Contacts of the strand formed by residues 276 - 282 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215F LEU* 3.7 18.8 - - + +
216F ALA* 5.6 4.7 - - - -
219F ALA* 4.8 12.6 - - + +
221F SER 5.0 3.0 + - - +
234F LEU* 5.8 8.5 - - + -
235F GLU* 5.7 7.6 - - + +
268F ILE* 3.9 8.5 - - + -
269F ASN 3.5 3.8 - - - -
270F PHE* 3.6 25.8 - - + -
275F TYR* 1.3 75.3 - - - +
277F VAL* 1.3 58.8 + - - +
278F GLY* 3.3 30.3 - - - +
279F ALA* 6.0 0.4 - - + -
466F SER* 5.3 3.3 - - - -
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Residues in contact with VAL 277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269F ASN* 3.0 38.8 + - + +
271F ASP* 3.7 28.7 - - + +
276F ILE* 1.3 75.7 - - - +
278F GLY* 1.3 56.5 + - - +
465F ARG* 3.4 5.3 - - + +
466F SER* 2.8 36.4 + - - -
467F PRO 3.9 19.5 - - - +
468F ARG* 5.5 3.6 - - - -
469F GLN 5.6 0.9 - - - +
470F GLY* 2.9 32.3 - - - +
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Residues in contact with GLY 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235F GLU* 6.0 4.0 - - - -
268F ILE* 4.0 1.0 - - - +
269F ASN* 3.0 27.5 + - - +
276F ILE* 3.3 17.0 - - - +
277F VAL* 1.3 81.4 - - - +
279F ALA* 1.3 61.6 + - - +
464F ASP 4.4 5.2 - - - -
465F ARG* 4.1 14.8 - - - -
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Residues in contact with ALA 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235F GLU* 5.4 13.2 - - + +
238F LEU* 5.5 11.0 - - + -
266F ILE* 5.2 4.9 - - + -
267F ARG 3.2 17.3 - - - +
268F ILE* 4.3 11.2 - - + -
269F ASN* 3.9 5.8 + - - -
276F ILE* 6.0 0.2 - - + -
278F GLY* 1.3 74.9 - - - +
280F ASN* 1.3 64.5 + - - +
281F ILE* 6.2 0.4 - - + -
460F ASN 5.1 0.9 - - - +
463F LEU* 3.6 27.3 - - + +
464F ASP 5.0 3.3 + - - +
465F ARG* 5.2 1.4 - - - +
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Residues in contact with ASN 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266F ILE* 3.8 1.6 - - - +
267F ARG* 2.9 65.0 + - - +
269F ASN* 3.7 16.6 + - - +
279F ALA* 1.3 74.5 - - - +
281F ILE* 1.3 69.6 + - - +
282F GLU* 3.7 14.7 + - - +
460F ASN* 3.8 24.9 - - + +
463F LEU* 4.1 1.8 - - - -
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Residues in contact with ILE 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238F LEU* 4.5 16.2 - - + -
241F ALA* 5.7 6.1 - - + -
245F LEU* 4.3 17.3 - - + -
264F LYS* 4.1 16.8 - - + -
265F PHE 3.5 4.7 - - - +
266F ILE* 3.6 37.7 - - + -
279F ALA* 6.2 0.4 - - + -
280F ASN* 1.3 77.1 - - - +
282F GLU* 1.3 80.0 + - - +
283F THR* 4.3 1.8 - - + -
456F VAL* 3.7 19.4 - - + +
459F LEU* 5.2 9.2 - - + -
460F ASN* 2.9 35.3 + - - +
463F LEU* 4.4 9.6 - - + -
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Residues in contact with GLU 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264F LYS* 3.8 0.2 - - - -
265F PHE* 2.6 47.3 + - + +
267F ARG* 2.8 36.2 + - - +
280F ASN* 3.7 10.6 + - - +
281F ILE* 1.3 80.0 - - - +
283F THR* 1.3 65.7 + - - +
284F TYR* 2.1 47.6 + - + -
456F VAL* 4.6 2.7 - - - -
460F 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