Contacts of the strand formed by residues 15 - 26 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24H THR 5.8 1.1 - - - -
42H ALA* 3.5 3.6 - - - +
43H ASN* 2.7 42.2 + - - +
45H MET* 5.9 2.9 - - - +
13P ALA 4.8 2.7 + - - -
14P PRO* 1.3 75.0 - - - +
16P ASN* 1.3 76.6 + - - +
17P PHE* 3.3 4.6 + - - -
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Residues in contact with ASN 16 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H SER* 3.6 7.0 + - - +
42H ALA* 4.1 2.4 - - - -
43H ASN* 3.6 28.9 - - - +
15P SER* 1.3 87.9 + - - +
17P PHE* 1.3 66.4 + - - +
18P GLU* 3.3 11.7 + - + +
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Residues in contact with PHE 17 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H ILE* 4.1 13.5 - - + -
24H THR* 3.3 48.0 - - + +
25H THR* 3.8 18.4 - - + -
40H TYR* 3.8 39.5 - + + -
41H SER 3.3 10.5 - - - -
42H ALA* 4.6 2.2 - - + +
15P SER 3.3 4.6 - - - -
16P ASN* 1.3 77.8 - - - +
18P GLU* 1.3 68.2 + - - +
19P HIS* 4.3 19.5 - + + -
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Residues in contact with GLU 18 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H TYR* 3.2 7.1 - - - +
41H SER* 2.9 49.3 + - - +
16P ASN* 3.8 8.7 - - + +
17P PHE* 1.3 84.7 - - - +
19P HIS* 1.3 60.0 + - - +
20P ARG* 3.5 9.6 + - + -
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Residues in contact with HIS 19 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H ASP* 2.9 30.7 + - - -
39H ASN 3.5 9.0 - - - -
40H TYR* 3.7 20.9 - + - -
17P PHE* 4.3 16.3 - - + -
18P GLU* 1.3 72.4 - - - +
20P ARG* 1.3 60.4 + - - +
21P VAL 3.1 18.8 + - - -
22P HIS* 3.7 18.9 - + + +
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Residues in contact with ARG 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H ASN* 2.9 28.8 + - - +
41H SER* 3.4 31.4 - - - +
18P GLU* 4.0 10.5 - - + +
19P HIS* 1.3 74.9 - - - +
21P VAL* 1.3 67.9 + - + +
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Residues in contact with VAL 21 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H PHE* 3.9 15.3 - - + -
38H ASP* 3.3 2.8 - - - -
39H ASN* 3.0 41.4 + - + -
19P HIS* 3.1 12.2 + - - -
20P ARG* 1.3 88.4 - - + +
22P HIS* 1.3 63.9 + - - +
23P THR* 3.4 22.0 - - - +
34P GLY 3.7 9.4 - - - +
35P LEU 4.6 0.4 - - - +
36P PRO* 3.9 26.2 - - + -
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Residues in contact with HIS 22 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E GLU* 4.9 11.9 + - - -
33H ILE* 6.6 0.4 - - + -
38H ASP* 2.6 27.6 + - - +
19P HIS* 3.7 17.5 - + + +
21P VAL* 1.3 75.8 - - - +
23P THR* 1.3 74.9 + - - +
24P GLY* 4.0 3.5 + - - -
33P THR 4.8 0.2 - - - -
34P GLY* 3.5 15.6 + - - +
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Residues in contact with THR 23 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H VAL* 3.5 28.2 + - + +
37H PHE* 2.9 31.9 + - + +
38H ASP* 5.0 0.2 - - - +
67H LEU* 4.6 2.5 - - + -
21P VAL* 3.4 13.0 - - - +
22P HIS* 1.3 88.0 - - - +
24P GLY* 1.3 71.2 + - - +
32P PHE* 4.4 3.8 - - + -
33P THR 3.3 13.0 - - - +
34P GLY 2.8 15.6 + - - -
35P LEU* 3.7 23.9 - - + -
36P PRO* 3.8 4.5 - - - +
39P TRP* 6.0 0.2 - - + -
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Residues in contact with GLY 24 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H VAL* 4.1 11.4 - - - -
22P HIS* 4.0 5.2 + - - -
23P THR* 1.3 80.0 - - - +
25P PHE* 1.3 61.5 + - - +
32P PHE* 3.3 8.3 - - - -
33P THR* 2.8 39.4 + - - +
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Residues in contact with PHE 25 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E GLY 5.1 4.5 - - - +
36H VAL* 4.4 4.0 - - + +
64H TYR* 3.1 27.8 - + + +
66H ARG* 3.5 27.4 - - - -
24P GLY* 1.3 73.6 - - - -
26P ASP* 1.3 70.5 + - - +
27P GLN* 3.6 35.8 + - - +
30P GLN* 3.5 51.1 - - - -
31P LYS 3.7 4.3 - - - -
32P PHE* 3.5 32.3 - + + -
33P THR* 3.8 3.5 + - - -
1205P CL 3.9 8.5 - - - +
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Residues in contact with ASP 26 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25P PHE* 1.3 74.5 - - - +
27P GLN* 1.3 59.1 + - - +
28P HIS* 2.8 32.8 + - - +
29P GLU* 3.5 26.3 - - + +
30P GLN* 2.8 26.0 + - - -
31P LYS* 2.8 22.7 + - + +
33P THR* 4.0 15.9 - - + +
1205P CL 3.9 6.5 - - - +
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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