Contacts of the helix formed by residues 288 - 297 (chain S) in PDB entry 1I84
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 288 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232S GLU 4.3 5.6 + - - -
233S ALA* 3.7 11.6 + - - +
236S ASN* 3.0 26.9 + - + -
237S ALA* 3.4 14.9 + - + -
238S LYS 4.0 2.7 + - - -
243S ASP 3.5 17.7 + - - -
244S ASN* 2.9 34.4 + - + -
285S ARG* 4.3 14.4 - - - +
286S THR 3.0 9.4 + - - -
287S PHE* 1.3 66.7 - - - +
289S ILE* 1.3 66.8 + - - +
290S PHE 2.6 2.6 + - - -
291S TYR* 2.8 16.2 + - - +
292S TYR* 2.9 46.2 + + + -
323S ILE* 4.5 2.9 - - + +
326S GLN* 3.8 19.3 - - - -
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Residues in contact with ILE 289 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233S ALA* 3.7 7.8 + - + +
234S PHE* 3.2 63.9 - - + +
287S PHE* 2.8 16.0 + - + +
288S HIS* 1.3 74.6 - - - +
290S PHE* 1.3 65.1 + - + +
292S TYR* 3.7 17.9 - - + -
293S LEU* 2.8 30.3 + - + +
332S PHE* 4.9 3.4 - - + -
335S THR* 5.3 7.2 - - - +
336S LEU* 6.3 0.2 - - + -
339S MET* 5.6 4.0 - - + -
353S LEU* 4.5 21.3 - - + -
356S VAL* 4.4 16.6 - - + -
435S PHE* 4.9 4.9 - - + -
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Residues in contact with PHE 290 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277S ALA* 4.0 16.6 - - + -
286S THR* 3.4 37.7 - - + +
287S PHE* 2.7 24.0 + + + +
288S HIS 2.6 4.8 + - - -
289S ILE* 1.3 76.9 - - + +
291S TYR* 1.3 70.1 + - + +
293S LEU* 3.0 2.9 + - - +
294S ILE* 2.9 28.1 + - - +
315S PHE* 6.1 1.1 - + + -
316S LEU* 4.7 9.2 - - + -
356S VAL* 3.2 33.4 - - + -
359S VAL* 3.7 27.6 - - + -
360S LEU* 3.3 29.5 - - + +
435S PHE* 3.8 20.6 - + - -
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Residues in contact with TYR 291 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280S GLN* 4.5 5.5 + - - -
284S GLU 4.5 1.0 + - - -
285S ARG* 3.2 62.8 - - + +
286S THR* 3.1 49.7 + - - -
288S HIS* 2.8 12.0 + - - +
290S PHE* 1.3 75.8 - - + +
292S TYR* 1.3 70.6 + - - +
294S ILE* 3.2 1.5 + - - +
295S ALA* 3.1 22.7 + - - +
310S PHE* 3.3 38.4 - + + -
316S LEU* 4.7 11.9 - - + +
317S SER 4.7 1.9 + - - -
319S GLY 4.2 21.4 + - - -
320S HIS* 4.9 1.8 - + - -
321S VAL* 4.3 8.7 - - - +
328S ASP* 4.1 11.4 - - - +
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Residues in contact with TYR 292 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233S ALA* 5.1 6.0 - - + -
285S ARG* 4.3 1.1 - - - -
288S HIS* 2.9 54.0 + + + -
289S ILE* 3.3 17.3 - - + +
291S TYR* 1.3 76.9 - - + +
293S LEU* 1.3 53.4 + - - +
295S ALA* 3.7 0.3 - - - +
296S GLY 2.4 34.7 + - - -
326S GLN* 3.4 11.4 + - - -
328S ASP* 3.5 34.5 - - - +
331S MET* 3.4 37.7 - - + +
332S PHE* 3.1 19.9 - - + +
335S THR* 3.4 33.9 - - + -
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Residues in contact with LEU 293 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289S ILE* 2.8 17.0 + - + +
290S PHE* 3.4 9.0 - - - +
292S TYR* 1.3 68.9 - - - +
294S ILE* 1.3 60.2 + - + +
295S ALA 2.8 10.7 + - - -
297S ALA* 2.9 29.1 + - + +
301S MET* 3.2 31.2 - - + -
305S LEU* 4.2 0.4 - - + -
307S LEU* 3.7 21.7 - - + +
332S PHE* 3.3 13.9 - - + -
353S LEU* 3.3 54.5 - - + +
356S VAL* 3.8 16.2 - - + -
357S SER 4.6 0.2 - - - +
360S LEU* 6.2 1.3 - - + -
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Residues in contact with ILE 294 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290S PHE* 2.9 23.9 + - - +
291S TYR 3.8 0.2 - - - +
293S LEU* 1.3 74.1 - - + +
295S ALA* 1.3 56.3 + - - +
297S ALA* 4.6 5.0 - - - +
302S ARG* 6.0 1.2 - - - +
307S LEU* 5.2 13.8 - - + +
308S GLU 3.8 21.9 - - - +
309S GLY* 3.9 7.0 - - - -
310S PHE* 3.2 55.8 - - + -
313S TYR* 5.0 9.2 - - + -
316S LEU* 4.0 31.9 - - + -
360S LEU* 4.4 13.0 - - + -
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Residues in contact with ALA 295 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291S TYR 3.1 13.6 + - - +
292S TYR* 3.7 1.1 - - - +
293S LEU 2.8 1.8 + - - -
294S ILE* 1.3 79.5 - - - +
296S GLY* 1.3 59.0 + - - +
297S ALA* 2.9 16.3 + - - +
310S PHE* 4.1 12.3 - - + -
328S ASP* 5.1 4.7 - - + -
329S ASP* 4.8 22.0 - - - +
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Residues in contact with GLY 296 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292S TYR 2.4 21.7 + - - -
295S ALA* 1.3 71.0 - - - +
297S ALA* 1.3 62.1 + - - +
298S SER* 3.4 2.9 + - - -
329S ASP* 4.1 9.7 + - - +
332S PHE* 3.2 42.6 - - - -
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Residues in contact with ALA 297 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293S LEU* 2.9 23.4 + - + +
294S ILE 4.6 3.8 - - - +
295S ALA 2.9 9.4 - - - +
296S GLY* 1.3 80.3 - - - +
298S SER* 1.3 63.3 + - - +
299S GLU 3.7 1.4 + - - -
301S MET* 3.7 26.2 - - + -
302S ARG* 4.3 15.9 - - + +
307S LEU* 4.1 13.5 - - + -
332S PHE* 4.2 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