Contacts of the strand formed by residues 15 - 26 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24F THR 5.9 0.7 - - - -
42F ALA* 3.3 3.5 - - - +
43F ASN* 2.7 46.4 + - - +
13N ALA 4.8 3.0 + - - -
14N PRO* 1.3 73.9 - - - +
16N ASN* 1.3 78.0 + - - +
17N PHE* 3.2 4.8 + - - -
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Residues in contact with ASN 16 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F SER* 3.7 5.9 + - - +
42F ALA* 3.9 2.9 - - - -
43F ASN* 2.7 30.9 + - - +
15N SER* 1.3 86.4 + - - +
17N PHE* 1.3 68.4 + - - +
18N GLU* 3.4 12.3 + - + +
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Residues in contact with PHE 17 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F ILE* 4.4 9.6 - - + -
24F THR* 3.3 49.1 - - + +
25F THR* 4.1 21.3 - - + -
40F TYR* 3.8 36.1 - + + -
41F SER 3.3 13.0 - - - -
42F ALA* 4.5 2.9 - - + +
15N SER* 3.2 4.6 - - - +
16N ASN* 1.3 76.4 - - - +
18N GLU* 1.3 70.1 + - - +
19N HIS* 4.2 20.4 - - + -
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Residues in contact with GLU 18 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F TYR* 3.3 7.4 - - - +
41F SER* 2.8 41.2 + - - +
16N ASN* 3.7 10.6 - - - +
17N PHE* 1.3 87.8 - - - +
19N HIS* 1.3 61.3 + - - +
20N ARG* 2.8 35.2 + - + +
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Residues in contact with HIS 19 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F ASP* 2.6 32.3 + - - -
39F ASN 3.5 4.3 - - - -
40F TYR* 3.4 30.0 - + + -
17N PHE* 4.2 13.6 - - + -
18N GLU* 1.3 72.9 - - - +
20N ARG* 1.3 58.6 + - - +
21N VAL 3.0 20.3 + - - -
22N HIS* 3.6 19.3 - + + +
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Residues in contact with ARG 20 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F ASN* 2.9 27.1 + - - +
41F SER* 2.5 37.3 + - - +
18N GLU* 2.8 27.4 + - + +
19N HIS* 1.3 75.2 - - - +
21N VAL* 1.3 69.8 + - + +
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Residues in contact with VAL 21 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F PHE* 3.9 14.1 - - + -
38F ASP* 3.2 2.4 - - - -
39F ASN* 2.9 44.1 + - + +
19N HIS* 3.0 14.1 + - - -
20N ARG* 1.3 89.2 - - + +
22N HIS* 1.3 61.5 + - - +
23N THR* 3.4 24.0 - - - +
34N GLY 3.6 10.3 - - - +
35N LEU 4.6 0.4 - - - -
36N PRO* 4.0 24.5 - - + -
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Residues in contact with HIS 22 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F ASP* 2.7 32.9 + - - +
94H ARG* 6.0 5.6 - - + -
148H GLU* 5.6 6.5 - - - -
19N HIS* 3.6 16.5 - + + +
21N VAL* 1.3 71.2 - - - +
23N THR* 1.3 72.6 + - - +
24N GLY* 4.1 3.2 + - - -
34N GLY* 3.6 16.1 + - - +
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Residues in contact with THR 23 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F VAL* 3.6 26.8 + - + +
37F PHE* 2.9 33.0 + - + +
38F ASP* 4.9 0.2 - - - +
67F LEU* 4.6 3.4 - - + -
21N VAL* 3.4 13.3 - - - +
22N HIS* 1.3 88.0 - - - +
24N GLY* 1.3 68.2 + - - +
32N PHE* 4.3 3.8 - - + -
33N THR 3.1 18.6 - - - +
34N GLY 2.8 15.3 + - - +
35N LEU* 4.1 20.6 - - + -
36N PRO* 3.8 4.7 - - - +
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Residues in contact with GLY 24 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F VAL* 4.1 10.5 - - - -
22N HIS* 4.1 4.8 + - - -
23N THR* 1.3 80.2 - - - +
25N PHE* 1.3 63.3 + - - +
32N PHE* 3.4 8.1 - - - -
33N THR* 2.8 37.0 + - - +
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Residues in contact with PHE 25 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F VAL* 4.5 2.7 - - + +
64F TYR* 3.3 29.8 - + + +
66F ARG* 3.5 27.8 - - - -
24N GLY* 1.3 72.8 - - - +
26N ASP* 1.3 66.5 + - - +
27N GLN* 3.6 43.2 + - - +
30N GLN* 3.6 33.2 - - - -
31N LYS* 3.6 26.0 - - - -
32N PHE* 3.6 22.7 - + + -
33N THR* 3.8 3.2 + - - +
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Residues in contact with ASP 26 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147H ARG* 4.3 16.3 + - - +
25N PHE* 1.3 73.3 - - - +
27N GLN* 1.3 54.2 + - - +
28N HIS* 3.2 32.1 + - - +
29N GLU* 3.3 29.7 + - + +
30N GLN* 2.7 35.2 + - - -
31N LYS* 2.9 19.8 + - + +
33N THR* 4.1 15.0 - - + +
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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