Contacts of the strand formed by residues 15 - 26 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24E THR 5.8 2.5 - - - -
42E ALA* 3.5 4.3 - - - +
43E ASN* 2.9 35.0 + - - -
13M ALA 4.8 2.4 + - - -
14M PRO* 1.3 76.6 + - - +
16M ASN* 1.3 83.0 + - - +
17M PHE 3.2 3.7 + - - -
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Residues in contact with ASN 16 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E SER* 3.9 4.2 - - - +
42E ALA* 4.4 2.1 - - - -
43E ASN* 3.3 25.3 + - - +
15M SER* 1.3 85.9 + - - +
17M PHE* 1.3 68.9 + - - +
18M GLU* 3.3 9.7 + - - +
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Residues in contact with PHE 17 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E ILE* 4.1 13.5 - - + -
24E THR* 3.5 44.6 - - - +
25E THR* 3.8 17.5 - - + -
40E TYR* 3.8 37.2 - + + -
41E SER 3.4 11.4 - - - -
42E ALA* 4.7 2.0 - - - +
15M SER 3.2 4.7 + - - -
16M ASN* 1.3 77.9 - - - +
18M GLU* 1.3 66.7 + - - +
19M HIS* 4.1 24.2 - + + -
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Residues in contact with GLU 18 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E TYR* 3.2 7.6 - - - +
41E SER* 2.9 46.1 + - - +
16M ASN 3.3 6.5 + - - +
17M PHE* 1.3 83.3 - - - +
19M HIS* 1.3 61.0 + - - +
20M ARG* 3.6 10.7 + - + -
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Residues in contact with HIS 19 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E ASP* 2.7 32.5 + - - -
39E ASN 3.5 7.6 - - - -
40E TYR* 3.7 19.8 - + - -
17M PHE* 4.1 19.0 - - + -
18M GLU* 1.3 72.3 - - - +
20M ARG* 1.3 61.7 + - - +
21M VAL 3.0 22.6 + - - -
22M HIS* 3.7 18.4 - + + +
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Residues in contact with ARG 20 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E ASN* 2.8 29.9 + - - +
41E SER* 3.1 35.4 - - - +
18M GLU* 4.3 10.8 - - + +
19M HIS* 1.3 76.5 - - - +
21M VAL* 1.3 68.6 + - + +
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Residues in contact with VAL 21 (chain M).
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* 3.8 12.8 - - + -
38E ASP* 3.3 2.3 - - - -
39E ASN* 2.9 44.5 + - + +
19M HIS* 3.0 13.3 + - - -
20M ARG* 1.3 87.6 - - + +
22M HIS* 1.3 63.0 + - - +
23M THR* 3.5 22.0 - - - +
34M GLY 3.5 12.3 - - - +
36M PRO* 4.0 25.1 - - + -
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Residues in contact with HIS 22 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E ASP* 2.7 29.1 + - - +
19M HIS* 3.7 17.9 - + + +
21M VAL* 1.3 73.1 - - - +
23M THR* 1.3 70.8 + - - +
24M GLY* 4.1 1.9 + - - -
33M THR 4.7 0.2 - - - -
34M GLY* 3.6 16.8 + - - +
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Residues in contact with THR 23 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E VAL* 3.5 25.3 + - + +
37E PHE* 2.9 47.3 + - + +
38E ASP* 4.9 0.7 - - - +
67E LEU* 4.8 1.3 - - + -
21M VAL* 3.5 2.9 - - - +
22M HIS* 1.3 85.3 + - - +
24M GLY* 1.3 66.5 + - - +
32M PHE* 4.3 3.1 - - + -
33M THR 3.1 16.8 - - - +
34M GLY 3.2 12.0 + - - +
35M LEU* 4.0 24.9 - - + -
36M PRO* 4.1 3.5 - - - +
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Residues in contact with GLY 24 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E VAL* 4.1 11.7 - - - -
22M HIS* 4.1 1.9 + - - -
23M THR* 1.3 74.5 - - - +
25M PHE* 1.3 60.9 + - - +
32M PHE* 3.2 12.8 - - - -
33M THR* 2.8 39.5 + - - +
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Residues in contact with PHE 25 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E VAL* 4.5 3.2 - - + +
64E TYR* 3.3 29.8 - + + +
66E ARG* 3.6 26.9 - - - -
30H GLY 5.5 3.3 - - - +
24M GLY* 1.3 73.5 - - - +
26M ASP* 1.3 69.4 + - - +
27M GLN* 3.6 37.8 + - - +
30M GLN* 3.5 51.4 - - - -
31M LYS 3.6 15.0 - - - -
32M PHE* 3.7 22.4 - + + -
33M THR* 3.8 2.9 + - - -
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Residues in contact with ASP 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M PHE* 1.3 74.1 - - - +
27M GLN* 1.3 57.8 + - - +
28M HIS* 2.8 31.9 + - - +
29M GLU* 2.9 26.4 + - + +
30M GLN* 2.8 29.6 + - - -
31M LYS* 2.7 19.3 + - + +
33M THR* 4.0 16.5 - - + +
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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