Contacts of the strand formed by residues 264 - 270 (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 LYS 264 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205G THR* 4.2 13.2 + - - +
241G ALA* 5.7 1.2 - - - +
242G ASN* 3.5 25.7 + - - +
245G LEU* 4.0 19.6 - - + +
262G PHE* 3.6 28.9 - - + -
263G GLY* 1.3 73.7 - - - -
265G PHE* 1.3 61.3 + - - +
266G ILE* 3.7 32.7 - - + +
281G ILE* 4.1 15.7 - - + -
282G GLU 3.8 2.2 - - - -
283G THR* 4.9 0.2 - - - -
476G ILE 3.2 3.3 - - - +
477G LEU* 3.3 4.7 - - - +
478G ASP* 2.6 62.0 + - + +
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Residues in contact with PHE 265 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193G SER* 4.4 4.7 - - - -
263G GLY 4.2 0.4 - - - -
264G LYS* 1.3 73.8 - - - +
266G ILE* 1.3 60.4 + - - +
267G ARG* 3.4 45.1 + - + -
281G ILE* 3.5 1.9 - - - +
282G GLU* 2.6 58.8 + - + +
284G TYR* 3.8 20.4 - + + -
473G PHE* 4.1 10.3 - + - -
475G GLY* 3.5 28.7 - - - -
476G ILE 3.4 7.6 - - - -
477G LEU* 4.4 12.3 - - + -
681G LEU* 4.8 5.8 - - + -
684G THR* 5.1 7.2 - - - -
685G LEU* 3.4 33.4 - - + -
688G THR* 6.2 0.2 - - + -
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Residues in contact with ILE 266 (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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205G THR* 5.7 7.0 - - + -
208G THR* 4.7 18.8 - - + -
212G ILE* 5.7 7.6 - - + -
238G LEU* 5.3 11.9 - - + -
264G LYS* 3.7 27.6 - - + +
265G PHE* 1.3 72.8 - - - +
267G ARG* 1.3 67.9 + - - +
268G ILE* 3.8 14.3 + - + -
279G ALA* 5.2 4.0 - - + -
280G ASN 3.9 4.3 - - - +
281G ILE* 3.6 27.8 - - + -
474G LEU 3.3 6.1 - - - +
475G GLY* 3.4 0.8 - - - -
476G ILE* 2.8 52.0 + - + +
478G ASP* 6.0 2.0 - - + -
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Residues in contact with ARG 267 (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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265G PHE* 3.4 25.9 - - + +
266G ILE* 1.3 72.7 - - - +
268G ILE* 1.3 61.9 + - - +
269G ASN* 3.8 9.5 + - - +
279G ALA* 3.2 8.0 - - - +
280G ASN* 2.9 65.7 + - - +
282G GLU* 2.8 33.1 + - - -
284G TYR* 4.1 5.3 + - - -
473G PHE* 2.9 55.9 - - + -
474G LEU 3.7 4.3 - - - -
684G THR* 4.7 12.5 - - - +
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Residues in contact with ILE 268 (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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211G VAL* 6.1 0.2 - - + -
212G ILE* 4.1 23.8 - - + -
215G LEU* 3.9 22.4 - - + -
238G LEU* 6.1 2.2 - - + -
266G ILE* 4.4 12.3 - - + +
267G ARG* 1.3 75.5 - - - +
269G ASN* 1.3 60.0 + - - +
270G PHE* 3.2 36.5 - - + -
276G ILE* 3.9 15.7 - - + -
278G GLY 4.1 7.2 - - - +
279G ALA* 4.3 7.2 - - + -
473G PHE* 3.2 2.8 - - - -
474G LEU* 2.9 37.8 + - + +
476G ILE* 4.1 20.4 - - + -
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Residues in contact with ASN 269 (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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267G ARG* 4.5 5.7 - - - +
268G ILE* 1.3 73.0 - - - +
270G PHE* 1.3 65.6 + - - +
276G ILE* 3.5 2.9 - - - +
277G VAL* 3.0 45.8 + - + +
278G GLY 3.0 17.9 + - - +
279G ALA* 3.9 8.8 - - - -
280G ASN* 3.7 24.5 + - - +
470G GLY 4.7 1.6 - - - +
472G SER 3.4 5.3 + - - +
473G PHE* 3.6 22.6 - - - +
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Residues in contact with PHE 270 (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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182G TYR* 5.4 6.3 - + - -
185G MET* 3.3 43.5 - - + -
215G LEU* 3.1 45.1 - - + -
268G ILE* 3.2 42.0 - - + -
269G ASN* 1.3 77.8 - - - +
271G ASP* 1.3 61.6 + - - +
274G GLY* 4.9 7.9 - - - -
275G TYR 3.2 13.0 - - - +
276G ILE* 3.6 6.1 - - + -
470G GLY 3.9 1.1 - - - -
471G ALA* 2.7 24.3 + - - +
472G SER* 2.5 22.7 + - - +
474G LEU* 3.3 23.8 - - + -
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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