Contacts of the helix formed by residues 366 - 383 (chain A) in PDB entry 3RU0
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 HIS 366 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A PRO* 6.2 4.0 - - + -
213A SER* 5.9 0.7 - - - -
238A CYS* 5.8 3.2 - - + +
240A LEU 5.5 1.8 + - - -
242A MET* 3.3 34.4 - - + +
362A PHE* 3.6 34.0 + + + +
363A PRO* 4.6 4.9 - - + +
364A GLY 4.0 2.0 + - - -
365A SER* 1.3 74.9 - - - +
367A PRO* 1.4 79.3 - - + +
368A VAL* 3.1 47.6 + - + +
369A ARG* 3.1 5.1 + - + +
370A GLY 3.1 17.0 + - - -
399A ILE* 3.6 6.2 - - - +
403A THR* 3.6 3.5 - - - +
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Residues in contact with PRO 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A MET* 3.7 10.8 - - + -
213A SER* 3.3 28.5 - - - +
214A ILE 4.1 4.5 - - - +
215A VAL* 3.5 30.3 - - + -
366A HIS* 1.4 97.3 - - + +
368A VAL* 1.3 58.2 + - + +
370A GLY* 3.4 1.1 + - - +
371A VAL* 3.0 32.7 + - - +
403A THR* 3.5 22.2 - - + +
404A HIS* 3.5 8.3 - - + -
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Residues in contact with VAL 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A MET* 4.1 33.2 - - + -
358A TYR* 3.9 13.0 - - + +
362A PHE* 3.6 25.4 - - + -
366A HIS* 3.1 25.2 + - + +
367A PRO* 1.3 79.9 - - + +
369A ARG* 1.3 57.5 + - - +
371A VAL* 3.5 3.3 + - - +
372A GLN* 3.0 27.0 + - - +
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Residues in contact with ARG 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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355A MET 5.0 1.8 + - - -
358A TYR* 3.5 34.8 - - + +
359A ARG* 3.5 44.1 + - - +
362A PHE* 3.7 30.4 + - + +
364A GLY 4.5 10.0 + - - +
366A HIS* 3.1 11.4 + - + +
368A VAL* 1.3 77.6 - - - +
370A GLY* 1.3 65.0 + - - +
372A GLN* 3.1 1.4 + - - +
373A VAL* 2.9 36.8 + - + +
395A LEU* 3.9 27.7 - - - +
399A ILE* 3.7 25.7 - - + +
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Residues in contact with GLY 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A HIS 3.1 11.1 + - - -
367A PRO 3.4 3.1 + - - -
369A ARG* 1.3 75.3 - - - +
371A VAL* 1.3 62.7 + - - +
373A VAL* 3.5 1.1 + - - -
374A MET* 3.1 23.7 + - - +
396A ALA* 3.8 5.0 - - - +
399A ILE* 3.6 28.8 - - - +
400A MET* 3.5 20.5 - - - +
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Residues in contact with VAL 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ALA 3.7 25.8 - - - +
189A GLU* 4.2 8.1 - - - +
190A MET* 3.9 15.5 - - + -
367A PRO 3.0 20.9 + - - +
368A VAL 3.9 3.8 - - - +
370A GLY* 1.3 74.2 - - - +
372A GLN* 1.3 60.1 + - - +
374A MET* 3.4 8.9 + - + +
375A LYS* 2.9 54.1 + - + +
400A MET* 4.5 1.8 - - + -
404A HIS* 3.8 22.0 - - + +
410A LEU* 4.1 9.2 - - + -
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Residues in contact with GLN 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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332A ASP* 3.0 28.2 + - - +
335A MET* 3.4 24.8 - - - +
354A THR* 3.0 29.7 + - - +
355A MET* 3.4 19.7 - - + -
358A TYR* 3.5 28.3 + - + -
368A VAL* 3.0 18.8 + - - +
369A ARG 3.1 4.4 + - - +
371A VAL* 1.3 76.3 - - - +
373A VAL* 1.3 64.1 + - + +
375A LYS* 3.1 13.7 + - - +
376A VAL* 3.0 22.2 + - - +
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Residues in contact with VAL 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A MET* 3.9 24.0 - - + -
369A ARG* 2.9 42.0 + - + +
370A GLY* 4.0 3.6 - - - +
372A GLN* 1.3 73.1 - - - +
374A MET* 1.3 59.0 + - - +
376A VAL* 3.2 1.9 + - - +
377A GLY* 2.9 27.5 + - - -
392A ASN* 3.1 42.9 - - - +
395A LEU* 3.8 17.0 - - + -
396A ALA* 3.8 13.0 - - + +
399A ILE* 4.6 2.0 - - + -
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Residues in contact with MET 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A GLY 3.1 19.0 + - - +
371A VAL* 3.5 6.7 - - - +
373A VAL* 1.3 76.4 - - - +
375A LYS* 1.3 57.7 + - + +
377A GLY* 3.4 0.7 + - - -
378A LYS* 2.9 34.0 + - + +
393A LEU* 4.0 5.3 - - - +
396A ALA* 3.7 14.9 - - + +
400A MET* 4.0 26.0 - - - +
410A LEU* 3.6 29.8 - - + -
