Contacts of the helix formed by residues 362 - 372 (chain A) in PDB entry 4BEJ
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 GLY 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347A THR* 3.1 10.3 - - - -
348A ILE* 3.2 9.6 - - - +
361A CYS* 1.3 63.9 + - - -
363A GLY* 1.3 63.7 + - - -
364A ALA 3.4 0.7 - - - -
365A ARG* 3.2 5.4 - - - +
366A ILE* 3.2 23.4 - - - +
438A GLU* 2.8 22.5 + - - -
442A ILE* 3.6 22.7 - - - -
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Residues in contact with GLY 363 (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 THR 2.6 17.0 + - - -
348A ILE 3.2 11.9 - - - +
349A GLU* 4.3 2.2 - - - -
350A GLY* 3.7 15.7 - - - -
361A CYS* 2.9 15.9 - - - +
362A GLY* 1.3 72.9 - - - +
364A ALA* 1.3 58.9 + - - +
366A ILE* 4.5 1.6 - - - +
367A CYS* 3.8 18.4 + - - -
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Residues in contact with ALA 364 (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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361A CYS* 3.9 7.9 - - + +
363A GLY* 1.3 73.7 - - - +
365A ARG* 1.3 56.2 + - - +
366A ILE 2.9 2.5 - - - -
367A CYS* 3.5 10.5 - - + +
368A TYR* 2.4 38.4 + - - +
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Residues in contact with ARG 365 (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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361A CYS* 3.4 9.4 - - - +
362A GLY 3.2 11.7 - - - +
363A GLY 3.8 0.2 - - - -
364A ALA* 1.3 76.1 - - - +
366A ILE* 1.3 56.9 + - - +
368A TYR* 3.3 40.6 - - - +
369A ILE* 2.9 47.1 + - + +
373A THR* 5.7 0.6 + - - -
438A GLU* 3.2 42.3 + - + +
441A ARG* 5.4 1.8 - - - +
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Residues in contact with ILE 366 (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* 4.3 15.3 - - + +
362A GLY 3.2 20.8 + - - +
363A GLY 4.5 3.6 - - - +
364A ALA 2.9 0.4 - - - -
365A ARG* 1.3 76.8 - - - +
367A CYS* 1.3 69.4 + - - +
369A ILE* 2.9 10.7 + - - +
370A PHE* 2.8 30.1 + - + +
435A VAL* 4.5 11.2 - - + +
438A GLU* 4.0 20.0 - - + -
439A MET* 4.3 22.4 - - + -
442A ILE* 5.0 2.2 - - + -
645A MET* 3.5 27.4 - - + -
649A VAL* 4.4 19.5 - - + -
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Residues in contact with CYS 367 (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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363A GLY 3.8 16.4 - - - -
364A ALA* 3.0 11.9 + - + +
366A ILE* 1.3 82.1 - - - +
368A TYR* 1.3 54.9 + - - +
370A PHE* 2.7 9.5 + - - +
371A HIS* 2.5 41.1 + - + +
493B TYR* 3.6 28.5 - - - +
497B LYS* 6.6 0.2 - - - -
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Residues in contact with TYR 368 (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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364A ALA 2.4 31.6 + - - +
365A ARG* 3.3 47.1 - - - +
367A CYS* 1.3 66.2 - - - +
369A ILE* 1.3 59.2 + - + +
372A GLU* 2.5 68.2 + - + +
373A THR* 3.3 17.8 + - - -
376A ARG* 4.2 20.1 + - - -
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Residues in contact with ILE 369 (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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365A ARG* 2.9 37.0 + - - +
366A ILE* 2.9 10.7 + - - +
368A TYR* 1.3 79.9 - - + +
370A PHE* 1.3 64.2 + - + +
373A THR* 4.3 11.0 - - - +
374A PHE* 3.0 29.2 + - - +
431A CYS* 4.7 6.7 - - - +
434A LEU* 3.6 63.9 - - + +
435A VAL* 4.8 4.5 - - + +
437A GLU* 5.4 2.2 - - - +
438A GLU* 4.2 15.3 - - + -
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Residues in contact with PHE 370 (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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366A ILE* 2.8 13.5 + - + +
367A CYS* 2.7 17.6 + - - +
369A ILE* 1.3 77.6 - - - +
371A HIS* 1.3 71.4 + - + +
374A PHE* 3.7 19.2 - - - +
375A GLY* 3.9 4.9 + - - -
431A CYS* 3.4 26.2 - - - -
435A VAL* 3.3 28.7 - - + -
637A GLN 5.1 1.6 - - - +
641A PRO* 3.4 40.6 - - + +
644A VAL* 3.5 29.2 - - + -
645A MET* 3.2 31.6 - - + -
493B TYR* 4.5 11.9 - + - +
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Residues in contact with HIS 371 (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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367A CYS* 2.5 20.2 + - + +
368A TYR* 5.7 0.2 - - - -
370A PHE* 1.3 80.8 + - + +
372A GLU* 1.3 75.1 + - + +
375A GLY* 4.8 8.5 - - - +
376A ARG 5.5 0.2 + - - -
637A GLN* 5.0 19.5 + - - -
638A ASP* 5.9 0.9 - - + -
641A PRO* 5.9 3.6 - - + +
493B TYR* 4.1 18.4 - + - -
495B ASN* 3.6 31.1 + - + +
497B LYS* 3.3 50.5 + - + +
498B HIS* 5.1 0.7 - - - -
499B PRO* 6.1 0.7 - - + -
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Residues in contact with GLU 372 (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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368A TYR* 2.5 64.4 + - + +
371A HIS* 1.3 88.9 - - + +
373A THR* 1.3 60.0 + - - +
375A GLY 4.3 2.0 - - - -
376A ARG* 3.2 58.5 + - - +
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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
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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