Contacts of the helix formed by residues 15 - 26 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13H ALA 3.4 1.0 - - - -
14H VAL* 1.3 78.6 - - - +
16H LYS* 1.3 65.3 + - - +
17H THR 3.4 2.5 - - - -
18H CYS* 4.0 1.0 - - - +
19H LEU* 3.1 26.0 + - - +
115H THR* 4.9 6.3 - - - +
159H ALA* 5.1 0.3 - - - +
200H GCP 2.9 42.9 + - - -
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Residues in contact with LYS 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H VAL* 3.7 27.6 - - + +
9H VAL* 3.4 28.9 - - - -
10H GLY* 3.0 12.7 + - - +
11H ASP 3.0 18.4 + - - -
14H VAL* 3.6 11.9 - - + -
15H GLY* 1.3 78.4 - - - +
17H THR* 1.3 63.7 + - - +
19H LEU* 3.5 7.4 - - - +
20H LEU* 3.2 27.0 + - - +
57H ASP* 4.0 7.4 - - - +
58H THR* 3.2 27.8 - - - -
59H ALA 4.6 0.2 - - - -
60H GLY 4.0 1.8 - - - +
81H CYS* 4.1 8.3 - - - -
200H GCP 2.5 47.4 + - - +
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Residues in contact with THR 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H LYS* 1.3 73.2 - - - +
18H CYS* 1.3 68.4 + - - +
20H LEU* 3.1 4.5 + - - +
21H ILE* 2.9 31.9 + - + +
29H PRO* 5.0 7.0 - - + -
33H ILE 5.7 3.6 - - - +
35H THR* 2.8 5.0 + - - +
40H TYR* 3.8 12.3 - - - +
57H ASP* 2.5 27.1 + - - +
200H GCP 3.1 11.8 + - - -
202H MG 2.2 29.6 - - - -
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Residues in contact with CYS 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H GLY 4.0 0.2 - - - +
16H LYS 3.4 0.2 - - - -
17H THR* 1.3 76.8 - - - +
19H LEU* 1.3 53.2 + - - +
21H ILE* 4.1 0.2 - - - +
22H SER* 2.8 37.8 + - - -
28H PHE* 3.8 23.3 - - + -
29H PRO* 3.9 31.4 - - - +
31H GLU 5.4 2.5 - - - -
159H ALA* 3.6 2.5 - - + -
200H GCP 2.9 66.7 + - + +
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Residues in contact with LEU 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H VAL* 4.7 7.2 - - + -
15H GLY 3.1 17.6 + - - +
16H LYS* 3.5 10.3 - - - +
18H CYS* 1.3 76.2 - - - +
20H LEU* 1.3 71.2 + - + +
23H TYR* 3.2 24.6 + - - +
79H LEU* 4.3 11.4 - - + -
81H CYS* 4.7 6.1 - - - -
113H VAL* 4.0 16.6 - - + -
115H THR* 4.4 10.8 - - + -
157H CYS* 3.7 27.6 - - - -
159H ALA* 3.5 16.2 - - + +
165H LEU* 3.6 17.8 - - + +
168H VAL* 5.0 5.2 - - + -
169H PHE* 3.7 21.8 - - + -
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Residues in contact with LEU 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H VAL* 3.9 24.2 - - + -
16H LYS 3.2 10.5 + - - +
17H THR 3.1 7.4 + - - +
19H LEU* 1.3 82.1 - - + +
21H ILE* 1.3 58.5 + - - +
23H TYR* 3.5 4.0 + - - +
24H THR* 2.9 35.1 + - - +
40H TYR* 4.1 19.1 - - + -
55H LEU* 4.0 23.6 - - + -
57H ASP* 3.6 41.3 - - + +
169H PHE* 3.5 30.3 - - + -
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Residues in contact with ILE 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H THR* 2.9 33.8 + - + +
18H CYS 4.1 0.2 - - - +
20H LEU* 1.3 73.1 - - - +
22H SER* 1.3 60.6 + - - +
23H TYR 3.2 0.4 - - - -
24H THR* 3.8 2.0 - - - +
25H THR* 2.6 51.0 + - + +
27H ALA* 3.5 12.1 - - + +
29H PRO* 4.1 21.3 - - + -
40H TYR* 3.9 30.5 - - + +
17P PHE* 4.1 21.5 - - + -
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Residues in contact with SER 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H CYS 2.8 23.2 + - - -
19H LEU 4.0 0.2 - - - -
21H ILE* 1.3 72.3 - - - +
23H TYR* 1.3 58.6 + - - +
26H ASN* 2.9 18.4 + - - +
27H ALA 3.3 17.4 + - - -
28H PHE* 5.1 2.6 - - - +
159H ALA* 2.6 31.3 + - - -
162H GLN* 2.9 36.9 + - - +
165H LEU* 3.3 10.6 - - - +
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Residues in contact with TYR 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H LEU 3.2 17.2 + - - +
20H LEU 3.5 3.4 - - - +
21H ILE 3.2 0.2 - - - -
22H SER* 1.3 81.9 - - - +
24H THR* 1.3 74.2 + - + +
25H THR 3.7 0.2 + - - -
26H ASN* 4.5 5.9 + - - +
44H VAL* 4.1 14.0 - - - +
53H LEU* 4.0 16.2 - - + +
55H LEU* 4.7 0.7 - - + -
162H GLN* 4.9 0.7 - - - +
165H LEU* 3.6 16.8 - - + +
166H LYS* 4.6 18.2 - - + -
169H PHE* 3.3 60.6 - + + +
170H ASP* 4.8 4.5 + - - -
173H ILE* 4.6 5.5 - - - +
11P ILE* 5.6 0.2 - - - +
12P SER 4.8 2.8 + - - -
14P PRO* 3.3 47.5 - - + +
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Residues in contact with THR 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H LEU 2.9 19.6 + - - +
21H ILE* 3.8 3.5 - - - -
23H TYR* 1.3 86.6 - - + +
25H THR* 1.3 65.5 + - - +
26H ASN* 3.9 0.4 - - - -
40H TYR* 5.5 1.1 - - + -
42H ALA* 4.3 15.7 - - + -
55H LEU* 3.7 28.0 - - + -
14P PRO* 4.1 15.4 - - + +
15P SER* 5.8 0.7 - - - -
17P PHE* 3.3 45.5 - - + +
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Residues in contact with THR 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H ILE* 2.6 35.4 + - + +
24H THR* 1.3 92.6 - - - +
26H ASN* 1.3 71.1 + - - +
27H ALA* 3.1 17.7 + - - +
17P PHE* 3.8 31.0 - - + -
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Residues in contact with ASN 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H SER* 2.9 18.7 + - - +
23H TYR 4.5 5.4 - - - +
25H THR* 1.3 77.9 + - - +
27H ALA* 1.3 57.9 + - - +
28H PHE 4.3 0.3 + - - -
162H GLN* 3.2 30.6 + - - +
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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