Contacts of the strand formed by residues 39 - 45 (chain A) in PDB entry 1OVY
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 HIS 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ARG* 3.2 6.4 - - - +
36A SER* 2.5 42.1 + - - +
37A ASN* 5.2 0.7 - - + -
38A LYS* 1.3 111.6 - - + +
40A ILE* 1.3 58.9 + - - +
58A THR* 3.0 38.9 + - + +
66A ASP* 3.8 30.5 + - + -
67A SER 4.2 0.9 - - - -
68A THR* 3.6 17.6 + - + -
69A ASN* 3.1 33.4 + - + +
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Residues in contact with ILE 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A PHE 3.8 2.2 - - - +
35A ARG* 3.5 28.7 - - + -
39A HIS* 1.3 72.7 - - - +
41A TYR* 1.3 62.0 + - - +
42A ALA 3.5 0.3 + - - -
57A SER* 4.6 0.2 - - - -
68A THR* 2.9 39.1 - - - +
69A ASN 4.3 8.1 - - - +
71A ILE* 3.6 28.9 - - + -
74A ALA* 3.1 25.3 - - + +
105A ARG* 4.4 8.3 - - + -
106A VAL* 3.5 27.1 - - + +
109A LEU* 3.7 9.7 - - + +
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Residues in contact with TYR 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL* 3.8 0.2 - - - -
34A PHE* 2.6 54.4 + + + +
36A SER* 3.2 28.5 - - - +
39A HIS 3.7 3.4 + - - -
40A ILE* 1.3 68.1 - - - +
42A ALA* 1.3 81.3 - - - +
43A GLN* 3.8 21.0 + - + -
55A SER* 4.7 5.8 + - - -
56A ALA* 3.9 10.5 + - - -
57A SER* 2.7 35.9 - - - -
59A LEU* 4.5 16.0 - - + +
109A LEU* 3.1 10.5 - - - +
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Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A SER 4.3 0.7 - - - -
40A ILE 3.5 1.2 + - - -
41A TYR* 1.3 84.2 - - - +
43A GLN* 1.3 52.7 + - - +
44A ILE* 4.8 3.1 - - + -
55A SER* 2.4 36.5 + - - +
56A ALA 3.2 13.7 + - - +
74A ALA 4.2 0.2 - - - +
78A GLY* 3.8 15.7 - - - +
109A LEU* 3.1 42.5 - - + +
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Residues in contact with GLN 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 3.1 0.3 - - - +
32A SER* 2.4 63.1 + - - +
34A PHE* 3.4 40.8 - - + -
41A TYR* 3.8 12.5 + - + -
42A ALA* 1.3 75.5 - - - +
44A ILE* 1.3 65.7 + - - +
45A ILE* 4.5 9.6 - - + +
53A ILE 5.6 1.3 - - - -
54A VAL* 4.9 8.3 - - - -
55A SER* 3.4 6.1 - - - -
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Residues in contact with ILE 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 2.9 46.2 - - + -
42A ALA* 4.8 3.1 - - + -
43A GLN* 1.3 80.8 - - - +
45A ILE* 1.3 53.2 - - - +
52A THR* 2.4 40.8 - - - +
53A ILE* 3.3 0.3 - - - -
54A VAL 3.1 22.5 + - - +
55A SER* 4.4 1.3 - - - +
78A GLY 4.3 13.0 - - - +
81A VAL* 4.1 5.8 - - + -
82A ALA* 4.1 21.3 - - + -
85A ALA* 3.9 4.5 - - + -
92A GLN* 3.6 7.2 - - - +
93A VAL* 3.0 38.1 - - + -
109A LEU 5.4 3.4 - - - +
113A ALA* 5.3 0.2 - - + -
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Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLY* 3.3 37.7 - - - +
28A ARG 4.3 5.6 - - - +
30A ARG* 2.6 56.0 + - - +
31A LEU 3.6 0.5 + - - -
32A SER* 3.4 18.2 - - - +
43A GLN* 4.5 10.5 - - + +
44A ILE* 1.3 74.9 - - - +
46A ASP* 1.3 97.1 + - - +
51A ALA* 4.7 1.6 - - - -
52A THR 3.0 1.6 - - - -
53A ILE* 3.3 28.5 - - + -
93A VAL* 4.0 1.8 - - - +
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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