Contacts of the strand formed by residues 15 - 26 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24D THR 5.6 1.8 - - - -
42D ALA* 3.4 4.4 - - - +
43D ASN* 2.9 36.6 + - - +
13L ALA 4.9 3.1 + - - -
14L PRO* 1.3 74.6 - - - +
16L ASN* 1.3 86.7 + - - +
17L PHE* 3.2 4.0 + - - -
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Residues in contact with ASN 16 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D SER* 3.7 6.2 - - - +
42D ALA* 3.9 3.6 - - - -
43D ASN* 3.8 27.3 + - - +
15L SER* 1.3 95.7 + - - +
17L PHE* 1.3 67.1 + - - +
18L GLU* 3.4 5.5 + - - +
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Residues in contact with PHE 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ILE* 4.1 15.0 - - + -
24D THR* 3.2 47.3 - - + +
25D THR* 3.8 17.7 - - + -
40D TYR* 3.8 38.1 - + + -
41D SER 3.3 12.6 - - - -
42D ALA* 4.5 1.6 - - + +
15L SER 3.2 4.1 + - - -
16L ASN* 1.3 77.5 - - - +
18L GLU* 1.3 62.0 + - - +
19L HIS* 4.1 23.1 - + + -
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Residues in contact with GLU 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D TYR* 3.2 7.1 - - - +
41D SER* 2.8 51.4 + - - +
16L ASN 3.4 4.0 + - - +
17L PHE* 1.3 80.8 - - - +
19L HIS* 1.3 62.7 + - - +
20L ARG* 3.7 3.4 + - + +
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Residues in contact with HIS 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ASP* 2.8 31.4 + - - -
39D ASN 3.5 9.6 - - - -
40D TYR* 3.8 20.2 - + - -
17L PHE* 4.1 16.6 - - + -
18L GLU* 1.3 70.9 - - - +
20L ARG* 1.3 61.1 + - - +
21L VAL 3.0 20.6 + - - -
22L HIS* 3.7 16.6 - + + +
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Residues in contact with ARG 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ASN* 2.9 27.8 + - - +
41D SER* 4.4 12.8 - - - +
18L GLU* 3.7 5.0 + - + +
19L HIS* 1.3 75.4 - - - +
21L VAL* 1.3 68.8 + - + +
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Residues in contact with VAL 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D PHE* 3.8 7.2 - - + -
38D ASP* 3.3 2.3 - - - +
39D ASN* 3.1 40.1 + - + +
19L HIS* 3.0 17.2 + - - -
20L ARG* 1.3 88.3 - - + +
22L HIS* 1.3 63.4 + - - +
23L THR* 3.5 22.0 - - - +
34L GLY 3.7 9.4 - - - +
35L LEU 4.8 0.2 - - - -
36L PRO* 3.8 31.2 - - + -
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Residues in contact with HIS 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ILE* 6.5 1.1 - - + -
36D VAL 6.3 0.4 - - - -
38D ASP* 2.7 30.6 + - - +
19L HIS* 3.7 15.9 - + + +
21L VAL* 1.3 74.1 - - - +
23L THR* 1.3 75.2 + - - +
24L GLY* 4.1 3.8 + - - -
33L THR 4.9 0.2 - - - -
34L GLY* 3.7 14.1 + - - +
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Residues in contact with THR 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D VAL* 3.6 26.5 + - + +
37D PHE* 2.8 32.6 + - + +
67D LEU* 4.5 5.2 - - + -
21L VAL* 3.5 12.5 - - - +
22L HIS* 1.3 88.2 - - - +
24L GLY* 1.3 70.8 + - - +
32L PHE* 4.3 2.9 - - + -
33L THR 3.2 12.8 - - - +
34L GLY 2.9 13.6 + - - -
35L LEU* 3.9 23.6 - - + -
36L PRO* 3.7 5.4 - - - +
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Residues in contact with GLY 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D VAL* 4.2 11.0 - - - -
22L HIS* 4.1 4.6 + - - -
23L THR* 1.3 74.4 - - - +
25L PHE* 1.3 60.6 + - - -
32L PHE* 3.5 15.4 - - - -
33L THR* 2.7 39.8 + - - +
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Residues in contact with PHE 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D VAL* 4.6 3.1 - - + +
64D TYR* 3.3 27.8 - + + +
66D ARG* 3.5 28.3 - - - -
24L GLY* 1.3 74.5 - - - +
26L ASP* 1.3 68.7 - - - +
27L GLN* 3.6 35.2 + - - +
30L GLN* 3.5 39.3 - - - -
31L LYS 3.6 21.5 - - - -
32L PHE* 3.5 27.1 - + + -
33L THR* 3.6 4.1 + - - -
44L GLU 5.7 0.2 - - - -
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Residues in contact with ASP 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25L PHE* 1.3 75.5 - - - +
27L GLN* 1.3 53.2 + - - +
28L HIS* 3.7 19.0 + - - +
29L GLU* 2.8 42.8 + - + +
30L GLN* 2.7 35.7 + - - -
31L LYS* 2.8 19.6 + - + +
33L THR* 4.0 15.2 - - + +
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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