Contacts of the strand formed by residues 59 - 65 (chain A) in PDB entry 2OVI
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 ASN 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A TRP 3.9 0.6 + - - -
58A GLY* 1.3 72.3 - - - -
60A VAL* 1.3 58.3 - - - +
74A SER* 4.7 3.9 - - - -
75A GLY* 3.5 29.1 - - - +
76A GLU* 3.7 14.1 - - - +
138A GLY* 3.6 8.7 - - - -
146A LEU* 4.7 8.8 - - + +
149A GLN* 2.7 28.4 + - - +
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Residues in contact with VAL 60 (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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54A VAL* 5.1 4.3 - - + +
57A TRP* 4.7 18.4 - - + -
58A GLY 3.9 5.2 - - - +
59A ASN* 1.3 80.7 - - - +
61A THR* 1.3 64.1 + - - +
62A THR* 4.5 6.7 - - - +
73A PHE 3.4 1.9 - - - +
74A SER* 3.1 3.7 - - - -
75A GLY 2.9 35.7 + - - +
77A LEU* 4.2 23.6 - - + +
135A ILE* 3.7 22.4 - - + -
136A PHE 3.5 13.2 - - - +
137A LEU* 4.7 2.0 - - - -
138A GLY* 4.2 4.9 - - - +
149A GLN* 3.7 17.9 - - - +
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Residues in contact with THR 61 (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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60A VAL* 1.3 77.6 - - - +
62A THR* 1.3 63.6 + - - +
63A LEU* 3.9 3.9 + - + -
72A GLU* 3.6 41.6 + - + +
73A PHE 3.4 5.2 - - - +
74A SER* 3.2 19.0 + - - +
134A LYS 3.8 0.7 - - - +
135A ILE* 3.3 4.8 - - - -
136A PHE* 2.8 51.2 + - + +
137A LEU 5.3 2.0 + - - -
138A GLY* 5.4 3.1 - - - -
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Residues in contact with THR 62 (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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51A TRP* 5.5 0.7 - - + -
60A VAL* 4.5 4.0 - - - +
61A THR* 1.3 73.2 - - - +
63A LEU* 1.3 62.5 + - - +
71A LEU 3.7 0.5 - - - +
72A GLU* 3.1 4.0 - - - -
73A PHE* 2.8 36.2 + - - +
75A GLY 5.6 0.3 + - - -
77A LEU* 3.3 17.2 - - + +
95A MET* 3.6 32.8 - - + +
133A LEU* 3.8 25.8 - - + -
134A LYS 3.5 2.7 - - - -
135A ILE* 2.9 28.5 - - + +
71D LEU* 4.7 1.7 - - + +
73D PHE* 5.5 1.0 - - - -
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A THR* 5.0 1.8 - - + +
62A THR* 1.3 77.1 - - - +
64A VAL* 1.3 78.1 + - - +
65A HIS* 3.8 16.8 - - + +
70A ILE* 3.8 25.1 - - + -
71A LEU 3.3 7.0 - - - +
72A GLU* 4.1 19.7 - - + +
133A LEU* 3.4 7.0 - - - +
134A LYS* 2.8 59.4 + - + +
136A PHE* 4.1 23.1 - - + -
71D LEU* 6.1 0.2 - - - -
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Residues in contact with VAL 64 (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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63A LEU* 1.3 74.2 - - - +
65A HIS* 1.3 67.8 + - - +
66A THR* 5.0 2.9 - - - +
69A VAL* 3.9 2.5 - - + +
70A ILE* 3.5 3.3 - - - -
71A LEU* 3.0 35.3 + - + +
132A MET 4.6 8.5 - - - +
133A LEU* 3.3 16.8 - - + +
64D VAL* 4.3 26.0 - - + -
66D THR* 5.1 8.5 - - + +
69D VAL* 3.8 18.8 - - + -
71D LEU* 3.0 37.5 - - + -
73D PHE* 5.9 0.9 - - + -
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Residues in contact with HIS 65 (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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19A GLU* 5.0 23.1 - - + +
63A LEU* 3.8 15.3 + - + +
64A VAL* 1.3 77.7 - - - +
66A THR* 1.3 72.6 + - - +
67A ALA* 5.6 0.2 - - - -
69A VAL 3.6 1.8 - - - -
70A ILE* 3.2 37.0 - - + +
131A ALA* 5.0 10.3 + - + +
132A MET 5.4 1.6 + - - -
133A LEU* 6.1 0.2 - - - +
134A LYS* 5.3 8.7 - - - +
66D THR* 5.6 1.4 + - - -
86D TYR* 5.6 2.2 - - - -
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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