Contacts of the helix formed by residues 281 - 295 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499A LYS* 4.9 8.1 - - - +
501A LEU* 4.0 10.9 - - - +
279B ASP 3.7 1.4 + - - -
280B ALA* 1.3 68.8 - - - +
282B LEU* 1.3 58.8 + - - +
283B ASN* 2.9 24.8 + - - +
284B LEU* 3.1 29.2 + - + +
285B VAL* 2.9 27.7 + - - +
431B PHE* 5.7 0.6 - - - +
432B THR 5.6 0.8 - - - +
433B LYS* 4.1 26.8 - - - +
455B ASN* 5.7 1.8 + - - -
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Residues in contact with LEU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B VAL* 4.6 7.6 - - + -
277B PHE 4.9 0.7 - - - +
278B GLU 5.0 1.6 - - - +
280B ALA* 3.2 38.4 + - + +
281B ASP* 1.3 70.0 + - - +
283B ASN* 1.3 59.8 + - - +
285B VAL* 4.0 5.2 - - + -
286B VAL* 3.1 35.2 + - + +
313B VAL* 4.3 26.9 - - + -
316B ALA* 5.6 6.5 - - + -
317B VAL* 4.0 26.0 - - + -
320B ARG* 3.4 25.3 + - - +
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Residues in contact with ASN 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501A LEU* 3.7 29.4 - - + +
281B ASP* 2.9 12.5 + - - +
282B LEU* 1.3 77.4 - - - +
284B LEU* 1.3 57.2 + - - +
287B PRO* 3.1 24.0 - - - +
320B ARG* 3.0 24.5 + - - +
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Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A ASN* 3.7 12.3 - - - +
498A SER 5.7 2.7 - - - +
500A ASP 4.1 14.1 - - - +
501A LEU* 3.8 8.5 - - + -
502A PRO* 4.0 18.5 - - + +
281B ASP* 3.1 27.7 + - + +
283B ASN* 1.3 79.1 - - - +
285B VAL* 1.3 63.4 + - - +
286B VAL 3.4 0.4 - - - -
287B PRO* 3.2 3.3 - - - +
288B SER* 2.9 38.7 + - - +
431B PHE* 3.7 16.6 - - + -
455B ASN* 3.6 35.9 - - + +
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Residues in contact with VAL 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ILE* 5.7 0.7 - - + -
276B VAL* 3.6 31.2 - - + -
280B ALA* 3.9 13.5 - - + -
281B ASP 2.9 20.9 + - - +
282B LEU* 3.4 9.8 + - - +
284B LEU* 1.3 75.4 - - - +
286B VAL* 1.3 58.2 + - + +
288B SER* 3.2 3.1 + - - -
289B ALA* 2.8 39.8 + - + +
307B LEU* 5.4 0.4 - - + -
309B LEU* 5.2 0.2 - - + -
317B VAL* 4.4 18.2 - - + -
431B PHE* 3.7 39.7 - - + -
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Residues in contact with VAL 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A PHE* 3.6 27.4 - - + -
282B LEU* 3.1 17.4 + - + +
285B VAL* 1.3 77.1 - - + +
287B PRO* 1.3 68.7 - - + +
289B ALA* 3.4 1.6 + - - +
290B VAL* 3.1 27.8 + - + +
317B VAL* 4.5 12.1 - - + -
320B ARG* 3.8 56.3 - - + +
321B ILE* 4.3 17.9 - - + +
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Residues in contact with PRO 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A LEU* 5.9 0.9 - - + -
502A PRO* 3.6 25.4 - - + +
503A LEU 5.5 0.2 - - - +
509A PHE* 3.8 43.1 - - + -
283B ASN* 3.1 28.9 - - - +
284B LEU 3.2 7.2 - - - +
286B VAL* 1.3 92.7 - - + +
288B SER* 1.3 60.9 + - - +
290B VAL* 3.4 1.0 + - + +
291B PHE* 3.1 38.4 + - + -
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Residues in contact with SER 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A PRO* 4.3 7.7 - - - +
274B ILE* 5.5 0.2 - - - -
284B LEU* 2.9 38.6 + - - +
285B VAL 3.4 2.9 - - - -
287B PRO* 1.3 78.2 - - - +
289B ALA* 1.3 63.4 + - - +
291B PHE* 4.0 2.7 - - - +
292B ALA* 3.0 26.2 + - - +
431B PHE* 3.7 18.6 - - - -
457B PRO* 3.6 29.0 - - - +
