Contacts of the helix formed by residues 343 - 356 (chain A) in PDB entry 4JVS
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 343 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341A GLU 3.8 4.5 - - - +
342A GLN* 1.3 99.7 - - + +
344A PHE* 1.3 66.5 + - - +
345A PRO* 3.7 13.2 - - + -
346A GLU* 3.3 15.8 + - + +
347A LEU* 3.1 18.7 + - - +
376A CYS* 4.0 2.7 - - - +
380A TYR* 6.0 1.6 - - + -
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Residues in contact with PHE 344 (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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343A PRO* 1.3 71.1 - - - +
345A PRO* 1.3 71.2 - - + +
347A LEU* 3.2 4.5 + - + +
348A ILE* 2.9 52.6 + - + +
373A LEU* 3.4 31.9 - - + -
376A CYS* 3.5 29.3 + - - +
377A PHE* 3.6 39.0 - + + -
380A TYR* 4.0 8.6 - + + +
477A GLY* 3.9 19.5 - - - -
480A ILE* 4.1 10.1 - - + -
481A ILE* 4.6 2.7 - - + -
512A PHE* 3.5 37.9 - + - -
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Residues in contact with PRO 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A PRO* 3.4 13.7 - - + -
344A PHE* 1.3 95.3 - - + +
346A GLU* 1.3 61.8 + - + +
348A ILE* 3.4 2.3 + - + +
349A ARG* 3.0 27.2 + - - +
380A TYR* 3.6 39.9 - - + -
512A PHE* 4.2 14.8 - - + -
513A MET* 3.8 7.4 - - + +
516A LYS* 3.8 24.5 - - + +
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Residues in contact with GLU 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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339A GLU* 4.1 10.1 - - - +
342A GLN* 4.5 8.3 - - + +
343A PRO* 3.3 26.2 + - + +
345A PRO* 1.3 82.2 - - + +
347A LEU* 1.3 66.2 + - - +
349A ARG* 1.9 52.7 + - - +
350A THR* 3.0 27.5 + - - -
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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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337A GLN 3.5 6.5 - - - +
338A MET* 4.1 17.9 - - + -
339A GLU* 3.4 35.1 + - + +
342A GLN 5.0 1.3 - - - +
343A PRO 3.1 11.5 + - - +
344A PHE* 3.3 11.2 - - + +
346A GLU* 1.3 77.2 - - - +
348A ILE* 1.3 65.1 + - + +
350A THR* 3.3 2.9 + - - -
351A TRP* 3.0 73.1 + - + +
373A LEU* 4.2 10.1 - - + -
376A CYS* 4.0 24.9 - - - -
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Residues in contact with ILE 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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344A PHE* 2.9 48.7 + - + +
345A PRO 3.7 3.8 - - - +
347A LEU* 1.3 77.2 - - + +
349A ARG* 1.3 66.1 + - - +
351A TRP* 3.1 17.1 + - + +
352A ALA* 2.8 23.6 + - - +
480A ILE* 3.8 29.8 - - + -
509A LEU* 3.7 30.5 - - + +
512A PHE* 4.2 3.8 - - + -
513A MET* 3.8 24.0 - - + -
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Residues in contact with ARG 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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345A PRO 3.0 18.1 + - - +
346A GLU* 1.9 58.7 + - - +
348A ILE* 1.3 74.3 - - - +
350A THR* 1.3 82.7 + - - +
352A ALA* 3.9 3.5 - - - +
353A GLY* 3.1 19.9 + - - -
513A MET* 4.2 19.2 - - + +
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Residues in contact with THR 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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339A GLU* 3.6 24.9 + - - +
346A GLU 3.0 15.0 + - - -
347A LEU 3.3 9.2 - - - -
349A ARG* 1.3 96.3 + - - +
351A TRP* 1.3 72.7 + - + +
353A GLY* 3.2 3.8 + - - -
354A LEU* 3.1 31.7 + - + +
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Residues in contact with TRP 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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336A LEU* 3.6 35.2 - - + -
337A GLN 3.0 42.3 + - - +
338A MET* 3.9 16.4 - - + -
347A LEU* 3.0 45.7 + - + +
348A ILE* 3.9 23.6 - - + +
350A THR* 1.3 86.0 - - + +
352A ALA* 1.3 67.4 + - - +
354A LEU* 3.1 10.2 + - + +
355A LEU* 2.9 28.2 + - - +
368A VAL* 4.5 7.9 - - + -
373A LEU* 4.2 15.0 - - + -
480A ILE* 5.1 0.4 - - + -
484A LEU* 3.5 31.9 - - + -
505A LEU* 6.5 0.2 - - + -
509A LEU* 4.1 16.2 - - + -
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Residues in contact with ALA 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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348A ILE* 2.8 21.5 + - + +
349A ARG* 3.9 5.8 - - - +
351A TRP* 1.3 71.8 - - - +
353A GLY* 1.3 57.7 + - - +
355A LEU* 3.5 3.0 + - - +
356A GLY* 3.1 24.6 + - - -
506A GLN 5.7 0.2 - - - +
509A LEU* 3.7 29.9 - - + +
510A ASP* 4.2 14.4 - - - +
513A MET* 5.2 4.9 - - - -
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Residues in contact with GLY 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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349A ARG 3.1 14.7 + - - -
350A THR 3.2 4.2 + - - -
351A TRP 3.1 0.2 - - - -
352A ALA* 1.3 75.2 - - - +
354A LEU* 1.3 62.8 + - - +
356A GLY* 3.3 10.4 + - - -
357A GLN* 3.5 16.0 + - - +
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Residues in contact with LEU 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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334A PRO* 3.7 30.7 - - + +
335A LEU 4.0 22.7 - - - +
336A LEU* 4.9 2.2 - - + -
337A GLN 5.6 0.2 - - - +
350A THR* 3.1 25.5 + - + +
351A TRP* 3.1 22.2 + - + +
353A GLY* 1.3 75.1 - - - +
355A LEU* 1.3 63.9 + - + +
357A GLN* 3.5 35.9 - - - +
360A VAL* 4.0 2.6 - - - +
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Residues in contact with LEU 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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334A PRO* 3.4 28.5 - - + -
336A LEU* 4.4 12.1 - - + -
351A TRP 2.9 18.9 + - - +
352A ALA* 3.8 4.9 - - - +
354A LEU* 1.3 73.4 - - - +
356A GLY* 1.3 57.1 + - - +
357A GLN 3.2 5.5 - - - +
360A VAL* 3.3 22.8 - - + +
362A SER 4.4 3.6 - - - +
363A VAL* 3.8 24.2 - - + -
502A LEU* 4.9 7.0 - - + -
505A LEU* 3.5 33.0 - - + -
506A GLN* 3.7 27.1 + - + +
509A LEU* 4.1 14.6 - - + -
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Residues in contact with GLY 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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352A ALA 3.1 16.0 + - - -
353A GLY 3.3 4.6 + - - -
355A LEU* 1.3 75.5 - - - +
357A GLN* 1.3 66.4 + - - +
358A ILE* 3.7 0.9 + - - -
506A GLN* 5.6 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