Contacts of the helix formed by residues 293 - 303 (chain M) in PDB entry 2JA7
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 GLU 293 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88M LYS* 3.4 35.2 + - + +
89M PRO 5.2 6.4 - - - +
90M VAL* 5.7 1.2 - - + +
180M LYS* 4.6 12.6 + - - -
204M THR* 5.2 7.2 + - - -
205M GLU* 3.4 12.6 - - - +
276M LEU* 3.8 26.7 - - + -
289M ILE* 2.9 15.6 + - + +
290M GLU* 4.0 14.0 - - - +
291M GLU 4.0 0.2 - - - +
292M ALA* 1.3 76.8 - - - +
294M SER* 1.3 64.7 + - - +
295M LEU 3.1 1.3 - - - -
296M LEU* 3.4 7.4 + - + +
297M GLN* 3.2 21.1 + - - +
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Residues in contact with SER 294 (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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179M LEU* 5.5 0.7 - - - +
180M LYS* 3.8 30.5 - - - +
290M GLU 4.1 6.4 + - - -
291M GLU* 3.5 18.2 + - - -
292M ALA 4.2 0.2 - - - +
293M GLU* 1.3 81.9 + - - +
295M LEU* 1.3 58.5 + - - +
296M LEU 3.3 0.2 - - - -
297M GLN* 3.5 9.6 - - - +
298M PHE* 2.8 28.4 + - - +
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Residues in contact with LEU 295 (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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272M ALA* 3.8 26.0 - - + -
275M SER* 5.3 4.0 - - - +
291M GLU 4.7 3.1 - - - +
292M ALA* 3.7 22.2 - - + +
293M GLU 3.1 0.2 - - - -
294M SER* 1.3 81.2 + - - +
296M LEU* 1.3 59.1 + - - +
298M PHE* 3.3 12.5 - - + +
299M HIS* 3.0 46.1 + - + +
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Residues in contact with LEU 296 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86M LEU* 4.5 5.2 - - + -
87M ALA* 4.2 15.7 - - + +
88M LYS 4.3 14.6 - - - +
90M VAL* 4.4 7.2 - - + -
269M ILE* 3.5 28.3 - - + +
272M ALA* 4.1 12.3 - - + +
273M ASN* 3.3 37.7 - - + +
276M LEU* 4.6 6.7 - - + -
292M ALA 3.9 3.0 + - - +
293M GLU* 3.4 14.3 + - + +
294M SER 3.3 0.2 - - - -
295M LEU* 1.3 74.7 - - - +
297M GLN* 1.3 68.5 + - - +
298M PHE 3.0 1.7 + - - -
299M HIS* 4.6 0.7 - - - +
300M VAL* 2.9 49.9 + - + +
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Residues in contact with GLN 297 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89M PRO 4.7 0.3 - - - +
90M VAL* 2.9 36.2 - - + +
91M PHE* 2.7 49.8 + - - +
93M VAL 5.1 0.4 - - - +
96M ILE* 4.9 2.2 - - - +
179M LEU* 3.9 34.0 - - + +
180M LYS* 5.5 6.3 - - + -
204M THR* 4.2 6.6 + - - -
293M GLU* 3.2 13.1 + - - +
294M SER* 3.5 12.3 - - - +
296M LEU* 1.3 79.1 - - - +
298M PHE* 1.3 58.6 + - - +
301M ALA* 2.9 35.2 + - - +
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Residues in contact with PHE 298 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179M LEU* 3.9 17.0 - - + -
294M SER 2.8 18.2 + - - +
295M LEU* 3.3 16.4 - - + +
296M LEU 3.0 0.4 - - - -
297M GLN* 1.3 73.9 - - - +
299M HIS* 1.3 93.7 + + - +
301M ALA* 2.6 25.1 + - - +
302M THR* 2.7 19.9 + - - -
308M ILE* 6.6 0.2 - - + -
312M PRO* 4.3 24.7 - - + -
314M ALA* 3.5 39.0 - - + -
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Residues in contact with HIS 299 (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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265M LYS* 4.9 2.9 - - + +
268M ASP* 3.3 50.1 + - + +
269M ILE* 3.5 21.1 - - + -
272M ALA* 3.9 12.9 - - + +
295M LEU* 3.0 28.2 + - + +
296M LEU* 4.1 2.2 - - - +
298M PHE* 1.3 105.7 - + - +
300M VAL* 1.3 54.5 + - - +
301M ALA 2.5 12.6 + - - -
302M THR* 3.5 11.5 - - + +
303M TYR* 2.9 24.8 + - - +
314M ALA* 5.8 0.4 - - + -
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Residues in contact with VAL 300 (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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86M LEU* 4.4 8.1 - - + -
90M VAL* 4.4 16.4 - - + -
91M PHE 4.9 0.7 - - - +
93M VAL* 3.9 0.2 - - - +
236M LEU* 3.9 23.1 - - + +
239M LEU* 3.7 22.9 - - + -
269M ILE* 3.2 41.0 - - + +
296M LEU* 2.9 35.5 + - + +
297M GLN 4.0 0.7 - - - -
299M HIS* 1.3 68.3 - - - +
301M ALA* 1.3 58.0 + - - +
303M TYR* 4.4 2.8 - - + +
304M MET* 3.1 23.1 - - + +
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Residues in contact with ALA 301 (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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91M PHE 5.6 0.4 - - - -
93M VAL* 3.0 47.4 - - + +
179M LEU* 3.8 16.2 - - + -
297M GLN* 2.9 22.3 + - - +
298M PHE 2.6 14.2 + - - +
299M HIS 2.5 5.3 + - - -
300M VAL* 1.3 71.2 - - - +
302M THR* 1.3 58.6 + - - +
303M TYR 3.2 1.3 - - - -
304M MET 3.1 2.4 + - - -
305M ASP 3.0 17.2 + - - +
308M ILE* 5.5 0.9 - - + -
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Residues in contact with THR 302 (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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265M LYS* 4.4 16.4 - - + -
298M PHE* 2.7 21.5 + - - -
299M HIS* 3.5 22.0 - - + +
301M ALA* 1.3 71.3 - - - +
303M TYR* 1.3 69.0 + - - +
304M MET 3.2 0.2 + - - -
305M ASP 2.9 17.6 + - - +
306M ASN* 2.9 34.0 + - - +
308M ILE* 5.3 4.5 - - - +
312M PRO 5.4 0.7 + - - -
314M ALA* 3.4 22.5 - - + +
322M VAL* 5.0 1.4 - - + +
324M SER* 3.3 15.4 - - - -
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Residues in contact with TYR 303 (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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239M LEU* 4.4 15.5 - - + -
240M PRO 3.8 2.4 + - - -
242M PRO* 3.0 36.8 - - + +
262M LEU* 3.6 29.1 - - + +
265M LYS* 4.2 19.5 - - + -
266M LEU* 3.4 30.4 - - + +
269M ILE* 3.8 19.3 - - + -
299M HIS 2.9 15.2 + - - +
300M VAL 4.5 4.7 - - - -
301M ALA 3.2 0.2 - - - -
302M THR* 1.3 80.4 - - - +
304M MET* 1.3 78.5 + - + +
322M VAL* 6.1 0.2 - - - -
324M SER* 3.5 3.0 - - - +
325M ILE* 3.0 31.8 + - + +
1209N ALA* 3.6 22.0 + - - +
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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