Contacts of the strand formed by residues 15 - 26 (chain O) 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 SER 15 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24G THR 5.8 2.2 - - - -
42G ALA* 3.5 3.6 - - - -
43G ASN* 2.8 46.3 + - - +
13O ALA 4.8 2.2 - - - -
14O PRO* 1.3 75.0 - - - +
16O ASN* 1.3 81.6 + - - +
17O PHE 3.4 3.0 + - - -
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Residues in contact with ASN 16 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G SER* 3.7 5.4 - - - +
42G ALA* 4.1 2.6 - - - -
43G ASN* 3.7 22.4 + - - +
15O SER* 1.3 92.8 + - - +
17O PHE* 1.3 70.2 + - - +
18O GLU* 3.4 6.6 + - - +
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Residues in contact with PHE 17 (chain O).
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* 4.2 10.8 - - + -
24G THR* 3.6 42.8 + - - +
25G THR* 3.8 18.2 - - + -
40G TYR* 3.7 42.2 - + + -
41G SER 3.4 10.5 - - - -
42G ALA* 4.7 2.4 - - - +
15O SER 3.4 3.4 - - - -
16O ASN* 1.3 78.4 - - - +
18O GLU* 1.3 63.7 + - - +
19O HIS* 4.0 24.2 - + + -
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Residues in contact with GLU 18 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G TYR* 3.2 6.1 - - - +
41G SER* 2.8 48.3 + - - +
16O ASN 4.2 4.7 - - - +
17O PHE* 1.3 80.9 - - - +
19O HIS* 1.3 65.1 + - - +
20O ARG* 3.5 25.5 + - + +
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Residues in contact with HIS 19 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G ASP* 2.9 28.7 + - - -
39G ASN 3.5 8.3 - - - -
40G TYR* 3.6 21.1 - + - -
17O PHE* 4.0 20.5 - + + -
18O GLU* 1.3 73.8 - - - +
20O ARG* 1.3 62.6 + - - +
21O VAL 3.1 22.3 + - - -
22O HIS* 3.6 21.5 - + + +
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Residues in contact with ARG 20 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G ASN* 2.8 31.6 + - - +
41G SER* 2.9 32.1 - - - +
18O GLU* 3.9 32.5 - - - +
19O HIS* 1.3 74.5 - - - +
21O VAL* 1.3 63.4 + - + +
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Residues in contact with VAL 21 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G PHE* 4.2 3.1 - - + -
38G ASP* 3.4 2.1 - - - -
39G ASN* 3.0 48.3 + - + +
19O HIS* 3.1 13.2 + - - -
20O ARG* 1.3 84.4 - - + +
22O HIS* 1.3 61.8 + - - +
23O THR* 3.5 11.9 - - - +
34O GLY 3.3 22.7 - - - +
35O LEU 4.3 0.7 - - - +
36O PRO* 3.8 32.3 - - + -
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Residues in contact with HIS 22 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G ASP* 2.7 26.5 + - - -
19O HIS* 3.6 19.7 - + + +
21O VAL* 1.3 75.0 - - - +
23O THR* 1.3 73.8 + - - +
24O GLY* 3.9 2.4 + - - -
33O THR 4.0 0.3 - - - +
34O GLY* 3.6 15.4 + - - +
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Residues in contact with THR 23 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36G VAL* 3.5 26.7 + - + +
37G PHE* 2.9 36.5 + - + +
38G ASP* 5.0 0.7 - - - +
67G LEU* 4.6 3.8 - - + -
21O VAL* 3.5 11.1 - - - +
22O HIS* 1.3 84.8 - - - +
24O GLY* 1.3 69.7 + - - +
32O PHE* 4.2 3.8 - - + -
33O THR 3.2 13.9 - - - +
34O GLY 2.9 13.6 + - - -
35O LEU* 3.8 23.1 - - + -
36O PRO* 3.8 4.5 - - - +
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Residues in contact with GLY 24 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36G VAL* 4.2 11.2 - - - -
22O HIS* 3.9 4.3 + - - -
23O THR* 1.3 80.3 - - - +
25O PHE* 1.3 58.5 + - - +
32O PHE* 3.3 7.8 - - - -
33O THR* 2.8 42.3 + - - +
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Residues in contact with PHE 25 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36G VAL* 4.6 3.1 - - + +
64G TYR* 3.4 27.1 - + + +
66G ARG* 3.6 25.6 - - - -
24O GLY* 1.3 74.8 - - - +
26O ASP* 1.3 67.9 + - - +
27O GLN* 3.6 31.0 + - - +
30O GLN* 3.6 44.4 - - + -
31O LYS* 3.7 21.5 - - - -
32O PHE* 3.7 26.7 - + + -
33O THR* 3.7 2.1 + - - -
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Residues in contact with ASP 26 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25O PHE* 1.3 73.3 - - - +
27O GLN* 1.3 53.5 + - - +
28O HIS* 3.3 12.7 + - - +
29O GLU* 2.8 45.0 + - + +
30O GLN* 2.8 34.5 + - - -
31O LYS* 3.0 15.9 + - + +
33O THR* 4.0 16.2 - - + +
1209O CL 4.2 11.4 - - - +
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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