Contacts of the helix formed by residues 281 - 295 (chain G) in PDB entry 2JG7
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 ASP 281 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279G ASP 3.7 1.6 + - - -
280G ALA* 1.3 68.2 - - - +
282G LEU* 1.3 58.9 + - - +
283G ASN* 2.9 25.3 + - - +
284G LEU* 3.1 28.7 + - + +
285G VAL* 3.0 26.7 + - - +
431G PHE* 5.7 0.6 - - - +
432G THR 5.7 0.4 - - - -
433G LYS* 4.1 27.8 + - + +
455G ASN* 5.7 2.2 + - - -
499H LYS* 5.1 10.9 - - - +
501H LEU* 4.2 10.4 - - - +
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Residues in contact with LEU 282 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276G VAL* 4.6 8.5 - - + -
277G PHE 4.9 0.9 - - - +
278G GLU 4.9 1.8 - - - +
280G ALA* 3.2 37.7 + - + +
281G ASP* 1.3 73.5 + - - +
283G ASN* 1.3 58.1 + - - +
285G VAL* 3.7 6.7 - - + -
286G VAL* 3.1 34.6 + - + +
313G VAL* 4.4 26.9 - - + -
316G ALA* 5.6 6.5 - - + -
317G VAL* 4.1 24.2 - - + -
320G ARG* 3.4 27.2 + - - +
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Residues in contact with ASN 283 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281G ASP* 2.9 12.7 + - - +
282G LEU* 1.3 77.0 - - - +
284G LEU* 1.3 56.7 + - - +
287G PRO* 3.1 23.5 - - - +
320G ARG* 3.0 24.8 + - - +
501H LEU* 3.7 29.0 - - + +
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Residues in contact with LEU 284 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281G ASP* 3.1 28.1 + - + +
283G ASN* 1.3 78.4 - - - +
285G VAL* 1.3 64.0 + - - +
286G VAL 3.4 0.2 - - - -
287G PRO* 3.3 3.3 - - - +
288G SER* 2.8 40.2 + - - +
431G PHE* 3.7 19.1 - - + -
455G ASN* 3.5 34.3 - - + +
496H ASN* 3.8 12.6 - - - +
498H SER 5.8 2.0 - - - +
500H ASP 4.2 13.9 - - - +
501H LEU* 3.9 8.3 - - + +
502H PRO* 4.0 18.1 - - + +
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Residues in contact with VAL 285 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274G ILE* 5.7 1.1 - - + -
276G VAL* 3.6 31.0 - - + -
280G ALA* 3.9 13.5 - - + -
281G ASP 3.0 20.4 + - - +
282G LEU* 3.9 9.0 - - + +
284G LEU* 1.3 75.2 - - - +
286G VAL* 1.3 58.1 + - + +
288G SER* 3.1 2.4 + - - -
289G ALA* 2.8 40.1 + - + +
307G LEU* 5.3 0.4 - - + -
317G VAL* 4.4 17.9 - - + -
431G PHE* 3.7 38.8 - - + -
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Residues in contact with VAL 286 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282G LEU* 3.1 15.6 + - + +
285G VAL* 1.3 77.9 - - + +
287G PRO* 1.4 69.5 - - + +
289G ALA* 3.8 2.0 - - - +
290G VAL* 3.1 29.7 + - + +
317G VAL* 4.6 12.3 - - + -
320G ARG* 3.8 57.7 - - + +
321G ILE* 4.3 17.5 - - + +
509H PHE* 3.9 24.9 - - + -
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Residues in contact with PRO 287 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283G ASN* 3.1 28.0 - - - +
284G LEU 3.3 8.5 - - - +
286G VAL* 1.4 93.2 - - + +
288G SER* 1.3 60.7 + - - +
290G VAL* 3.8 1.5 - - + +
291G PHE* 3.1 37.7 + - + -
501H LEU* 6.0 0.7 - - + -
502H PRO* 3.7 25.4 - - + +
509H PHE* 3.8 43.5 - - + -
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Residues in contact with SER 288 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274G ILE* 5.0 0.2 - - - -
284G LEU* 2.8 36.7 + - - +
285G VAL 3.1 3.9 + - - -
287G PRO* 1.3 78.6 - - - +
289G ALA* 1.3 63.1 + - - +
291G PHE* 4.0 2.6 - - - +
292G ALA* 3.0 26.9 + - - +
431G PHE* 3.7 18.2 - - - -
457G PRO* 3.6 30.0 - - - +
502H PRO* 4.4 8.1 - - - +
