Contacts of the strand formed by residues 276 - 282 (chain G) in PDB entry 5JLH
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 ILE 276 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215G LEU* 3.6 17.7 - - + +
216G ALA* 5.6 4.7 - - - -
219G ALA* 4.9 13.2 - - + +
221G SER 5.0 3.9 + - - +
234G LEU* 5.8 8.3 - - + -
235G GLU* 5.7 7.4 - - + +
268G ILE* 3.9 8.7 - - + -
269G ASN 3.5 4.3 - - - +
270G PHE* 3.6 25.8 - - + -
275G TYR* 1.3 74.3 - - - +
277G VAL* 1.3 59.6 + - - +
278G GLY* 3.3 30.5 - - - +
466G SER* 5.2 3.5 - - - -
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Residues in contact with VAL 277 (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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269G ASN* 3.0 38.3 + - + +
271G ASP* 3.7 29.6 - - + +
275G TYR 3.4 0.4 + - - +
276G ILE* 1.3 74.1 - - - +
278G GLY* 1.3 55.9 + - - +
465G ARG* 3.4 5.5 - - + +
466G SER* 2.8 36.0 + - - -
467G PRO 3.9 20.2 - - - +
468G ARG* 5.5 3.8 - - - -
469G GLN 5.5 0.7 - - - +
470G GLY* 2.9 31.6 - - - +
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Residues in contact with GLY 278 (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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235G GLU* 6.0 4.3 - - - -
268G ILE* 4.0 1.2 - - - +
269G ASN* 3.0 29.1 + - - +
276G ILE* 3.3 16.6 - - - +
277G VAL* 1.3 81.8 - - - +
279G ALA* 1.3 61.9 + - - +
464G ASP 4.4 4.3 - - - -
465G ARG* 4.2 15.5 - - - -
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Residues in contact with ALA 279 (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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235G GLU* 5.3 13.2 - - + +
238G LEU* 5.5 11.7 - - + -
266G ILE* 5.2 5.2 - - + -
267G ARG 3.2 17.3 - - - +
268G ILE* 4.3 11.9 - - + -
269G ASN* 3.9 6.0 + - - -
276G ILE* 6.0 0.2 - - + -
278G GLY* 1.3 75.1 - - - +
280G ASN* 1.3 64.8 + - - +
281G ILE* 6.2 0.2 - - + -
460G ASN 5.1 1.2 - - - +
463G LEU* 3.6 27.4 - - + +
464G ASP 5.0 3.3 + - - +
465G ARG* 5.2 1.2 - - - +
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Residues in contact with ASN 280 (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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266G ILE* 3.8 1.7 - - - +
267G ARG* 2.9 67.1 + - - +
269G ASN* 3.7 17.6 + - - +
279G ALA* 1.3 75.4 - - - +
281G ILE* 1.3 70.3 + - - +
282G GLU* 3.7 14.3 + - - +
460G ASN* 3.7 24.7 - - + +
463G LEU* 4.1 1.3 - - - -
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Residues in contact with ILE 281 (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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238G LEU* 4.5 15.7 - - + -
241G ALA* 5.7 5.2 - - + -
245G LEU* 4.3 13.7 - - + -
264G LYS* 4.1 17.3 - - + -
265G PHE 3.5 4.0 - - - +
266G ILE* 3.6 37.9 - - + -
279G ALA* 6.2 0.7 - - + -
280G ASN* 1.3 76.0 - - - +
282G GLU* 1.3 80.0 + - - +
283G THR* 4.3 5.2 - - + -
456G VAL* 3.7 20.6 - - + +
459G LEU* 5.2 9.4 - - + -
460G ASN* 2.9 37.2 + - - +
463G LEU* 4.4 9.9 - - + -
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Residues in contact with GLU 282 (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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264G LYS* 3.8 0.3 - - - -
265G PHE* 2.6 45.5 + - + +
267G ARG* 2.8 36.4 + - - +
280G ASN* 3.7 10.2 + - - +
281G ILE* 1.3 81.2 - - - +
283G THR* 1.3 64.9 + - - +
284G TYR* 2.1 47.0 + - + -
456G VAL* 4.6 2.5 - - - -
460G ASN* 5.4 0.4 - - - +
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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