Contacts of the strand formed by residues 78 - 83 (chain A) in PDB entry 2OSL
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 THR 78 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A SER* 4.2 5.6 - - - +
22A CYS 3.3 25.1 - - - +
23A LYS* 4.2 9.3 - - + +
29A PHE* 3.6 5.4 - - - -
72A ALA* 3.5 2.4 - - - -
73A ASP* 3.2 34.2 + - - +
76A SER* 2.8 25.2 + - - -
77A SER* 1.3 75.8 + - - +
79A ALA* 1.3 62.7 + - - +
80A TYR* 3.6 36.1 + - + +
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A SER* 3.6 2.6 - - - -
22A CYS* 2.8 42.8 + - + +
29A PHE* 3.8 12.7 - - + -
34A MET* 3.8 31.0 - - + -
36A TRP* 3.7 8.7 - - + +
51A ILE* 4.9 2.2 - - + -
71A THR 3.6 8.3 - - - +
72A ALA* 4.1 4.5 - - + -
78A THR* 1.3 75.0 - - - +
80A TYR* 1.3 61.4 + - - +
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Residues in contact with TYR 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LYS* 3.9 37.2 - - + -
20A MET 3.2 16.6 - - - +
21A SER* 3.7 19.6 - - - -
36A TRP* 3.9 5.3 + - - -
51A ILE* 6.0 0.2 - - - +
70A LEU* 3.4 6.9 - - - +
71A THR* 2.7 57.8 + - - +
72A ALA* 4.7 2.0 - - - -
73A ASP* 4.0 11.0 - - - -
76A SER* 5.1 3.1 + - - -
78A THR* 3.6 36.9 + - + +
79A ALA* 1.3 76.3 - - - +
81A MET* 1.3 61.0 + - - +
82A GLN 4.3 0.2 - - - -
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Residues in contact with MET 81 (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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18A VAL 3.8 0.9 - - - +
19A LYS* 3.5 3.7 - - - -
20A MET* 2.8 58.0 + - + +
36A TRP* 3.8 43.0 - - + -
48A ILE* 3.7 29.2 - - + -
68A ALA* 4.4 3.8 - - + -
69A THR 3.5 4.0 - - - +
70A LEU* 3.7 10.8 - - + -
80A TYR* 1.3 74.8 - - - +
82A GLN* 1.3 63.4 + - - +
83A LEU* 3.5 31.1 + - + -
94A TYR* 3.7 19.3 - - + -
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Residues in contact with GLN 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A SER* 4.3 17.4 + - - -
18A VAL 3.4 7.8 - - - +
19A LYS* 4.0 26.9 - - + +
67A LYS 3.3 7.6 - - - +
68A ALA* 3.3 3.1 - - - -
69A THR* 2.8 48.3 + - - +
71A THR* 5.8 0.4 + - - +
81A MET* 1.3 73.2 - - - +
83A LEU* 1.3 63.7 + - - +
84A SER* 3.7 21.6 + - - +
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Residues in contact with LEU 83 (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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17A SER* 3.2 6.9 - - - -
18A VAL* 2.8 45.1 + - + -
20A MET* 3.6 15.7 - - + -
48A ILE* 5.4 0.9 - - + -
67A LYS* 3.5 13.9 - - + +
68A ALA* 4.8 4.0 - - + -
81A MET* 3.5 40.3 + - + -
82A GLN* 1.3 74.5 - - - +
84A SER* 1.3 59.7 + - - +
86A LEU* 3.7 30.9 - - + +
90A ASP* 4.8 0.4 - - + -
94A TYR* 3.5 37.7 - - + +
117A VAL* 4.7 0.7 - - + -
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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