Contacts of the helix formed by residues 354 - 369 (chain A) in PDB entry 3JRQ
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 THR 354 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A ARG* 5.3 2.0 - - - +
350A TRP* 3.9 3.3 - - - -
353A MET* 1.3 81.5 - - - +
355A ASP* 1.3 64.7 + - - +
356A GLU* 3.8 13.5 + - - +
357A GLU* 3.3 31.6 + - - +
358A ALA* 3.3 19.2 + - - +
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Residues in contact with ASP 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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263A ARG* 3.1 30.0 + - - +
265A VAL* 3.3 26.5 - - + +
272A ALA* 3.6 17.7 - - + -
274A PRO* 4.0 19.8 - - + +
350A TRP* 4.2 7.5 - - - -
354A THR* 1.3 75.7 - - - +
356A GLU* 1.3 72.9 + - - +
357A GLU 3.2 0.2 + - - -
358A ALA* 3.3 2.1 + - - +
359A CYS* 3.0 29.3 + - - -
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Residues in contact with GLU 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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270A LYS 6.0 1.6 - - - +
271A THR* 4.9 5.1 + - - +
272A ALA* 3.8 34.0 + - + +
354A THR* 3.4 11.2 - - - +
355A ASP* 1.3 88.5 + - - +
357A GLU* 1.3 54.5 + - + +
359A CYS* 3.6 2.1 - - - +
360A GLU* 2.7 37.9 + - - +
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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 MET* 3.8 8.1 - - + +
354A THR* 3.3 33.8 + - - +
355A ASP 3.1 0.2 - - - -
356A GLU* 1.3 77.8 - - + +
358A ALA* 1.3 64.6 + - - +
360A GLU* 4.4 5.1 - - - +
361A MET* 3.0 27.4 + - - +
405A LEU* 5.4 3.4 - - + +
409A ARG* 3.3 36.6 + - - -
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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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343A ILE* 3.8 13.0 - - + -
349A VAL* 5.0 0.7 - - + -
350A TRP* 3.6 37.2 - - + -
353A MET* 4.1 11.3 - - - -
354A THR 3.3 5.1 + - - +
355A ASP 3.7 3.8 - - - +
357A GLU* 1.3 78.2 - - - +
359A CYS* 1.3 53.5 + - - +
361A MET* 3.4 1.6 - - - +
362A ALA* 2.7 37.6 + - - +
402A LEU* 3.8 17.7 - - + +
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Residues in contact with CYS 359 (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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265A VAL* 3.6 23.8 - - - -
266A LEU 4.3 0.2 - - - -
267A CYS* 3.8 35.5 - - + -
270A LYS 5.6 0.7 - - - +
271A THR 5.2 0.4 - - - -
272A ALA* 3.6 24.9 - - + +
341A CYS* 4.8 0.7 - - - -
343A ILE* 3.7 8.0 - - - +
355A ASP 3.0 17.7 + - - +
356A GLU 3.6 4.5 - - - +
358A ALA* 1.3 78.3 - - - +
360A GLU* 1.3 55.3 + - - +
362A ALA* 4.6 0.2 - - - -
363A ARG* 2.8 39.7 + - - +
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Residues in contact with GLU 360 (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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356A GLU 2.7 23.4 + - - +
357A GLU* 4.4 4.4 - - - +
359A CYS* 1.3 71.3 - - - +
361A MET* 1.3 53.7 + - - +
363A ARG* 4.1 20.7 - - - +
364A LYS* 2.8 67.4 + - + +
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Residues in contact with MET 361 (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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357A GLU 3.0 21.1 + - - +
358A ALA 3.4 3.1 - - - +
360A GLU* 1.3 75.5 - - - +
362A ALA* 1.3 52.1 + - - +
364A LYS* 3.0 10.2 + - + +
365A ARG* 2.7 76.1 + - + +
398A ALA 5.4 0.2 - - - +
401A TYR* 4.3 28.9 - - + +
