Contacts of the helix formed by residues 345 - 357 (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 PRO 345 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335A ASP* 3.4 11.9 - - - +
343A LYS 3.6 9.6 - - - +
344A ILE* 1.3 84.1 - - - +
346A ALA* 1.3 67.8 + - - +
347A LEU* 3.9 11.2 - - + +
348A GLU* 3.1 38.4 + - + +
349A VAL* 2.9 25.1 + - - +
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Residues in contact with ALA 346 (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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333A ILE* 4.6 1.6 - - - +
334A LYS* 3.6 26.5 - - - +
335A ASP* 2.7 20.4 + - - +
345A PRO* 1.3 72.7 - - - +
347A LEU* 1.3 53.6 + - - +
349A VAL* 3.2 2.8 + - - +
350A ALA* 2.8 36.7 + - - +
386A PRO* 3.6 35.2 - - + -
389A THR* 4.8 1.3 - - - +
390A ILE* 4.0 6.7 - - + +
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Residues in contact with LEU 347 (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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345A PRO* 3.1 8.6 - - + +
346A ALA* 1.3 79.6 - - - +
348A GLU* 1.3 61.3 + - + +
350A ALA* 3.4 2.9 + - - +
351A SER* 2.9 35.3 + - - +
389A THR* 3.5 46.3 + - + +
390A ILE* 4.0 13.7 - - + -
393A ALA* 3.9 20.0 - - + -
394A TYR* 4.1 11.2 - - + -
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Residues in contact with GLU 348 (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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307A LEU* 5.3 1.0 - - - +
343A LYS 5.1 1.3 - - - +
344A ILE* 3.8 17.5 - - + +
345A PRO* 3.1 35.3 + - + +
347A LEU* 1.3 81.2 - - + +
349A VAL* 1.3 65.5 + - - +
351A SER* 3.5 8.7 + - - -
352A LEU* 3.1 23.2 + - - +
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Residues in contact with VAL 349 (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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307A LEU* 4.3 14.6 - - + -
332A GLY 3.7 22.7 - - - +
333A ILE* 4.3 5.2 - - + -
334A LYS 3.4 18.8 - - - +
336A ILE* 3.6 15.7 - - + -
344A ILE* 3.5 19.1 - - + +
345A PRO 2.9 19.7 + - - +
346A ALA* 3.6 6.7 - - - +
348A GLU* 1.3 76.0 - - - +
350A ALA* 1.3 62.5 + - - +
352A LEU* 3.3 7.2 + - + +
353A TYR* 3.1 46.0 + - + -
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Residues in contact with ALA 350 (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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333A ILE* 4.2 8.7 - - + +
346A ALA 2.8 17.7 + - - +
347A LEU 3.5 4.7 - - - +
349A VAL* 1.3 74.4 - - - +
351A SER* 1.3 54.2 + - - +
353A TYR* 3.1 5.5 + - - +
354A PHE* 2.8 54.9 + - + -
361A VAL* 4.3 10.8 - - + -
390A ILE* 3.6 27.8 - - + -
394A TYR* 5.5 0.4 - - + -
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Residues in contact with SER 351 (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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347A LEU* 2.9 27.6 + - - +
348A GLU* 3.6 10.4 - - - -
349A VAL 3.4 0.2 - - - -
350A ALA* 1.3 75.2 - - - +
352A LEU* 1.3 56.9 + - - +
354A PHE* 3.4 6.2 + - - +
355A ARG* 2.9 41.4 + - - +
394A TYR* 2.7 33.1 + - - -
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Residues in contact with LEU 352 (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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307A LEU* 3.6 37.9 - - + -
308A LYS* 4.4 12.1 - - + +
313A LEU* 3.7 26.0 - - + -
348A GLU 3.1 12.8 + - - +
349A VAL* 3.4 9.4 - - - +
350A ALA 3.2 0.2 - - - -
351A SER* 1.3 75.6 - - - +
353A TYR* 1.3 55.4 - - + +
355A ARG* 3.5 10.5 + - + +
356A SER* 2.6 43.1 + - - +
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Residues in contact with TYR 353 (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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298A ASN* 3.3 19.2 + - - -
307A LEU* 5.5 6.1 - - + +
310A THR* 3.6 17.0 - - + +
312A MET* 3.9 22.4 - - + +
313A LEU* 3.5 30.5 - - + -
316A LEU* 3.5 17.2 - - + +
329A VAL* 3.9 19.7 - - + -
331A GLY 4.4 2.9 + - - -
332A GLY* 4.7 5.1 + - - -
333A ILE* 3.3 26.7 - - + -
349A VAL* 3.1 39.1 + - + -
350A ALA* 3.1 7.9 + - - +
352A LEU* 1.3 74.1 - - + +
354A PHE* 1.3 64.6 + - - +
356A SER* 3.2 4.2 + - - -
357A GLY 3.1 6.9 + - - -
358A ALA* 3.0 30.8 + - + +
361A VAL* 4.6 2.2 - - + -
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Residues in contact with PHE 354 (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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12A GLY* 4.1 15.3 - - - -
13A ASN* 3.2 23.4 - - - +
350A ALA* 2.8 23.5 + - + +
351A SER* 3.5 5.4 - - - +
353A TYR* 1.3 76.1 - - - +
355A ARG* 1.3 58.1 + - - +
357A GLY 3.0 15.9 + - - -
358A ALA* 3.4 21.4 - - + +
359A ASP* 3.8 5.8 - - - -
360A LYS* 3.8 19.5 - - - -
361A VAL* 3.6 29.8 - - + -
390A ILE* 4.1 8.7 - - + -
394A TYR* 3.6 48.5 - + + -
398A ALA* 3.8 23.6 - - + -
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Residues in contact with ARG 355 (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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8A ASP* 4.7 3.2 + - - -
10A GLU* 3.0 61.4 + - - +
11A SER* 3.6 1.0 - - - +
12A GLY 3.5 26.0 + - - +
13A ASN* 5.1 0.2 - - - -
14A LEU 5.1 1.6 + - - -
15A GLN* 3.1 28.2 + - - +
32A LYS* 4.9 6.1 - - - +
351A SER* 2.9 28.0 + - - +
352A LEU* 3.5 11.1 + - + +
354A PHE* 1.3 76.3 - - - +
356A SER* 1.3 56.7 + - - +
394A TYR* 5.9 0.4 - - - -
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Residues in contact with SER 356 (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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15A GLN* 3.8 7.0 - - - +
313A LEU* 3.4 40.2 - - - +
316A LEU* 3.4 3.8 - - - -
317A LYS* 3.1 35.8 + - - +
352A LEU* 2.6 27.3 + - - +
353A TYR 3.4 6.7 - - - -
354A PHE 3.1 0.4 - - - -
355A ARG* 1.3 79.4 - - - +
357A GLY* 1.3 55.0 + - - +
358A ALA 3.9 0.4 - - - -
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Residues in contact with GLY 357 (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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13A ASN* 3.4 29.7 + - - -
15A GLN* 3.9 6.3 - - - +
196A LYS* 4.5 0.2 + - - -
316A LEU* 4.4 4.5 - - - -
320A ALA* 4.4 7.9 - - - +
327A LEU* 3.4 26.4 - - - +
354A PHE 3.0 4.4 + - - -
355A ARG 3.3 1.0 - - - -
356A SER* 1.3 81.1 - - - +
358A ALA* 1.3 65.0 + - - +
359A ASP* 3.9 0.7 + - - +
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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