Contacts of the helix formed by residues 276 - 289 (chain A) in PDB entry 1JVN
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 LEU 276 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A ASP* 5.5 4.4 - - - +
254A LEU* 3.9 46.9 + - + +
277A GLY* 1.3 70.9 + - - +
278A LYS 3.4 3.1 - - - -
279A PRO* 3.1 17.7 - - - +
280A VAL* 3.3 22.4 - - + +
311A PRO* 4.5 10.1 - - + +
314A GLU* 3.3 37.2 - - + +
315A VAL* 4.3 2.2 - - + +
318A GLN* 4.3 15.3 - - + -
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Residues in contact with GLY 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A LEU 5.0 0.2 + - - -
276A LEU* 1.3 84.0 - - - +
278A LYS* 1.3 52.9 + - - +
280A VAL* 3.1 6.3 + - - +
281A GLN* 2.7 51.8 + - - +
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Residues in contact with LYS 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A LEU 4.0 6.0 + - - +
255A VAL* 4.4 13.7 - - + -
256A VAL* 4.1 12.0 - - + +
261A ASP* 3.6 45.6 + - - +
276A LEU 3.4 0.2 - - - -
277A GLY* 1.3 73.1 - - - +
279A PRO* 1.3 69.2 - - + +
281A GLN* 3.9 8.4 + - - +
282A LEU* 3.1 25.5 + - - +
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Residues in contact with PRO 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LEU* 3.4 21.3 - - + +
246A VAL* 4.0 15.7 - - + -
254A LEU* 3.5 24.7 - - + +
255A VAL* 4.7 0.4 - - - +
256A VAL* 3.7 17.5 - - + -
276A LEU 3.1 25.4 - - - +
278A LYS* 1.3 91.1 - - + +
280A VAL* 1.3 59.2 + - - +
283A ALA* 3.2 21.7 + - - +
296A PHE* 4.0 1.0 - - - -
315A VAL* 3.9 28.0 - - + -
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Residues in contact with VAL 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A LEU* 3.3 33.2 - - + +
277A GLY* 3.1 9.8 + - - +
279A PRO* 1.3 77.8 - - - +
281A GLN* 1.3 58.4 + - + +
283A ALA* 3.3 7.9 + - - +
284A GLN* 3.1 43.9 + - - +
315A VAL* 3.8 30.1 - - + +
318A GLN* 3.9 22.4 - - + +
319A ALA* 4.0 12.3 - - - +
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Residues in contact with GLN 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A GLY* 2.7 33.0 + - - +
278A LYS* 4.1 6.6 + - - +
280A VAL* 1.3 71.6 - - + +
282A LEU* 1.3 60.6 + - - +
284A GLN* 3.6 18.5 + - - +
285A LYS* 3.1 26.0 + - - +
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Residues in contact with LEU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LEU* 3.8 12.3 - - + -
256A VAL* 3.6 27.1 - - + -
278A LYS 3.1 17.6 + - - +
279A PRO 4.0 3.8 - - - +
281A GLN* 1.3 75.1 - - - +
283A ALA* 1.3 60.3 + - - +
285A LYS* 3.3 21.1 + - + +
286A TYR* 2.9 66.1 + - + +
526A PHE 5.2 0.7 - - - +
527A HIS* 3.5 34.5 - - + +
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Residues in contact with ALA 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LEU* 4.5 2.6 - - + +
279A PRO 3.2 15.1 + - - +
280A VAL 3.3 10.1 + - - +
282A LEU* 1.3 78.0 - - - +
284A GLN* 1.3 58.1 + - - +
286A TYR* 3.4 5.3 + - - +
287A TYR* 3.0 27.7 + - - +
294A VAL* 4.0 18.7 - - + +
296A PHE* 3.6 28.5 - - + -
319A ALA* 4.4 9.0 - - + -
323A VAL* 3.9 7.1 - - + +
327A LEU* 5.7 0.2 - - + -
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Residues in contact with GLN 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A VAL* 3.1 29.4 + - + +
281A GLN* 3.6 26.7 + - - +
282A LEU 3.3 0.2 - - - -
283A ALA* 1.3 73.8 - - - +
285A LYS* 1.3 59.9 + - - +
287A TYR* 3.4 2.6 + - - +
288A GLN* 2.8 53.6 + - - +
318A GLN 4.8 5.7 + - - -
319A ALA* 4.9 2.0 - - - +
322A THR* 2.7 38.2 + - - +
323A VAL* 3.8 14.4 - - + -
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Residues in contact with LYS 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A GLN 3.1 19.7 + - - +
282A LEU* 3.5 23.2 - - + +
284A GLN* 1.3 73.4 - - - +
286A TYR* 1.3 60.9 + - + +
288A GLN* 3.2 11.1 + - - -
289A GLN* 2.9 69.9 + - + +
526A PHE 5.2 5.9 + - - -
527A HIS 5.5 3.4 + - - -
529A GLY* 5.2 12.3 - - - -
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Residues in contact with TYR 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A ALA* 3.3 31.9 - - + -
243A CYS 3.7 19.5 + - - -
244A LEU* 3.7 30.5 - - + +
282A LEU* 2.9 41.8 + - + +
283A ALA 3.4 8.5 - - - +
285A LYS* 1.3 79.2 - - + +
287A TYR* 1.3 60.3 + - - +
289A GLN* 3.1 20.0 + - - +
290A GLY 3.3 0.7 + - - -
291A ALA* 3.0 25.9 + - + +
294A VAL* 4.1 5.8 - - + -
523A ALA 3.8 0.7 + - - -
526A PHE* 3.7 29.1 - - + -
527A HIS* 3.3 31.2 + - - +
533A VAL* 4.5 4.8 - - + +
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Residues in contact with TYR 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A GLY* 3.7 17.0 - - - -
199A LYS 4.0 0.9 + - - -
283A ALA 3.0 14.0 + - - +
284A GLN* 3.6 7.0 - - - +
285A LYS 3.3 0.2 - - - -
286A TYR* 1.3 74.2 - - - +
288A GLN* 1.3 78.2 + - + +
290A GLY* 3.0 15.2 + - - -
291A ALA* 4.0 11.1 + - - +
294A VAL* 4.6 0.6 - - + +
322A THR* 3.3 25.4 - - - -
323A VAL* 3.8 19.7 - - + -
324A PHE* 3.7 17.3 - - - +
325A VAL* 3.5 37.9 - - + -
548A ARG* 4.2 13.6 + - - -
550A ASP 5.7 0.7 - - - +
552A GLU* 2.6 35.0 + - + +
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Residues in contact with GLN 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLN* 2.8 47.3 + - - +
285A LYS* 3.6 8.0 - - - +
287A TYR* 1.3 89.1 - - + +
289A GLN* 1.4 61.1 + - + +
290A GLY 3.7 0.9 + - - -
322A THR* 5.3 3.6 + - - -
534A ASN* 4.5 4.9 + - - -
551A GLU* 4.9 13.7 - - - +
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Residues in contact with GLN 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LYS* 2.9 54.8 + - + +
286A TYR* 3.5 12.8 - - - +
287A TYR 3.0 1.0 - - - -
288A GLN* 1.4 81.0 - - + +
290A GLY* 1.3 55.2 + - - -
291A ALA 3.6 0.4 - - - -
526A PHE 5.3 3.6 - - - +
532A THR* 3.6 39.6 - - + +
533A VAL* 3.5 6.0 + - + +
534A ASN* 2.9 42.1 + - - +
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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