Contacts of the helix formed by residues 368 - 384 (chain B) in PDB entry 6MZL
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 TRP 368 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B SER 5.1 1.1 - - - -
366B ASP 4.4 4.5 - - - -
367B GLU* 1.3 74.8 - - - +
369B VAL* 1.3 87.9 + - + +
370B LEU 3.2 0.4 - - - -
371B LYS* 3.6 1.5 + - - +
372B GLY* 2.9 26.9 + - - -
414B LEU* 3.6 46.8 + - + +
415B HIS 4.5 11.1 + - - -
416B PRO* 6.0 0.6 - - - +
449B PHE* 3.6 28.4 - + + -
453B ALA* 4.0 9.4 - - + +
456B VAL* 4.4 6.5 - - + -
457B MET* 3.6 28.7 - - + -
460B ILE* 5.5 4.3 - - + -
500B THR* 3.4 33.6 + - + +
503B PHE* 5.3 4.3 - + - -
519B ILE* 5.7 5.2 - - + -
523B VAL* 3.7 37.7 - - + +
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Residues in contact with VAL 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B ILE* 5.9 5.6 - - + -
366B ASP 4.8 1.8 - - - +
367B GLU 2.6 6.8 + - - +
368B TRP* 1.3 112.3 - - + +
370B LEU* 1.3 57.3 + - + +
372B GLY* 4.7 1.1 - - - -
373B ILE* 2.9 45.2 + - + +
457B MET* 5.0 2.0 - - + -
498B VAL 5.2 5.4 - - - +
499B SER* 5.7 0.9 - - - -
500B THR* 3.9 16.4 - - - +
503B PHE* 3.5 42.4 - - + -
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Residues in contact with LEU 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B TYR* 4.3 2.5 - - - +
352B GLN* 6.2 0.2 - - - -
355B PHE* 3.4 42.4 - - + +
359B ILE* 3.5 34.1 - - + +
360B SER* 4.0 3.8 - - - +
361B ARG* 3.5 38.6 - - + +
366B ASP 5.5 0.2 - - - +
367B GLU* 2.5 44.5 + - + +
369B VAL* 1.3 74.0 - - + +
371B LYS* 1.3 59.2 + - + +
373B ILE* 5.3 0.7 - - - -
374B SER* 3.0 30.7 + - - -
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Residues in contact with LYS 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B GLN* 3.4 10.3 - - - +
352B GLN* 3.4 28.3 - - + +
367B GLU* 3.2 28.8 + - - +
368B TRP 3.6 2.9 + - - +
369B VAL 3.5 0.2 - - - -
370B LEU* 1.3 77.0 - - + +
372B GLY* 1.3 64.4 + - - +
374B SER* 2.9 17.6 + - - +
375B GLY* 2.9 11.1 + - - -
446B TYR* 2.3 41.6 + - - -
449B PHE* 3.8 24.9 - - + -
450B GLN* 3.6 23.9 - - + +
453B ALA* 3.7 15.3 - - + +
454B HIS* 5.1 0.9 + - - -
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Residues in contact with GLY 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B TRP 2.9 20.4 + - - -
369B VAL 3.6 1.6 - - - -
370B LEU 3.2 0.2 - - - -
371B LYS* 1.3 76.2 - - - +
373B ILE* 1.3 56.8 + - - +
376B TYR* 2.9 32.4 + - - +
453B ALA* 3.4 26.7 - - - +
457B MET* 3.4 14.3 - - - +
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Residues in contact with ILE 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B PHE* 3.5 25.6 - - + -
359B ILE* 5.9 2.9 - - + -
369B VAL* 2.9 37.7 + - + +
370B LEU* 4.2 0.4 - - - +
372B GLY* 1.3 73.0 - - - +
374B SER* 1.3 57.0 + - - +
376B TYR* 3.8 4.7 - - + +
377B ILE* 2.8 43.7 + - + +
457B MET* 3.8 17.5 - - - -
473B PHE* 3.5 44.2 - - + -
476B LEU* 4.6 6.7 - - + -
503B PHE* 3.9 15.0 - - + -
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Residues in contact with SER 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B ALA* 3.3 16.3 - - - +
352B GLN* 3.6 38.4 + - - +
355B PHE* 3.7 19.0 - - - -
370B LEU 3.0 15.2 + - - -
371B LYS* 2.9 15.9 + - - +
373B ILE* 1.3 76.5 - - - +
375B GLY* 1.3 72.9 + - - +
377B ILE* 3.2 2.5 + - - +
378B TYR* 3.1 18.5 + - - -
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Residues in contact with GLY 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B LYS 2.9 8.3 + - - -
374B SER* 1.3 85.1 + - - +
376B TYR* 1.3 56.3 + - - +
378B TYR* 3.2 16.9 - - - -
379B GLY* 2.9 24.6 + - - -
394B TRP* 4.7 0.3 - - - -
454B HIS* 3.4 32.8 + - - -
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Residues in contact with TYR 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B GLY 2.9 20.4 + - - +
373B ILE* 3.8 5.4 - - - +
375B GLY* 1.3 76.5 - - - +
377B ILE* 1.3 62.4 + - + +
379B GLY* 3.1 2.3 + - - +
380B LEU* 2.9 61.1 + - + +
391B TYR* 4.8 5.6 - - - -
