Contacts of the helix formed by residues 281 - 295 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499E LYS* 4.9 9.5 - - - +
501E LEU* 3.9 15.1 - - - +
279F ASP 3.7 1.6 + - - -
280F ALA* 1.3 69.0 - - - +
282F LEU* 1.3 57.9 + - - +
283F ASN* 2.9 25.9 + - - +
284F LEU* 3.1 25.4 + - + +
285F VAL* 2.9 27.4 + - - +
431F PHE* 5.7 0.6 - - - +
432F THR 5.7 0.4 - - - -
433F LYS* 4.1 27.1 + - - +
455F ASN* 5.8 1.4 + - - -
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Residues in contact with LEU 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276F VAL* 4.6 7.4 - - + -
277F PHE 4.9 0.7 - - - +
278F GLU 5.0 1.8 - - - +
280F ALA* 3.2 38.2 + - + +
281F ASP* 1.3 73.7 + - - +
283F ASN* 1.3 58.2 + - - +
285F VAL* 4.0 6.3 - - + -
286F VAL* 3.1 34.8 + - + +
313F VAL* 4.4 28.0 - - + -
316F ALA* 5.6 6.7 - - + -
317F VAL* 4.0 24.2 - - + -
320F ARG* 3.4 26.6 + - - +
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Residues in contact with ASN 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501E LEU* 3.8 28.8 - - + +
509E PHE* 6.0 0.9 - - - +
281F ASP* 2.9 11.5 + - - +
282F LEU* 1.3 76.7 - - - +
284F LEU* 1.3 57.3 + - - +
287F PRO* 3.0 24.9 - - - +
320F ARG* 3.0 24.5 + - - +
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Residues in contact with LEU 284 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496E ASN* 3.8 13.5 - - - +
498E SER 5.7 2.0 - - - +
500E ASP 4.1 13.9 - - - +
501E LEU* 3.7 13.2 - - + +
502E PRO* 3.8 19.2 - - + +
281F ASP* 3.1 24.2 + - + +
283F ASN* 1.3 78.1 - - - +
285F VAL* 1.3 63.6 + - - +
286F VAL 3.4 0.2 - - - -
287F PRO* 3.2 3.3 - - - +
288F SER* 2.9 39.3 + - - +
431F PHE* 3.7 15.5 - - + -
455F ASN* 3.6 35.7 - - + +
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Residues in contact with VAL 285 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274F ILE* 5.7 1.1 - - + -
276F VAL* 3.6 31.6 - - + -
280F ALA* 3.9 13.5 - - + -
281F ASP 2.9 21.2 + - - +
282F LEU* 3.4 9.8 + - - +
284F LEU* 1.3 75.0 - - - +
286F VAL* 1.3 57.5 + - + +
288F SER* 3.2 2.6 + - - -
289F ALA* 2.8 39.3 + - + +
307F LEU* 5.4 0.7 - - + -
309F LEU* 5.3 0.2 - - + -
317F VAL* 4.4 17.7 - - + -
431F PHE* 3.7 39.8 - - + -
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Residues in contact with VAL 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509E PHE* 3.4 28.9 - - + -
282F LEU* 3.1 16.7 + - + +
285F VAL* 1.3 77.0 - - + +
287F PRO* 1.4 66.7 - - + +
289F ALA* 3.8 1.7 - - - +
290F VAL* 3.1 28.2 + - + +
317F VAL* 4.6 11.7 - - + -
320F ARG* 3.8 56.8 - - + +
321F ILE* 4.3 18.1 - - + +
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Residues in contact with PRO 287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501E LEU* 6.0 0.9 - - + -
502E PRO* 3.6 24.9 - - + +
509E PHE* 3.8 41.1 - - + -
283F ASN 3.0 29.4 - - - +
284F LEU 3.2 7.6 - - - +
286F VAL* 1.4 89.2 - - + +
288F SER* 1.3 63.1 + - - +
290F VAL* 3.8 1.0 - - + +
291F PHE* 3.1 39.0 + - + -
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Residues in contact with SER 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502E PRO* 4.1 8.8 - - - +
284F LEU* 2.9 36.6 + - - +
285F VAL 3.2 3.9 + - - -
287F PRO* 1.3 79.7 - - - +
289F ALA* 1.3 61.6 + - - +
291F PHE* 4.1 2.2 - - - +
292F ALA* 3.0 27.6 + - - +
431F PHE* 3.7 18.0 - - - -
457F PRO* 3.6 29.0 - - - +
