Contacts of the strand formed by residues 15 - 26 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B THR 5.7 1.3 - - - -
42B ALA* 3.5 3.9 - - - +
43B ASN* 2.9 40.8 + - - +
13J ALA 5.0 1.6 - - - -
14J PRO* 1.3 74.6 - - - +
16J ASN* 1.3 81.7 + - - +
17J PHE* 3.3 3.8 + - - -
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Residues in contact with ASN 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B SER 3.5 4.7 - - - +
42B ALA* 4.1 1.9 - - - -
43B ASN* 3.5 27.0 + - - +
15J SER* 1.3 92.8 + - - +
17J PHE* 1.3 67.1 + - - +
18J GLU* 3.2 16.2 + - + +
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Residues in contact with PHE 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ILE* 4.2 9.9 - - + -
24B THR* 3.3 49.4 - - + +
25B THR* 3.8 19.3 - - + -
40B TYR* 3.8 37.7 - + + -
41B SER 3.3 10.8 - - - -
42B ALA* 4.7 1.8 - - + +
15J SER 3.3 4.1 - - - -
16J ASN* 1.3 77.2 - - - +
18J GLU* 1.3 64.5 + - - +
19J HIS* 3.9 24.5 - + + -
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Residues in contact with GLU 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TYR* 3.2 6.2 - - - +
41B SER* 2.8 49.3 + - - +
16J ASN* 3.2 16.4 - - + +
17J PHE* 1.3 81.0 - - - +
19J HIS* 1.3 60.5 + - - +
20J ARG* 3.5 11.5 + - + -
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Residues in contact with HIS 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ASP* 2.8 29.6 + - - -
39B ASN 3.5 9.0 - - - -
40B TYR* 3.6 22.8 - + - -
17J PHE* 3.9 17.9 - - + -
18J GLU* 1.3 72.7 - - - +
20J ARG* 1.3 59.4 + - - +
21J VAL 3.2 19.4 + - - -
22J HIS* 3.8 17.3 - + + +
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Residues in contact with ARG 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ASN* 2.8 30.3 + - - +
41B SER* 3.7 33.0 - - - +
18J GLU* 3.5 9.8 + - + +
19J HIS* 1.3 76.4 - - - +
21J VAL* 1.3 64.0 + - + +
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Residues in contact with VAL 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B PHE* 4.1 6.3 - - + -
38B ASP* 3.2 4.9 - - - -
39B ASN* 2.9 46.5 + - + +
19J HIS* 3.2 10.6 + - - -
20J ARG* 1.3 86.3 - - + +
22J HIS* 1.3 63.6 + - - +
23J THR* 3.7 11.4 - - - +
34J GLY 3.6 20.9 - - - +
35J LEU 4.7 0.4 - - - -
36J PRO* 3.8 29.8 - - + -
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Residues in contact with HIS 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLU* 5.2 8.5 + - - -
33B ILE* 6.4 2.5 - - + -
38B ASP* 2.4 36.6 + - - +
94E ARG* 6.4 2.5 - - - -
19J HIS* 3.8 17.3 - + + +
21J VAL* 1.3 75.7 - - - +
23J THR* 1.3 73.3 + - - +
24J GLY* 4.0 3.4 + - - -
34J GLY* 3.6 15.5 + - - +
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Residues in contact with THR 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B VAL* 3.5 26.7 + - + +
37B PHE* 2.8 39.2 + - + +
38B ASP* 4.8 0.3 - - - +
67B LEU* 4.6 1.3 - - + -
21J VAL* 3.7 11.1 - - - +
22J HIS* 1.3 85.2 - - - +
24J GLY* 1.3 71.2 + - - +
32J PHE* 4.2 3.8 - - + -
33J THR 3.3 13.2 - - - +
34J GLY 3.0 13.5 + - - +
35J LEU* 3.9 22.2 - - + -
36J PRO* 3.8 6.2 - - - +
39J TRP* 5.1 0.2 - - - -
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Residues in contact with GLY 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B VAL* 4.2 9.9 - - - -
22J HIS* 4.0 4.8 + - - -
23J THR* 1.3 80.9 - - - +
25J PHE* 1.3 61.0 + - - +
32J PHE* 3.4 8.3 - - - -
33J THR* 2.8 37.9 + - - +
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Residues in contact with PHE 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLY 4.9 8.1 - - - +
36B VAL* 4.4 4.4 - - + +
64B TYR* 3.2 27.8 - + + +
66B ARG* 3.7 26.0 - - - -
24J GLY* 1.3 74.6 - - - +
26J ASP* 1.3 67.6 + - - +
27J GLN* 3.6 37.5 + - - +
30J GLN* 3.5 42.4 - - - -
31J LYS 3.5 22.2 - - - -
32J PHE* 3.7 24.9 - + - -
33J THR* 3.7 4.1 + - - -
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Residues in contact with ASP 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E ALA* 6.6 0.2 - - - -
147E ARG* 4.0 21.7 + - - +
148E GLU 5.5 0.2 + - - -
25J PHE* 1.3 75.2 - - - +
27J GLN* 1.3 59.2 + - - +
28J HIS* 3.6 23.2 + - - +
29J GLU* 3.1 28.2 + - + +
30J GLN* 2.8 25.3 + - - -
31J LYS* 2.9 24.8 + - + +
33J THR* 4.1 16.0 - - + +
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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