Contacts of the strand formed by residues 287 - 293 (chain G) in PDB entry 1II4
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 HIS 287 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66C ALA* 3.8 11.9 - - + -
67C GLU 3.5 6.5 + - - -
68C GLU* 3.4 33.6 - - + -
69C ARG* 3.5 25.3 + - + +
70C GLY 5.2 0.2 - - - +
285G GLN 4.2 0.2 + - - -
286G PRO* 1.3 73.2 - - - +
288G ILE* 1.3 70.8 + - - +
289G GLN* 3.9 25.3 + - + -
314G ALA* 4.1 13.3 - - + +
315G ALA* 3.0 37.1 + - + -
343G LEU* 3.4 2.8 - - - +
344G ALA* 3.3 3.1 - - - -
345G GLY 2.8 31.6 + - - +
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Residues in contact with ILE 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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26C PHE* 4.1 17.9 - - + -
278G CYS* 4.9 0.7 - - - -
280G VAL* 3.4 34.3 - - + -
286G PRO* 4.1 6.3 + - + +
287G HIS* 1.3 83.7 - - - +
289G GLN* 1.3 66.6 + - - +
290G TRP* 5.2 0.9 - - - +
315G ALA* 2.8 32.3 + - - +
321G ASP* 5.4 1.8 - - - +
324G ILE* 3.6 30.9 - - + +
325G GLU* 4.1 16.6 - - + -
342G CYS* 3.7 28.5 - - - -
343G LEU 3.3 5.4 - - - +
344G ALA* 4.3 5.6 - - + -
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Residues in contact with GLN 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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287G HIS* 3.9 20.5 + - + +
288G ILE* 1.3 77.9 - - - +
290G TRP* 1.3 65.0 + - - +
291G ILE* 4.0 9.2 - - + +
311G VAL* 3.2 30.1 - - + +
313G LYS 3.0 17.0 - - - +
314G ALA* 3.8 11.7 - - + +
324G ILE* 4.9 0.2 - - - -
341G THR 3.8 0.2 - - - +
342G CYS* 3.8 2.3 - - - -
343G LEU* 3.0 62.3 + - + +
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Residues in contact with TRP 290 (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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263G PRO* 4.0 9.4 - - + -
276G PHE* 3.0 45.8 - + + -
277G VAL 3.8 1.8 - - - -
278G CYS* 3.6 21.5 - - + -
288G ILE* 5.2 1.6 - - + +
289G GLN* 1.3 74.8 - - - +
291G ILE* 1.3 64.8 + - - +
311G VAL* 3.6 2.6 - - - +
312G LEU* 2.9 29.8 + - + -
313G LYS* 2.7 39.4 + - + +
324G ILE* 2.6 27.9 + - + +
325G GLU 3.2 24.5 - - - -
326G VAL 4.2 1.8 - - - -
327G LEU* 3.6 36.6 - - + +
340G TYR* 5.2 2.9 - - + -
341G THR 3.4 21.8 - - - -
342G CYS* 3.9 19.1 - - + -
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Residues in contact with ILE 291 (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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289G GLN* 4.0 21.3 - - + +
290G TRP* 1.3 81.0 - - - +
292G LYS* 1.3 65.2 + - - +
293G HIS* 4.4 1.6 + - + -
309G LEU* 3.6 44.4 - - + -
310G LYS 3.3 14.6 - - - +
311G VAL* 4.5 5.8 - - + +
312G LEU* 4.7 3.4 - - - -
339G GLU 3.9 0.3 - - - +
340G TYR* 3.5 2.5 - - - +
341G THR* 2.7 52.2 + - + +
343G LEU* 3.6 34.1 - - + -
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Residues in contact with LYS 292 (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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291G ILE* 1.3 75.1 - - - +
293G HIS* 1.3 67.4 + - - +
294G VAL* 3.5 8.7 - - + +
309G LEU* 3.6 1.6 - - - -
310G LYS* 2.9 33.8 + - + +
312G LEU* 3.9 28.0 - - + +
339G GLU 3.6 6.3 - - - +
340G TYR* 4.5 16.2 - - + +
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Residues in contact with HIS 293 (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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291G ILE* 4.4 2.2 + - + -
292G LYS* 1.3 76.9 - - - +
294G VAL* 1.3 60.2 + - - +
307G PRO* 5.6 5.6 - - + -
308G TYR 3.5 6.1 - - - +
309G LEU* 3.6 23.3 - - + +
338G GLY* 5.4 3.3 - - - -
339G GLU* 3.0 58.5 + - + +
341G THR* 3.0 32.5 - - + -
354G SER* 4.5 1.5 + - - -
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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