Contacts of the strand formed by residues 284 - 289 (chain A) in PDB entry 7ODC
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 PHE 284 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A TYR* 3.6 27.4 - + + -
42A VAL 3.5 3.4 - - - -
43A ALA* 3.7 25.1 - - + -
71A ASN* 3.5 26.0 - - - -
73A SER* 4.3 4.9 - - - -
76A ILE* 3.6 30.5 - - + -
280A VAL* 3.9 7.4 - - + -
281A ALA 3.9 1.4 + - - -
282A SER 3.3 1.4 - - - +
283A ALA* 1.3 87.3 - - + +
285A THR* 1.3 60.9 + - - +
385A ASN 3.5 7.4 + - - -
386A MET 3.0 31.1 + - - +
387A GLY* 3.5 28.3 - - - +
391A VAL* 4.9 3.8 - - + -
405A ILE* 4.0 24.7 - - + -
407A TYR* 4.4 4.3 - + - -
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Residues in contact with THR 285 (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 LEU* 3.6 31.3 - - + +
41A TYR* 3.3 6.0 - - - -
42A VAL* 3.0 36.6 + - - +
282A SER 4.9 3.8 + - - -
283A ALA 4.1 0.8 + - - -
284A PHE* 1.3 74.2 + - - +
286A LEU* 1.3 69.6 + - - +
287A ALA 4.0 0.3 + - - -
382A LEU* 4.5 5.4 - - + -
383A PHE 3.5 17.0 - - - +
384A GLU* 4.0 21.9 - - + +
385A ASN 4.7 0.5 + - - -
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Residues in contact with LEU 286 (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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39A ALA* 4.5 0.2 - - + -
40A PHE 3.6 18.4 - - - +
41A TYR* 3.6 34.0 - - + +
284A PHE 4.2 0.4 - - - -
285A THR* 1.3 75.2 - - - +
287A ALA* 1.3 66.3 + - - +
288A VAL* 3.8 21.3 + - + -
320A ASP* 3.6 22.9 - - - +
325A SER* 4.0 11.4 - - - -
326A PHE* 3.9 24.5 - - + -
381A MET 3.8 0.7 - - - +
382A LEU* 3.4 4.0 - - - -
383A PHE* 2.8 42.6 + - + +
386A MET* 4.1 9.6 - - + +
403A PRO* 4.2 6.5 - - + -
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Residues in contact with ALA 287 (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 LEU* 3.9 11.7 - - + -
28A ILE* 4.5 1.3 - - + -
39A ALA* 3.2 6.8 - - - +
40A PHE* 2.9 60.1 + - + +
285A THR 4.0 1.0 + - - -
286A LEU* 1.3 72.6 - - - +
288A VAL* 1.3 60.0 + - - +
380A TRP* 3.9 9.3 - - + -
381A MET 3.5 4.9 - - - -
382A LEU* 3.8 19.1 - - + -
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Residues in contact with VAL 288 (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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39A ALA* 4.1 3.4 - - + -
286A LEU* 3.8 26.7 - - + -
287A ALA* 1.3 77.5 - - - +
289A ASN* 1.3 58.9 + - - +
318A VAL* 3.7 30.7 - - + -
319A ASN* 3.7 9.0 - - - +
320A ASP* 3.9 22.2 - - + +
326A PHE* 4.5 6.1 - - + -
380A TRP* 3.3 9.0 - - - -
381A MET* 3.0 44.5 + - + +
383A PHE* 3.8 19.5 - - + -
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Residues in contact with ASN 289 (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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37A LYS* 3.3 37.5 - - - +
288A VAL* 1.3 74.6 - - - +
290A ILE* 1.3 72.9 + - - +
291A ILE* 3.2 9.9 + - + +
318A VAL* 3.2 20.6 - - - -
319A ASN* 2.9 17.7 + - - +
377A VAL* 5.5 0.2 - - - +
378A GLY* 3.0 41.4 + - - -
379A ASP 3.4 3.6 + - - -
380A TRP* 3.2 29.8 - - + -
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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