Contacts of the strand formed by residues 282 - 287 (chain B) in PDB entry 5DO7
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 LEU 282 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B LYS* 4.4 25.4 - - + +
99B GLN* 3.2 39.5 - - + +
100B MET 2.8 17.7 + - - +
101B LEU* 3.7 17.3 - - + -
102B ALA* 2.8 30.5 + - - +
280B PHE* 4.1 2.9 - - - +
281B ASP* 1.3 80.8 - - - +
283B VAL* 1.3 58.6 + - - +
294B LEU* 5.1 7.0 - - + -
295B GLY* 3.6 31.0 - - - +
296B ALA* 3.7 8.7 - - + +
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Residues in contact with VAL 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 3.7 3.4 - - - -
102B ALA 3.4 6.5 - - - +
104B ILE* 3.4 27.4 - - + -
277B PHE* 4.3 4.7 - - + -
280B PHE* 3.8 27.6 - - + -
282B LEU* 1.3 79.7 - - - +
284B LEU* 1.3 63.7 + - - +
285B LEU 4.2 0.4 - - - -
293B TYR 4.4 0.7 - - - +
294B LEU* 3.6 5.2 - - - +
295B GLY 2.8 45.1 + - - +
296B ALA 4.0 1.3 - - - +
297B ALA* 3.7 23.3 - - - +
300B MET* 4.6 4.9 - - + +
314B TYR* 3.7 21.5 - - + +
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Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 5.1 2.2 - - + -
93B PHE* 3.3 37.7 - - + -
101B LEU* 3.8 8.3 - - + +
102B ALA 2.8 11.3 + - - +
103B ILE* 3.5 17.1 - - + +
104B ILE* 2.8 29.2 + - - -
114B LEU* 5.0 1.1 - - + -
283B VAL* 1.3 73.6 - - - +
285B LEU* 1.3 67.7 + - - +
286B MET* 4.0 23.0 + - + -
291B PRO* 4.1 26.0 - - + -
293B TYR 4.3 0.9 - - - -
294B LEU* 3.6 29.6 - - + +
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ILE* 3.5 31.9 - - + +
283B VAL 4.2 0.4 - - - -
284B LEU* 1.3 75.2 - - - +
286B MET* 1.3 64.4 + - - +
287B THR* 4.8 1.8 - - - +
291B PRO* 3.7 1.2 - - - +
292B ILE* 2.8 45.6 + - + +
293B TYR 3.5 7.9 + - - -
300B MET* 4.2 10.5 - - + +
304B PHE* 5.1 4.7 - - + -
314B TYR* 3.4 41.7 - - + +
315B SER* 5.1 1.3 - - - -
317B PRO* 4.8 2.0 - - + -
318B ALA* 3.6 42.2 - - + +
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Residues in contact with MET 286 (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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88B ILE* 5.3 5.2 - - + -
91B LEU* 3.7 27.1 - - + -
103B ILE* 4.6 7.2 - - + -
105B GLY* 3.0 17.6 - - - -
106B SER* 2.8 26.5 + - - -
109B CYS* 4.2 12.8 - - - +
114B LEU* 4.2 19.3 - - + -
284B LEU* 4.0 26.9 - - + -
285B LEU* 1.3 80.1 - - - +
287B THR* 1.3 61.3 + - - +
288B SER 4.0 0.8 + - - -
289B GLY* 4.1 11.9 - - - +
290B THR 2.7 43.7 - - - +
291B PRO* 3.8 1.8 - - + -
292B ILE* 4.1 1.6 - - - +
318B ALA* 6.1 0.2 - - - +
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Residues in contact with THR 287 (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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225A CYS* 6.2 0.2 - - - -
106B SER* 3.1 17.0 + - - +
285B LEU* 4.8 0.5 - - - +
286B MET* 1.3 73.7 + - - +
288B SER* 1.3 77.2 + - - +
289B GLY 3.2 1.9 + - - -
290B THR* 3.1 22.3 + - - -
292B ILE* 3.9 16.4 - - - +
318B ALA* 3.4 23.5 + - - +
321B TYR 3.4 26.4 - - - +
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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