394B TRP* 6.3 0.4 - - - -
454B HIS* 3.8 10.5 + - - +
457B MET* 3.7 26.7 - - + -
458B ARG* 4.7 17.7 - - + +
461B GLU* 2.4 41.9 + - + +
466B MET* 4.6 4.0 - - - +
469B MET* 3.6 30.2 - - + +
473B PHE* 4.8 13.0 - + - -
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Residues in contact with ILE 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B PHE* 4.5 0.7 - - - -
291B TYR* 3.7 30.7 - - + +
294B ILE* 3.9 16.2 - - + -
295B LEU* 4.8 16.2 - - + -
351B ALA* 4.3 4.9 - - + -
354B PHE* 6.3 2.5 - - + -
355B PHE* 3.8 17.9 - - + -
373B ILE* 2.8 41.2 + - + +
374B SER* 3.2 5.4 + - - +
376B TYR* 1.3 82.4 - - + +
378B TYR* 1.3 59.6 + - - +
380B LEU* 3.0 18.3 + - + +
381B TRP* 2.9 22.7 + - - +
473B PHE* 4.5 13.9 - - + -
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Residues in contact with TYR 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B TYR* 3.6 17.7 - - - +
344B ARG* 2.9 51.4 + - - -
347B ALA* 3.5 28.7 - - + +
348B GLN* 2.7 45.9 + - + -
351B ALA* 4.4 0.9 - - + -
374B SER 3.1 11.1 + - - +
375B GLY* 3.2 36.3 + - - -
377B ILE* 1.3 75.6 - - - +
379B GLY* 1.3 60.8 + - - +
381B TRP* 3.3 11.9 - + - +
382B MET* 2.9 27.3 + - - +
394B TRP* 3.9 7.4 - + - -
454B HIS* 4.1 10.2 + + - -
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Residues in contact with GLY 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375B GLY 2.9 14.9 + - - -
376B TYR* 3.1 6.7 + - - -
378B TYR* 1.3 77.8 - - - +
380B LEU* 1.3 57.5 + - - +
382B MET* 3.0 9.2 + - - +
383B LYS 3.0 22.9 + - - -
391B TYR* 3.3 22.4 - - - -
394B TRP* 4.4 16.2 - - - -
458B ARG* 4.9 2.0 - - - -
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Residues in contact with LEU 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B PHE* 3.2 24.0 - - + -
294B ILE* 5.1 14.8 - - + -
376B TYR* 2.9 59.8 + - + +
377B ILE* 3.0 18.4 + - + +
379B GLY* 1.3 75.7 - - - +
381B TRP* 1.3 61.9 + - - +
383B LYS* 3.3 46.2 - - + +
384B LYS* 3.4 2.4 + - - +
466B MET* 4.6 10.5 - - + -
470B LEU* 6.1 2.9 - - + -
473B PHE* 5.8 2.2 - - + -
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Residues in contact with TRP 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B GLU* 5.7 2.4 - - - +
287B VAL* 3.9 32.1 - - + +
290B PHE* 3.4 35.3 - + + -
291B TYR* 4.4 6.3 - + + -
343B ARG* 3.8 33.7 - - + -
344B ARG* 4.2 7.9 - - - -
347B ALA* 3.6 27.6 - - + -
377B ILE 2.9 12.0 + - - +
378B TYR* 3.3 13.0 - + + +
380B LEU* 1.3 77.9 - - - +
382B MET* 1.3 91.9 + - + +
384B LYS 3.1 2.6 + - - -
385B THR* 2.5 68.8 + - + +
386B PHE* 3.5 21.3 - + - -
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Residues in contact with MET 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ARG* 2.8 39.9 - - - +
378B TYR* 2.9 22.3 + - - +
379B GLY* 3.0 10.9 + - - +
381B TRP* 1.3 95.1 - - + +
383B LYS* 1.3 64.2 + - - +
385B THR* 4.6 2.5 - - - +
386B PHE* 2.9 46.5 + - + +
387B GLY 4.0 4.5 - - - +
390B GLU* 4.7 8.7 - - + +
391B TYR* 4.3 10.3 - - + +
394B TRP* 4.1 32.5 - - + -
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Residues in contact with LYS 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B GLY 3.0 8.8 + - - +
380B LEU* 3.3 33.9 - - + +
381B TRP 3.1 0.4 - - - -
382B MET* 1.3 80.4 - - - +
384B LYS* 1.3 76.0 + - + +
385B THR 3.1 4.8 + - - -
386B PHE 3.8 5.9 + - - +
388B VAL* 3.5 30.7 - - + +
391B TYR* 3.3 55.8 - - + -
392B ARG* 5.2 5.7 - - - +
461B GLU* 3.8 10.3 + - - -
466B MET* 3.8 23.7 - - + +
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Residues in contact with LYS 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B PHE* 3.5 32.5 - - + -
380B LEU 3.4 2.4 + - - +
381B TRP 3.1 3.8 + - - -
383B LYS* 1.3 94.0 - - + +
385B THR* 1.3 63.8 + - - +
388B VAL* 5.7 5.7 - - + +
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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
------------------------------------------------------------
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