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Residues in contact with ALA 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274F ILE* 4.3 16.5 - - + +
285F VAL* 2.8 23.3 + - + +
286F VAL 3.8 3.6 - - - +
288F SER* 1.3 73.7 - - - +
290F VAL* 1.3 62.2 + - - +
292F ALA* 3.5 0.9 + - - +
293F SER* 2.9 32.3 + - - +
304F THR* 6.4 0.4 - - + -
307F LEU* 4.5 17.5 - - + -
321F ILE* 3.8 26.9 - - + -
404F LEU* 5.5 2.2 - - + -
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Residues in contact with VAL 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507E ILE* 4.7 3.4 - - + -
509E PHE* 4.4 3.1 - - + -
286F VAL 3.1 20.6 + - - +
287F PRO* 3.8 5.2 - - + +
288F SER 3.4 0.2 - - - -
289F ALA* 1.3 77.6 - - - +
291F PHE* 1.3 72.9 + - + +
293F SER* 3.8 1.0 - - - -
294F VAL* 2.9 36.4 + - + +
321F ILE* 4.0 20.2 - - + +
324F ALA* 3.6 30.5 - - + -
325F TYR* 4.5 14.6 - - + -
328F VAL* 4.4 23.1 - - + -
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Residues in contact with PHE 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502E PRO* 5.1 7.6 - - + -
503E LEU 3.3 20.0 - - - -
504E ALA 3.5 12.6 - - - -
505E GLN* 3.3 43.3 - - + +
507E ILE* 4.0 22.9 - - + -
509E PHE* 4.5 4.7 - + - -
287F PRO* 3.1 37.6 + - + +
288F SER* 4.3 2.7 - - - +
290F VAL* 1.3 80.4 - - + +
292F ALA* 1.3 58.4 + - - +
294F VAL* 4.9 5.8 - - + -
295F GLY* 3.0 30.4 + - - +
300F ARG* 3.7 9.0 + - - +
339F LEU* 4.7 6.3 - - + -
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Residues in contact with ALA 292 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274F ILE* 4.5 0.9 - - + -
288F SER 3.0 20.2 + - - +
289F ALA 4.0 2.5 - - - +
291F PHE* 1.3 77.8 - - - +
293F SER* 1.3 57.8 + - - +
295F GLY 4.7 0.7 + - - +
300F ARG* 4.0 7.8 + - - +
303F THR* 3.2 22.9 - - - +
304F THR* 3.2 26.8 + - - +
457F PRO* 3.6 22.8 - - + +
458F THR* 4.5 1.3 - - - +
459F SER* 4.0 15.4 + - - +
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Residues in contact with SER 293 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289F ALA* 2.9 21.0 + - - +
290F VAL 3.8 1.3 - - - -
292F ALA* 1.3 76.8 - - - +
294F VAL* 1.3 63.2 + - - +
295F GLY 3.5 0.2 - - - -
298F GLY* 3.5 11.1 + - - -
303F THR* 3.5 21.1 - - - +
304F THR* 3.8 13.0 - - - +
325F TYR* 3.4 22.4 - - - -
402F PRO* 4.8 7.1 - - - +
403F ILE 6.4 0.2 - - - -
404F LEU* 3.4 29.4 - - - +
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Residues in contact with VAL 294 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290F VAL* 2.9 19.4 + - + +
291F PHE* 5.2 7.0 - - + +
293F SER* 1.3 75.1 - - - +
295F GLY* 1.3 69.5 + - - +
296F THR 3.5 0.2 + - - -
297F ALA* 3.0 18.0 + - - -
298F GLY 4.2 0.7 - - - +
325F TYR* 3.7 37.2 - - + +
328F VAL* 3.8 34.3 - - + -
339F LEU* 4.9 7.2 - - + +
340F TYR* 3.4 15.9 - - + +
382F PRO* 3.9 17.3 - - + -
402F PRO* 5.6 1.3 - - + -
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Residues in contact with GLY 295 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F GLU* 4.5 2.2 - - - -
291F PHE* 3.0 13.1 + - - -
292F ALA 4.5 0.4 - - - +
293F SER 3.5 1.7 - - - +
294F VAL* 1.3 79.0 - - - +
296F THR* 1.3 66.4 + - - -
298F GLY* 2.9 21.1 + - - -
299F GLN 4.0 0.5 + - - -
300F ARG* 3.4 28.3 - - - +
303F THR* 4.4 1.7 + - - +
339F LEU 5.3 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
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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