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Residues in contact with ALA 289 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274G ILE* 4.3 16.9 - - + +
285G VAL* 2.8 22.3 + - + +
286G VAL 3.8 1.6 - - - +
288G SER* 1.3 73.3 - - - +
290G VAL* 1.3 60.7 + - - +
292G ALA* 4.0 0.9 - - - +
293G SER* 2.9 32.1 + - - +
304G THR* 6.3 0.4 - - + -
307G LEU* 4.5 17.9 - - + -
321G ILE* 3.8 28.3 - - + -
404G LEU* 5.5 2.2 - - + -
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Residues in contact with VAL 290 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286G VAL* 3.1 21.7 + - + +
287G PRO* 3.8 6.1 - - + +
288G SER 3.3 0.2 - - - -
289G ALA* 1.3 76.5 - - - +
291G PHE* 1.3 73.2 + - + +
293G SER* 3.7 1.4 - - - -
294G VAL* 2.9 35.1 + - + +
321G ILE* 4.0 20.9 - - + +
324G ALA* 3.6 29.8 - - + -
325G TYR* 4.5 13.9 - - + -
328G VAL* 4.4 23.3 - - + -
507H ILE* 5.0 3.4 - - + -
509H PHE* 4.7 2.2 - - + -
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Residues in contact with PHE 291 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287G PRO* 3.1 36.5 + - + +
288G SER* 4.3 2.5 - - - +
290G VAL* 1.3 82.1 - - + +
292G ALA* 1.3 59.1 + - - +
294G VAL* 4.9 6.5 - - + -
295G GLY* 3.0 29.3 + - - +
300G ARG* 3.7 9.9 + - - +
328G VAL* 6.4 0.2 - - + -
339G LEU* 4.5 6.5 - - + -
502H PRO* 5.1 8.7 - - + -
503H LEU 3.5 18.4 - - - -
504H ALA 3.7 11.7 - - - -
505H GLN* 3.6 43.5 - - + +
507H ILE* 4.0 23.1 - - + -
509H PHE* 4.3 7.9 - + - -
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Residues in contact with ALA 292 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274G ILE* 4.4 1.3 - - + -
288G SER 3.0 18.9 + - - +
289G ALA 4.0 2.7 - - - +
291G PHE* 1.3 76.9 - - - +
293G SER* 1.3 58.9 + - - +
295G GLY 4.6 0.9 + - - +
300G ARG* 4.0 14.4 + - - +
303G THR* 3.2 22.7 - - - +
304G THR* 3.3 25.6 + - - +
457G PRO* 3.6 23.6 - - + -
458G THR* 4.5 1.1 - - - +
459G SER* 4.1 6.5 - - - +
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Residues in contact with SER 293 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289G ALA* 2.9 21.7 + - - +
290G VAL 3.7 0.7 - - - -
292G ALA* 1.3 78.1 - - - +
294G VAL* 1.3 61.0 + - - +
298G GLY* 3.5 11.3 + - - -
303G THR* 3.5 21.4 - - - +
304G THR* 3.8 12.0 - - - +
325G TYR* 3.4 22.4 - - - -
402G PRO* 4.8 6.6 - - - +
404G LEU* 3.4 30.6 - - - +
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Residues in contact with VAL 294 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290G VAL* 2.9 19.1 + - + +
291G PHE* 5.2 6.3 - - + -
293G SER* 1.3 74.2 - - - +
295G GLY* 1.3 69.7 + - - +
296G THR 3.5 0.2 + - - -
297G ALA* 3.1 17.5 + - - -
298G GLY 4.2 0.9 - - - +
325G TYR* 3.7 31.2 - - + +
328G VAL* 3.8 34.3 - - + -
339G LEU* 4.8 7.9 - - + +
340G TYR* 3.5 15.7 - - + +
382G PRO* 3.9 23.3 - - + -
402G PRO* 5.6 1.6 - - + -
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Residues in contact with GLY 295 (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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113G GLU* 4.5 2.0 - - - -
291G PHE* 3.0 12.0 + - - +
292G ALA 4.6 0.2 - - - -
293G SER 3.5 1.8 - - - +
294G VAL* 1.3 80.9 - - - +
296G THR* 1.3 65.0 + - - -
298G GLY* 2.9 21.1 + - - -
299G GLN 4.0 0.5 + - - -
300G ARG* 3.4 28.7 - - - +
303G THR* 4.4 1.9 + - - +
339G LEU 5.2 4.3 - - - -
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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
------------------------------------------------------------
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