413A ASP* 4.3 4.7 - - + -
414A LEU* 4.0 33.4 - - + +
417A LEU* 3.9 24.2 - - + -
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Residues in contact with LYS 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A GLU* 2.9 45.2 + - + +
190A MET* 5.3 0.4 - - - +
335A MET* 4.0 17.2 - - + +
336A ASP* 2.8 34.1 + - - +
339A ILE* 3.9 22.7 - - + -
371A VAL* 2.9 30.5 + - + +
372A GLN* 3.1 14.6 + - - +
374A MET* 1.3 76.0 - - + +
376A VAL* 1.3 59.2 + - - +
378A LYS* 3.5 7.0 + - + +
379A LEU* 3.0 34.9 + - - +
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Residues in contact with VAL 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A MET* 4.7 6.3 - - - -
348A LEU* 3.9 11.4 - - + -
351A GLY* 3.7 27.6 - - - -
352A THR* 4.3 6.5 - - + +
355A MET* 3.6 37.2 - - + -
372A GLN 3.0 9.5 + - - +
373A VAL 3.2 5.6 + - - +
375A LYS* 1.3 75.5 - - - +
377A GLY* 1.3 57.7 + - - +
379A LEU* 3.3 9.0 + - + +
380A GLN* 2.8 48.7 + - - +
392A ASN* 3.9 10.8 - - - +
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Residues in contact with GLY 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A VAL 2.9 15.7 + - - -
374A MET 3.7 1.6 - - - -
376A VAL* 1.3 76.7 - - - +
378A LYS* 1.3 54.0 + - - +
380A GLN* 3.3 12.8 + - - -
381A LEU* 2.9 26.9 + - - +
389A ALA* 3.4 12.8 - - - +
392A ASN* 3.9 11.1 - - - +
393A LEU* 3.9 15.5 - - - -
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Residues in contact with LYS 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A MET* 2.9 25.3 + - + +
375A LYS* 3.7 7.6 - - + +
377A GLY* 1.3 68.7 - - - +
379A LEU* 1.3 62.3 + - + +
381A LEU* 3.4 8.4 + - + +
382A HIS* 2.9 28.0 + - + +
393A LEU* 3.9 4.5 - - - +
417A LEU* 4.0 37.0 - - + +
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Residues in contact with LEU 379 (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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335A MET* 4.8 4.5 - - + -
339A ILE* 4.5 17.5 - - + -
344A LEU* 3.7 45.3 - - + +
347A ALA* 3.7 15.5 - - + +
348A LEU* 3.6 38.8 - - + +
375A LYS 3.0 24.3 + - - +
376A VAL* 3.5 10.8 - - + +
378A LYS* 1.3 75.7 - - + +
380A GLN* 1.3 58.3 + - - +
382A HIS* 3.3 6.0 + - + +
383A GLN* 2.9 33.9 + - - +
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Residues in contact with GLN 380 (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 LEU* 3.7 20.1 - - + +
352A THR* 4.6 6.1 + - - +
376A VAL* 2.8 30.8 + - - +
377A GLY 3.5 3.1 - - - +
379A LEU* 1.3 69.6 - - - +
381A LEU* 1.3 63.3 + - - +
383A GLN* 3.0 3.3 + - - +
384A GLY 3.0 5.0 + - - -
385A MET* 2.8 46.7 + - + +
388A GLN* 3.2 31.0 + - - +
389A ALA* 3.5 16.0 - - + +
392A ASN* 2.9 34.2 + - - +
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Residues in contact with LEU 381 (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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377A GLY 2.9 15.9 + - - +
378A LYS* 3.7 5.8 - - + +
380A GLN* 1.3 75.1 - - - +
382A HIS* 1.3 63.4 + - - +
384A GLY* 3.1 13.6 + - - +
386A PHE* 3.8 16.9 - - + -
389A ALA* 3.4 12.0 - - + +
393A LEU* 4.6 3.1 - - + -
417A LEU* 3.8 39.0 - - + +
420A GLU* 4.0 24.7 - - + +
421A CYS* 3.7 19.5 - - + -
424A ASN* 3.7 26.7 - - - +
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Residues in contact with HIS 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU* 3.6 36.8 - - + +
378A LYS* 2.9 15.7 + - + +
379A LEU* 3.4 12.3 - - - +
381A LEU* 1.3 78.0 - - - +
383A GLN* 1.3 76.8 + - - +
384A GLY* 3.1 4.2 + - - -
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Residues in contact with GLN 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU* 4.4 3.2 - - + +
345A GLU* 3.7 48.0 + - - +
348A LEU* 3.7 16.8 - - + +
379A LEU 2.9 20.4 + - - +
380A GLN 3.0 4.7 + - - +
382A HIS* 1.3 97.4 + - - +
384A GLY* 1.3 61.0 + - - +
385A MET* 3.2 21.7 + - - +
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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
------------------------------------------------------------
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