Contacts of the strand formed by residues 283 - 289 (chain G) in PDB entry 5U07
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 283 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7G HIS 5.2 1.8 - - - +
8G ALA* 3.1 5.6 - - - +
9G ILE* 2.9 42.9 + - + +
281G PRO* 4.0 0.2 - - - +
282G ASP* 1.3 81.9 - - - +
284G VAL* 1.3 81.1 + - - +
285G HIS* 4.2 12.1 - - + +
315G CYS* 4.0 22.2 - - + +
318G LEU* 4.4 12.8 - - + -
337G TYR* 5.2 0.2 - - + -
338G ALA 3.7 3.8 - - - +
339G THR* 3.4 28.0 - - + +
341G GLU* 4.0 5.2 - - - +
346G LEU* 3.6 22.7 - - + -
349G LEU* 4.2 13.7 - - + -
356G TYR* 4.3 0.2 - - - -
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Residues in contact with VAL 284 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G ILE* 4.2 10.8 - - + -
7G HIS 3.5 8.5 - - - +
8G ALA* 4.4 2.0 - - + -
264G LEU* 3.7 31.6 - - + -
281G PRO* 4.1 7.0 - - + -
283G LEU* 1.3 82.3 - - - +
285G HIS* 1.3 63.5 + - - +
286G ILE* 4.0 14.6 - - + -
337G TYR* 3.1 6.4 - - - +
338G ALA 2.9 33.3 + - - +
356G TYR* 3.6 30.1 - - + +
359G LEU* 3.9 18.6 - - + -
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Residues in contact with HIS 285 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G HIS* 2.9 57.5 + + + -
283G LEU* 4.3 11.4 - - + -
284G VAL* 1.3 74.9 - - - +
286G ILE* 1.3 59.3 + - - +
287G ALA* 3.8 26.0 - - + -
296G PHE* 4.1 16.5 - + - -
318G LEU* 4.8 2.5 - - + -
322G ALA* 5.2 1.2 - - + +
335G ARG* 4.1 17.0 - - + +
336G GLY 3.5 7.0 - - - -
337G TYR* 4.3 1.8 - - + -
349G LEU* 3.3 57.7 + - + +
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Residues in contact with ILE 286 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G VAL* 3.9 22.4 - - + -
5G ASP 3.6 10.3 - - - +
6G ILE* 4.0 17.3 - - + -
260G LEU* 3.6 24.9 - - + -
284G VAL* 4.0 15.0 - - + -
285G HIS* 1.3 76.5 - - - +
287G ALA* 1.3 64.0 + - - +
288G VAL* 5.0 0.2 - - + -
336G GLY 2.8 33.6 + - - +
359G LEU* 4.1 20.6 - - + +
360G ILE* 4.1 15.9 - - + -
363G MET* 3.5 29.8 - - + +
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Residues in contact with ALA 287 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G VAL* 3.7 2.3 - - - -
5G ASP* 2.6 52.0 + - - +
7G HIS* 5.0 0.4 - - - +
285G HIS* 3.8 20.8 + - + -
286G ILE* 1.3 77.5 - - - +
288G VAL* 1.3 63.4 + - - +
289G ARG* 4.9 1.6 - - + +
296G PHE* 6.4 0.2 - - + -
333G ALA* 5.3 4.0 - - + -
334G ILE 3.5 5.8 - - - -
335G ARG* 4.2 14.1 - - + +
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Residues in contact with VAL 288 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G THR 4.5 9.2 - - - +
3G PHE 3.7 4.5 - - - +
4G VAL* 4.3 19.3 - - + -
287G ALA* 1.3 75.4 - - - +
289G ARG* 1.3 59.6 + - - +
290G PHE* 3.9 26.9 + - + -
333G ALA* 3.1 23.2 - - - +
334G ILE* 2.9 28.9 + - + +
363G MET* 4.2 32.3 - - + +
366G ALA* 5.3 2.7 - - + +
367G ALA* 4.3 19.3 - - + +
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Residues in contact with ARG 289 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G THR 3.2 1.1 + - - -
3G PHE* 2.9 41.7 + - + +
5G ASP* 4.5 8.1 - - - +
287G ALA* 3.7 2.5 - - + -
288G VAL* 1.3 72.6 - - - +
290G PHE* 1.3 61.4 + - - +
291G ASP* 4.2 4.5 - - - +
292G ARG 3.1 32.1 - - - +
293G PRO* 4.4 4.0 - - + -
294G ILE* 5.5 0.4 - - + +
331G ASP* 5.7 1.1 - - - +
333G ALA* 3.6 12.6 - - + -
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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