Contacts of the helix formed by residues 348 - 358 (chain A) in PDB entry 4J15
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 TYR 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347A GLU* 1.3 71.5 - - - +
349A CYS* 1.3 58.0 + - - +
351A ALA* 3.1 5.8 + - + +
352A LEU* 2.9 55.0 + - + +
362A MET* 3.6 7.0 - - + +
364A ASP 4.0 9.6 - - - -
366A ASP 2.5 27.9 + - - -
367A ASP* 3.5 2.3 - - - -
368A LEU* 3.3 23.9 + - + -
391A LEU* 3.8 24.0 - - + +
392A ASP 2.9 9.8 + - - +
393A LYS* 3.1 22.3 - - - +
394A TYR* 3.6 38.3 - + - -
395A PRO* 3.5 23.1 - - + -
412A GLN* 3.9 8.0 - - + +
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Residues in contact with CYS 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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347A GLU* 3.2 27.2 - - - -
348A TYR* 1.3 77.9 - - - +
350A GLU* 1.3 71.1 - - - +
352A LEU* 3.4 15.0 + - + +
353A ALA* 3.0 27.4 + - - +
412A GLN* 4.5 10.4 - - - +
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Residues in contact with GLU 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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345A ARG 4.3 1.7 - - - +
346A LEU* 3.2 25.2 - - + +
347A GLU* 2.6 40.2 + - + +
349A CYS* 1.3 87.1 - - - +
351A ALA* 1.3 58.8 + - - +
353A ALA* 3.4 7.9 + - - +
354A MET* 3.0 36.8 + - + +
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Residues in contact with ALA 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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346A LEU* 5.2 3.3 - - + +
347A GLU 3.2 4.0 + - - -
348A TYR* 3.1 11.5 + - + +
350A GLU* 1.3 73.8 - - - +
352A LEU* 1.3 60.4 + - + +
354A MET* 3.2 5.4 + - - +
355A LEU* 2.9 38.0 + - + +
368A LEU* 5.7 1.8 - - + -
376A LEU* 3.6 36.3 - - + +
391A LEU* 3.8 22.9 - - + -
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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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348A TYR* 2.9 34.1 + - + +
349A CYS* 3.6 14.8 - - + +
351A ALA* 1.3 76.2 - - + +
353A ALA* 1.3 61.7 + - - +
355A LEU* 3.5 7.6 + - + +
356A ARG* 3.0 51.9 + - - +
362A MET* 3.7 29.1 - - + +
363A GLY 3.6 21.5 - - - +
364A ASP* 3.8 34.3 - - + +
368A LEU* 6.2 0.2 - - + -
412A GLN* 6.3 0.2 - - - +
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Residues in contact with ALA 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 CYS 3.0 14.1 + - - +
350A GLU* 3.6 11.4 - - - +
351A ALA 3.2 0.2 - - - -
352A LEU* 1.3 74.5 - - - +
354A MET* 1.3 62.3 + - + +
356A ARG* 3.1 11.4 + - - +
357A GLU* 3.0 31.1 + - + +
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Residues in contact with MET 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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346A LEU* 4.1 20.0 - - - -
350A GLU* 3.0 23.4 + - + +
351A ALA 3.6 5.2 - - - +
353A ALA* 1.3 74.9 - - + +
355A LEU* 1.3 63.3 + - - +
357A GLU* 3.4 17.7 + - - +
358A ALA 3.3 15.4 + - - -
376A LEU* 4.1 18.8 - - + -
379A LEU* 3.8 53.0 - - + +
380A VAL* 4.3 9.4 - - + +
383A LYS* 4.6 22.2 - - + +
384A TYR* 4.8 5.4 - - + -
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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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351A ALA* 2.9 27.3 + - + +
352A LEU* 4.0 4.7 - - + +
354A MET* 1.3 72.6 - - - +
356A ARG* 1.3 59.2 + - + +
358A ALA* 3.0 19.9 + - - +
360A VAL* 3.1 30.4 + - + +
362A MET* 4.0 18.6 - - + -
368A LEU* 3.7 30.3 - - + -
372A ASN* 3.7 28.3 - - + +
375A LEU* 3.6 30.1 - - + -
376A LEU* 4.1 15.7 - - + -
379A LEU* 4.7 2.2 - - + -
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Residues in contact with ARG 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 LEU* 3.0 42.5 + - - +
353A ALA* 3.1 8.8 + - - +
355A LEU* 1.3 74.8 - - + +
357A GLU* 1.3 58.2 + - - +
359A GLY* 2.8 24.8 + - - -
360A VAL 3.4 19.7 - - - +
361A GLU* 5.3 0.2 - - - -
362A MET* 2.5 38.7 + - + +
363A GLY 3.8 1.2 - - - -
364A ASP* 2.6 35.5 + - - +
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Residues in contact with GLU 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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353A ALA* 3.0 17.2 + - + +
354A MET* 3.5 20.8 - - - +
356A ARG* 1.3 75.9 - - - +
358A ALA* 1.3 57.0 + - - +
359A GLY 3.1 3.2 + - - -
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Residues in contact with ALA 358 (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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354A MET 3.3 8.2 + - - +
355A LEU 3.0 12.9 + - - +
357A GLU* 1.3 76.9 - - - +
359A GLY* 1.3 61.0 + - - +
360A VAL* 3.3 3.8 + - - +
375A LEU* 4.2 25.2 - - + +
379A LEU* 4.6 11.2 - - + -
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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