Contacts of the strand formed by residues 87 - 92 (chain B) in PDB entry 5ODS
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 87 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82B LEU 3.9 1.0 - - - +
83B LYS* 3.6 0.9 - - - -
84B ALA* 2.7 48.7 + - + +
85B GLY 3.3 0.6 - - - -
86B LYS* 1.3 81.1 + - - +
88B LEU* 1.3 70.4 + - - +
89B GLN* 5.4 2.9 - - + +
101B ALA* 6.1 2.0 - - + -
102B HIS 3.7 3.6 - - - +
103B THR* 3.8 24.0 + - - +
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B LEU 3.7 3.8 - - - -
83B LYS* 4.6 12.6 - - + -
86B LYS* 3.7 18.8 - - - +
87B THR* 1.3 80.3 - - - +
89B GLN* 1.3 64.4 + - - +
101B ALA* 3.4 4.0 - - - +
102B HIS* 2.6 38.0 + - + +
104B MET* 4.0 18.2 - - + -
108B VAL* 4.2 13.9 - - + -
111B TRP* 3.8 20.2 - - + -
121B LEU* 3.5 44.0 - - + -
130B TRP* 3.7 17.5 - - + -
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Residues in contact with GLN 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ILE 3.9 0.2 - - - +
81B ALA* 3.5 2.5 - - - -
82B LEU* 3.0 56.4 + - + +
87B THR* 5.4 3.3 - - + +
88B LEU* 1.3 78.3 - - - +
90B ILE* 1.3 69.5 + - - +
91B PHE* 3.5 30.7 + - - +
98B LYS* 3.5 18.6 - - + +
100B LYS 3.6 12.6 - - - +
101B ALA* 4.2 5.2 - - + +
111B TRP* 5.2 0.6 - - - -
130B TRP* 4.2 2.1 - - - -
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Residues in contact with ILE 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B VAL* 3.7 24.7 - - + -
80B ILE 3.6 3.8 - - - +
81B ALA* 4.4 11.4 - - + +
89B GLN* 1.3 71.2 - - - +
91B PHE* 1.3 55.1 + - - +
98B LYS* 3.8 1.0 - - - -
99B MET* 2.8 40.7 + - + +
100B LYS* 3.0 37.8 + - + +
113B TRP* 4.7 5.2 - - + -
119B VAL* 4.5 9.6 - - + -
130B TRP* 3.9 32.1 - - + -
131B SER 4.3 0.2 - - - +
132B MET* 3.8 36.6 - - + -
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Residues in contact with PHE 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ARG* 5.4 3.8 - - - -
66B ILE* 5.4 8.5 - - + -
79B VAL* 3.7 2.6 - - - +
80B ILE* 2.7 60.5 + - + +
82B LEU* 4.1 9.9 - - + -
89B GLN* 3.5 26.4 + - - +
90B ILE* 1.3 74.5 - - - +
92B ASN* 1.3 71.9 + - - +
93B ILE* 3.5 15.3 + - + -
96B LYS* 3.5 26.9 - - + -
97B SER 3.4 28.7 - - - -
98B LYS* 3.6 16.8 - - + -
99B MET* 4.1 4.5 - - - +
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Residues in contact with ASN 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B LYS 4.1 3.7 - - - +
79B VAL* 4.1 12.3 - - - +
91B PHE* 1.3 73.2 - - - +
93B ILE* 1.3 60.6 + - - +
94B GLU* 3.4 10.0 + - - +
95B MET* 3.1 33.1 + - + +
96B LYS* 3.0 26.7 + - - -
97B SER* 2.8 29.0 + - - +
99B MET* 3.9 29.9 - - + +
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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