402A LEU* 3.7 21.1 - - + -
405A LEU* 4.2 23.3 - - + -
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Residues in contact with ALA 362 (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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341A CYS* 4.4 8.5 - - - -
343A ILE* 4.1 19.5 - - + -
358A ALA 2.7 20.5 + - - +
359A CYS 3.9 2.0 - - - +
361A MET* 1.3 71.0 - - - +
363A ARG* 1.3 65.4 + - - +
365A ARG 3.5 0.2 + - - -
366A ILE* 3.1 31.5 + - - +
398A ALA* 3.6 22.8 - - + +
402A LEU* 4.2 11.0 - - + -
419A VAL* 4.7 4.0 - - + -
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Residues in contact with ARG 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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267A CYS* 3.3 24.8 - - - -
269A GLY* 4.4 4.8 - - - -
270A LYS* 2.8 40.4 + - - +
340A ASP* 3.4 31.6 - - + +
341A CYS* 4.2 8.1 - - - -
359A CYS* 2.8 18.0 + - - +
360A GLU* 4.1 27.0 - - - +
362A ALA* 1.3 71.1 - - - +
364A LYS* 1.3 82.7 + - - +
365A ARG 3.3 0.2 + - - -
366A ILE* 4.0 4.7 - - + +
367A LEU* 3.2 41.0 + - + +
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Residues in contact with LYS 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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360A GLU* 2.8 60.5 + - + +
361A MET* 3.0 9.6 + - + +
363A ARG* 1.3 89.5 - - + +
365A ARG* 1.3 70.4 + - - +
367A LEU* 3.3 5.7 + - - +
368A LEU* 2.9 37.8 + - + +
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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 MET* 2.7 49.8 + - + +
362A ALA 4.2 0.7 - - - +
363A ARG 3.3 0.2 - - - -
364A LYS* 1.3 78.6 - - - +
366A ILE* 1.3 52.4 + - - +
368A LEU* 3.2 32.4 + - - +
369A TRP* 2.7 36.7 + - - +
394A ALA 4.7 2.5 - - - -
397A SER* 4.6 2.5 + - - +
398A ALA* 4.2 16.2 - - - +
401A TYR* 3.3 62.3 + - + -
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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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341A CYS* 4.1 17.9 - - + -
362A ALA 3.1 19.5 + - - +
363A ARG* 4.0 4.7 - - + +
365A ARG* 1.3 75.3 - - - +
367A LEU* 1.3 70.4 + - + +
368A LEU 3.0 1.4 + - - -
369A TRP* 3.2 18.5 + - - +
394A ALA* 3.6 39.2 - - + +
395A ALA* 4.2 2.2 - - - +
398A ALA* 4.0 2.5 - - + -
419A VAL* 4.0 25.4 - - + -
421A ASP* 4.2 33.9 - - + +
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Residues in contact with LEU 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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340A ASP* 5.8 2.2 - - - +
363A ARG* 3.2 38.5 + - + +
364A LYS* 3.8 4.7 - - - +
366A ILE* 1.3 84.4 - - + +
368A LEU* 1.3 63.7 + - + +
369A TRP 4.4 2.9 - - - +
423A LYS* 6.1 8.5 - - + -
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Residues in contact with LEU 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 LYS* 2.9 25.3 + - + +
365A ARG* 3.2 39.5 - - - +
366A ILE 3.0 0.4 - - - -
367A LEU* 1.3 81.6 - - + +
369A TRP* 1.3 64.5 + - - +
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Residues in contact with TRP 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 2.7 19.2 + - - +
366A ILE 3.2 7.6 + - - +
367A LEU 4.4 2.8 - - - +
368A LEU* 1.3 79.6 - - - +
392A ASP* 6.2 0.2 - - - -
393A PRO* 3.6 35.3 - - + +
394A ALA* 3.9 34.1 - - + -
397A SER* 4.4 22.0 - - - +
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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