Contacts of the strand formed by residues 37 - 46 (chain E) 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 PHE 37 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35E THR* 3.6 5.6 - - - -
36E VAL* 1.3 84.9 - - - +
38E ASP* 1.3 91.8 + - - +
39E ASN* 3.9 10.1 - - + -
56E TRP* 3.5 34.5 - + + -
57E ASP 3.6 10.1 - - - -
58E THR* 4.6 5.6 - - + -
67E LEU* 4.1 11.7 - - + -
71E SER* 3.2 24.5 - - - -
21M VAL* 3.8 19.3 - - + -
23M THR* 2.9 50.7 + - - +
36M PRO* 4.0 6.5 - - + -
39M TRP* 3.8 20.6 - + + -
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Residues in contact with ASP 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E THR* 3.6 16.5 + - - +
36E VAL 4.9 0.5 + - - -
37E PHE* 1.3 92.1 + - - +
39E ASN* 1.3 61.4 + - - +
40E TYR* 3.3 31.2 + - + +
57E ASP* 2.8 40.0 + - + +
19M HIS* 2.7 18.5 + - - -
21M VAL 3.3 3.6 - - - +
22M HIS* 2.7 37.5 + - - -
23M THR 4.9 0.9 - - - +
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Residues in contact with ASN 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E PHE* 3.9 8.3 - - + -
38E ASP* 1.3 73.4 - - - +
40E TYR* 1.3 59.6 + - - +
41E SER* 4.9 0.2 + - - -
54E GLY* 4.9 1.5 - - - -
55E LEU 3.2 12.8 + - - +
56E TRP* 3.2 44.5 - - - +
19M HIS* 3.5 4.9 - - - -
20M ARG* 2.8 56.5 + - - +
21M VAL* 2.9 32.2 + - + +
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Residues in contact with TYR 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E THR* 3.9 11.3 - - + +
20E LEU* 3.9 22.9 - - + -
21E ILE* 4.0 22.3 - - + +
24E THR* 5.3 0.4 - - + -
38E ASP* 3.3 19.4 + - + +
39E ASN* 1.3 83.0 - - - +
41E SER* 1.3 60.6 + - - +
54E GLY* 3.6 2.6 - - - -
55E LEU* 2.7 54.9 + - + +
57E ASP* 2.9 36.3 + - + -
17M PHE* 3.8 26.5 - + + -
18M GLU 3.2 8.1 - - - +
19M HIS* 3.7 33.4 - + - -
20M ARG* 4.8 0.7 - - - -
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Residues in contact with SER 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E THR* 5.6 0.4 - - - -
39E ASN* 4.9 0.2 + - - -
40E TYR* 1.3 75.5 + - - +
42E ALA* 1.3 64.2 + - - +
52E ASN* 3.9 21.0 + - - -
53E LEU 3.3 8.0 + - - -
54E GLY* 4.5 3.6 - - - -
55E LEU* 5.6 0.9 - - - -
16M ASN 4.6 1.1 - - - -
17M PHE* 3.4 5.9 - - - -
18M GLU* 2.9 40.7 + - - +
20M ARG* 3.1 30.8 - - - -
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Residues in contact with ALA 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E THR* 4.2 19.5 - - + +
41E SER* 1.3 78.8 - - - +
43E ASN* 1.3 59.8 + - - +
44E VAL* 5.3 0.7 - - + -
52E ASN* 3.5 6.5 + - - -
53E LEU* 2.8 48.6 + - + +
55E LEU* 5.4 1.3 - - + +
14M PRO* 3.9 21.5 - - + -
15M SER 3.5 13.5 - - - +
16M ASN 4.4 2.2 - - - -
17M PHE* 4.7 2.2 - - - -
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Residues in contact with ASN 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E ALA* 1.3 73.2 - - - +
44E VAL* 1.3 59.7 - - - +
50E PRO* 6.0 5.7 - - + +
51E VAL 3.5 9.0 + - - +
52E ASN* 3.3 25.6 - - - +
13M ALA 4.0 0.3 - - - +
14M PRO* 3.3 5.7 - - - +
15M SER* 2.9 43.3 + - - +
16M ASN* 3.3 30.3 + - - +
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Residues in contact with VAL 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E TYR* 3.6 23.3 - - - +
42E ALA 3.9 1.8 + - - +
43E ASN* 1.3 80.4 - - - +
45E MET* 1.3 66.1 + - - +
46E VAL* 3.8 11.2 - - + -
50E PRO* 3.7 1.0 - - - -
51E VAL* 2.8 41.2 + - + +
53E LEU* 4.5 15.9 - - + -
173E ILE* 4.1 7.2 - - + -
11M ILE* 3.5 31.2 - - + -
12M SER* 3.9 8.5 - - - +
14M PRO* 3.7 17.5 - - + -
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Residues in contact with MET 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E VAL* 1.3 73.5 - - - +
46E VAL* 1.3 59.1 + - - +
47E ASP 4.0 0.4 - - - -
48E GLY* 3.1 41.3 - - - +
49E LYS 3.5 7.2 - - - -
50E PRO* 3.6 25.8 - - + -
10M GLU 3.5 2.3 - - - +
11M ILE* 3.3 4.0 - - - -
12M SER* 2.8 51.6 + - - +
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Residues in contact with VAL 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E VAL* 3.8 18.8 - - + -
45E MET* 1.3 75.2 - - - +
47E ASP* 1.3 71.3 + - + +
49E LYS* 2.7 28.9 + - - +
51E VAL* 3.7 25.4 - - + -
173E ILE* 3.8 24.2 - - + -
174E ARG* 3.6 25.6 - - - +
177E LEU* 4.4 11.2 - - + -
10M GLU 3.6 2.5 - - - -
11M ILE* 4.2 10.5 - - + +
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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