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Residues in contact with ALA 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ILE* 4.3 15.2 - - + +
285B VAL* 2.8 22.4 + - + +
286B VAL 3.8 3.4 - - - +
288B SER* 1.3 73.5 - - - +
290B VAL* 1.3 62.3 + - - +
292B ALA* 3.9 0.7 - - - +
293B SER* 2.8 32.1 + - - +
304B THR* 6.3 0.4 - - + -
307B LEU* 4.5 17.9 - - + -
321B ILE* 3.8 26.5 - - + -
404B LEU* 5.5 2.5 - - + -
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Residues in contact with VAL 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A ILE* 4.9 3.4 - - + -
509A PHE* 4.4 3.6 - - + -
286B VAL 3.1 21.0 + - - +
287B PRO* 3.8 5.2 - - + +
288B SER 3.3 0.2 - - - -
289B ALA* 1.3 76.0 - - - +
291B PHE* 1.3 72.9 + - + +
293B SER* 3.8 1.2 - - - -
294B VAL* 2.9 36.1 + - + +
321B ILE* 3.9 21.1 - - + +
324B ALA* 3.7 29.8 - - + -
325B TYR* 4.4 16.2 - - + -
328B VAL* 4.4 22.2 - - + -
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Residues in contact with PHE 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A PRO* 5.0 8.3 - - + -
503A LEU 3.4 19.5 - - - -
504A ALA* 3.6 11.7 - - - -
505A GLN* 3.4 42.6 - - + +
507A ILE* 4.1 21.1 - - + -
509A PHE* 4.6 7.2 - + - -
287B PRO* 3.1 36.9 + - + +
288B SER* 4.3 2.7 - - - +
290B VAL* 1.3 83.1 - - + +
292B ALA* 1.3 57.1 + - - +
294B VAL* 4.9 6.3 - - + -
295B GLY* 2.9 30.3 + - - +
300B ARG* 3.7 8.6 + - - +
339B LEU* 4.5 6.7 - - + -
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ILE* 4.5 1.1 - - + -
288B SER 3.0 19.4 + - - +
289B ALA 4.0 2.0 - - - +
291B PHE* 1.3 77.7 - - - +
293B SER* 1.3 57.3 + - - +
295B GLY 4.6 0.9 + - - +
300B ARG* 4.0 15.0 + - - +
303B THR* 3.3 22.3 - - - +
304B THR* 3.3 26.6 + - - +
457B PRO* 3.6 23.8 - - + +
458B THR* 4.4 1.1 - - - +
459B SER* 4.0 7.4 + - - +
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Residues in contact with SER 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ALA* 2.8 21.2 + - - -
290B VAL 3.8 0.9 - - - -
292B ALA* 1.3 79.0 - - - +
294B VAL* 1.3 60.3 + - - +
295B GLY 3.5 0.2 - - - -
298B GLY* 3.5 12.1 - - - -
303B THR* 3.5 19.9 - - - +
304B THR* 3.8 13.1 - - - +
325B TYR* 3.4 22.0 - - - -
402B PRO* 4.8 6.6 - - - +
404B LEU* 3.5 30.6 - - - +
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Residues in contact with VAL 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B VAL* 2.9 19.9 + - + +
291B PHE* 5.2 6.7 - - + +
293B SER* 1.3 75.3 - - - +
295B GLY* 1.3 70.2 + - - +
296B THR 3.5 0.2 + - - -
297B ALA* 3.0 18.0 + - - -
298B GLY 4.2 0.9 - - - +
325B TYR* 3.7 32.3 - - + +
328B VAL* 3.8 34.5 - - + -
339B LEU* 4.8 8.3 - - + +
340B TYR* 3.5 15.5 - - + +
382B PRO* 3.9 22.9 - - + -
402B PRO* 5.6 1.1 - - + -
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Residues in contact with GLY 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B GLU* 4.5 2.5 - - - -
291B PHE* 2.9 12.4 + - - +
292B ALA 4.6 0.2 - - - -
293B SER 3.5 1.6 - - - +
294B VAL* 1.3 79.8 - - - +
296B THR* 1.3 65.4 + - - -
298B GLY* 2.9 21.7 + - - -
299B GLN 4.0 0.5 + - - -
300B ARG* 3.4 28.1 + - - +
303B THR* 4.4 1.9 + - - +
339B LEU 5.2 4.5 - - - -
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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
------------------------------------------------------------
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