Contacts of the helix formed by residues 285 - 292 (chain M) in PDB entry 2W4G
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 TYR 285 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231M ALA 4.0 4.0 - - - +
232M PHE 2.8 16.2 - - - +
233M GLY 3.3 2.7 - - - -
234M ASN 3.3 16.2 - - - +
235M ALA* 4.0 1.1 - - + +
245M ARG* 4.2 4.5 - - + -
270M LEU* 1.0 79.8 + - + -
271M GLU* 2.5 22.6 + - - +
274M ARG* 3.2 25.4 - - + -
275M VAL* 3.9 19.3 - - + -
284M SER* 1.4 98.2 + - - +
286M HIS* 1.3 65.9 + - - +
287M ILE* 3.4 1.1 - - + -
288M PHE* 4.0 14.1 + + + -
289M TYR* 3.2 11.6 - - - -
434M TYR* 3.7 21.3 - + - +
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Residues in contact with HIS 286 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230M GLU* 3.3 24.9 - - + -
231M ALA* 3.2 8.2 + - - +
234M ASN 3.2 9.1 + - - -
235M ALA* 3.4 29.2 + - - -
236M LYS 3.9 3.1 - - - -
241M ASP 3.9 9.2 - - - -
242M ASN* 2.5 30.1 + - - -
283M ARG* 3.5 24.0 + - - +
284M SER 4.3 0.2 - - - -
285M TYR* 1.3 70.1 - - - +
287M ILE* 1.3 57.1 + - - +
288M PHE 3.0 2.7 - - - -
289M TYR* 2.6 34.8 + - - +
290M GLN* 2.7 27.3 + - - +
325M ILE* 4.7 10.9 - - + +
327M ASP* 5.4 1.6 - - - +
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Residues in contact with ILE 287 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231M ALA* 2.7 30.5 + - + +
232M PHE* 3.0 45.1 - - + -
285M TYR* 4.4 1.6 - - + -
286M HIS* 1.3 72.3 - - - +
288M PHE* 1.3 80.1 + - + +
290M GLN* 2.9 16.6 + - + +
291M ILE* 2.8 35.4 + - + +
334M THR* 4.5 7.9 - - + -
352M TYR* 4.8 15.3 - - + -
355M THR* 4.3 13.2 - - + +
434M TYR* 4.0 18.4 - - - +
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Residues in contact with PHE 288 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275M VAL* 4.9 8.3 - - + -
284M SER* 4.0 17.3 - - - -
285M TYR* 4.0 23.6 - + + +
286M HIS 2.7 2.8 + - - -
287M ILE* 1.3 84.5 - - + +
289M TYR* 1.3 69.7 + - + +
291M ILE* 3.6 4.6 - - - +
292M MET* 3.2 28.7 + - - +
315M VAL* 4.0 33.4 - - + -
355M THR* 3.4 34.5 - - + -
358M VAL* 4.6 12.3 - - + -
359M MET* 3.8 28.9 - - + +
434M TYR* 3.9 31.6 - + - -
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Residues in contact with TYR 289 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278M GLN* 4.1 1.2 + - - -
283M ARG* 3.4 36.3 - - - +
284M SER* 3.3 30.5 + - - -
285M TYR 3.2 24.0 - - - -
286M HIS 2.6 11.1 + - - +
288M PHE* 1.3 72.9 - - + +
290M GLN* 1.3 68.3 + - - +
292M MET* 3.6 6.4 + - - +
293M SER* 3.3 17.5 + - - -
309M PRO* 4.7 9.4 - - + -
315M VAL* 2.3 46.5 + - + -
319M GLU 3.5 11.7 + - - -
320M ILE* 3.5 37.2 - - + +
327M ASP* 3.7 12.2 - - - +
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Residues in contact with GLN 290 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231M ALA* 3.5 17.5 - - - +
286M HIS* 2.7 27.7 + - - +
287M ILE* 3.0 16.5 - - + +
289M TYR* 1.3 77.2 - - - +
291M ILE* 1.3 51.6 + - + +
293M SER* 2.6 38.1 + - - -
327M ASP* 3.3 17.8 + - - +
330M GLU* 3.5 16.8 - - + +
331M LEU* 2.8 36.0 - - + +
334M THR* 2.4 39.9 + - - +
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Residues in contact with ILE 291 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287M ILE* 2.8 26.5 + - + +
288M PHE* 3.6 5.8 - - - +
290M GLN* 1.3 75.0 - - + +
292M MET* 1.3 59.1 + - + +
293M SER 3.0 1.1 + - - -
294M ASN* 3.8 2.9 + - - -
296M LYS 5.5 0.2 - - - +
299M LEU* 4.9 10.3 - - + +
300M ILE* 3.1 20.3 - - + +
303M LEU* 3.6 26.0 - - + -
305M ILE* 4.0 23.6 - - + -
331M LEU* 3.1 14.3 - - + +
352M TYR* 3.7 33.0 - - + -
355M THR* 4.7 18.8 - - + -
359M MET* 4.6 5.8 - - + -
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Residues in contact with MET 292 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288M PHE 3.2 21.4 + - - +
289M TYR* 4.0 7.2 - - + +
290M GLN 3.3 0.2 - - - -
291M ILE* 1.3 79.7 - - + +
293M SER* 1.3 62.4 + - - +
294M ASN* 3.2 2.6 + - - -
300M ILE* 4.2 7.0 - - - -
305M ILE* 4.3 11.7 - - + -
306M THR 3.8 13.0 - - - +
307M THR* 3.5 31.8 - - - +
308M ASN 3.4 6.3 - - - +
309M PRO* 3.0 57.9 - - + -
312M TYR* 4.4 8.3 - - + -
315M VAL* 4.8 6.3 - - - -
359M MET* 4.2 20.9 - - + +
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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