 4.1 0.2 - - - +
22G SER* 2.7 38.8 + - - -
28G PHE* 3.9 19.3 - - + -
29G PRO* 3.7 34.7 - - + +
31G GLU 5.7 1.3 - - - -
159G ALA* 3.6 2.7 - - + -
200G GCP 2.8 66.4 + - + +
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Residues in contact with LEU 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G VAL* 4.4 9.0 - - + -
15G GLY 3.0 17.1 + - - +
16G LYS* 3.5 12.1 - - - +
18G CYS* 1.3 77.0 - - - +
20G LEU* 1.3 62.3 + - + +
22G SER* 3.9 0.2 - - - -
23G TYR* 3.1 24.9 + - - +
79G LEU* 4.5 7.6 - - + -
81G CYS* 4.3 23.6 - - - -
113G VAL* 4.4 10.1 - - + -
115G THR* 5.0 5.8 - - + -
157G CYS* 3.3 33.2 - - - -
159G ALA* 3.6 14.1 - - + +
165G LEU* 3.4 20.2 - - + +
168G VAL* 4.7 4.3 - - + -
169G PHE* 4.0 20.6 - - + -
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Residues in contact with LEU 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G VAL* 3.9 29.2 - - + -
16G LYS 3.1 18.1 + - - +
17G THR 3.2 4.0 + - - +
19G LEU* 1.3 78.3 - - + +
21G ILE* 1.3 52.5 + - - +
23G TYR* 3.5 1.6 + - - +
24G THR* 2.7 41.3 + - - +
40G TYR* 4.1 19.1 - - + -
55G LEU* 3.8 22.4 - - + -
57G ASP* 3.5 41.7 - - + +
169G PHE* 3.5 32.3 - - + -
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Residues in contact with ILE 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G THR* 2.8 34.3 + - + +
18G CYS 4.1 1.1 - - - +
20G LEU* 1.3 74.7 - - - +
22G SER* 1.3 60.8 + - - +
24G THR* 3.6 11.4 - - - +
25G THR* 2.5 51.1 + - + +
26G ASN 3.5 0.3 + - - -
27G ALA* 3.6 13.0 - - + +
29G PRO* 4.2 17.0 - - + -
40G TYR* 3.8 34.1 - - + +
17O PHE* 4.2 13.7 - - + -
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Residues in contact with SER 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G CYS 2.7 22.8 + - - -
19G LEU 3.9 1.3 - - - -
21G ILE* 1.3 74.0 - - - +
23G TYR* 1.3 57.6 + - - +
26G ASN* 2.8 28.4 + - - +
27G ALA 3.3 19.5 + - - +
28G PHE* 5.1 2.6 - - - +
159G ALA* 2.8 30.7 + - - -
162G GLN* 3.0 25.6 + - - +
165G LEU* 3.4 8.9 - - - +
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Residues in contact with TYR 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G LEU 3.1 17.7 + - - +
20G LEU 3.7 2.7 - - - +
21G ILE 3.2 0.2 - - - -
22G SER* 1.3 79.9 - - - +
24G THR* 1.3 74.7 + - + +
26G ASN* 3.9 9.2 - - - +
42G ALA* 5.6 0.4 - - + -
44G VAL* 3.6 23.0 - - - +
53G LEU* 4.0 16.5 - - + +
55G LEU* 4.8 0.4 - - + -
162G GLN* 4.8 0.7 - - - +
165G LEU* 3.7 13.2 - - + +
166G LYS* 4.4 27.4 - - + -
169G PHE* 3.4 60.4 - + + +
170G ASP* 4.9 2.8 + - - -
173G ILE* 4.3 5.4 - - - +
12O SER 4.8 2.8 + - - -
14O PRO* 3.1 48.5 - - + +
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Residues in contact with THR 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G LEU 2.7 24.6 + - - +
21G ILE* 3.6 8.0 - - - +
23G TYR* 1.3 88.7 - - + +
25G THR* 1.3 64.2 + - - +
26G ASN* 5.6 0.6 - - - -
40G TYR* 5.3 2.1 - - + +
41G SER 5.4 0.4 - - - +
42G ALA* 4.3 17.8 - - + +
55G LEU* 3.5 28.9 - - + -
14O PRO* 4.1 14.7 - - - +
15O SER* 5.8 1.4 - - - -
17O PHE* 3.6 39.6 + - + +
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Residues in contact with THR 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G ILE* 2.5 39.8 + - + +
24G THR* 1.3 87.2 - - - +
26G ASN* 1.3 71.8 + - - +
27G ALA* 3.3 12.9 + - - +
17O PHE* 3.8 35.2 - - + -
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Residues in contact with ASN 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G SER* 2.8 24.1 + - - +
23G TYR* 3.9 9.5 - - - +
24G THR 5.6 0.4 - - - -
25G THR* 1.3 80.0 + - - +
27G ALA* 1.3 57.5 + - - +
162G GLN* 3.4 24.2 + - - +
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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