Contacts of the helix formed by residues 384 - 407 (chain I) 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 GLY 384 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380I LEU 4.0 0.4 + - - -
381I ALA 3.4 7.0 + - - +
382I GLU 3.2 4.1 - - - -
383I LEU* 1.3 82.6 - - - +
385I HIS* 1.3 65.2 + - - +
386I ASP 3.5 2.0 - - - -
387I VAL* 3.6 4.8 + - - +
388I ILE* 3.3 27.0 + - - +
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Residues in contact with HIS 385 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384I GLY* 1.3 71.8 - - - +
386I ASP* 1.3 83.6 + - - +
388I ILE* 3.3 6.9 + - - +
389I LYS* 2.9 47.8 + - - +
433I PRO 4.5 1.4 + - - -
434I VAL* 3.5 33.3 + - + +
437I LYS* 3.5 33.2 - - + +
438I LEU* 5.7 0.2 - - - -
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Residues in contact with ASP 386 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385I HIS* 1.3 83.1 - - - +
387I VAL* 1.3 60.9 + - + +
389I LYS* 2.9 37.1 + - + +
390I THR* 2.9 35.1 + - + +
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Residues in contact with VAL 387 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356I THR* 5.4 4.9 - - + -
380I LEU 3.5 19.7 - - - +
383I LEU* 3.6 43.7 - - + +
384I GLY* 3.6 9.2 - - - +
385I HIS 3.2 0.4 - - - -
386I ASP* 1.3 77.1 - - + +
388I ILE* 1.3 56.9 + - - +
390I THR* 2.3 28.2 + - - +
391I LEU* 2.9 32.2 + - + +
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Residues in contact with ILE 388 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377I ILE* 4.9 2.5 - - + +
380I LEU* 3.3 39.7 - - + +
381I ALA* 3.7 16.8 - - + +
384I GLY 3.3 12.8 + - - +
385I HIS* 3.3 8.3 + - - +
387I VAL* 1.3 75.4 - - + +
389I LYS* 1.3 61.3 + - - +
391I LEU* 4.1 2.2 - - + +
392I ILE* 2.7 56.8 + - + +
393I LEU 3.8 1.2 + - - -
431I CYS* 3.7 24.2 - - + +
434I VAL* 4.0 17.3 - - + -
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Residues in contact with LYS 389 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385I HIS* 2.9 38.4 + - - +
386I ASP* 2.9 37.1 + - + +
387I VAL 3.2 0.2 - - - -
388I ILE* 1.3 76.3 - - - +
390I THR* 1.3 60.6 + - + +
393I LEU* 3.3 24.8 - - - +
434I VAL* 5.0 7.1 - - + +
438I LEU* 5.3 13.5 - - + +
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Residues in contact with THR 390 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386I ASP* 2.9 17.5 + - + +
387I VAL* 2.3 32.6 + - - +
389I LYS* 1.3 81.1 - - + +
391I LEU* 1.3 73.4 + - - +
393I LEU* 3.8 4.0 - - - +
394I PRO* 3.7 13.9 - - - +
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Residues in contact with LEU 391 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356I THR* 5.7 3.4 - - + -
360I THR* 5.1 10.3 - - + +
380I LEU* 3.7 41.1 - - + -
387I VAL* 2.9 30.0 + - + +
388I ILE* 3.1 1.3 + - + -
390I THR* 1.3 84.8 + - - +
392I ILE* 1.3 74.7 + - + +
393I LEU 3.1 4.5 - - - -
394I PRO* 3.3 13.3 - - - +
395I ARG* 3.3 37.2 + - - +
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Residues in contact with ILE 392 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377I ILE* 4.9 12.1 - - + -
380I LEU* 5.6 1.8 - - + -
388I ILE* 2.7 47.2 + - + +
391I LEU* 1.3 83.1 - - + +
393I LEU* 1.3 60.8 + - - +
394I PRO 3.6 0.2 - - - -
395I ARG* 3.6 26.2 - - + +
396I LEU* 3.0 39.4 + - + +
399I GLU* 3.5 23.3 - - - +
431I CYS* 3.7 26.4 - - - -
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Residues in contact with LEU 393 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388I ILE 3.8 2.2 + - - -
389I LYS* 3.3 21.7 + - - +
390I THR* 3.7 4.4 + - - +
391I LEU 3.1 1.6 - - - -
392I ILE* 1.3 81.4 - - - +
394I PRO* 1.4 65.5 - - + +
396I LEU* 3.8 15.1 - - + +
397I GLN 4.9 0.3 + - - -
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Residues in contact with PRO 394 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390I THR 3.7 8.1 - - - +
391I LEU 3.3 17.0 - - - +
393I LEU* 1.4 87.5 - - + +
395I ARG* 1.3 61.6 + - + +
396I LEU 3.1 6.0 + - - -
397I GLN* 3.4 5.0 + - - +
398I GLN* 3.0 46.8 + - - +
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Residues in contact with ARG 395 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360I THR* 3.6 28.9 + - - +
363I TRP* 3.3 66.9 - - + +
364I VAL* 5.0 0.4 - - - +
377I ILE* 4.8 1.8 - - - +
380I LEU* 3.4 28.8 - - - +
391I LEU* 3.3 31.8 + - - +
392I ILE* 3.6 16.5 - - + +
393I LEU 3.4 0.4 - - - -
394I PRO* 1.3 78.2 - - + +
396I LEU* 1.3 57.7 + - - +
398I GLN* 4.0 9.6 - - - +
399I GLU* 2.8 61.7 + - - +
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Residues in contact with LEU 396 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392I ILE* 3.0 28.5 + - + +
393I LEU* 3.8 13.9 - - + +
395I ARG* 1.3 75.4 - - - +
397I GLN* 1.3 60.3 + - + +
399I GLU* 3.8 0.9 - - - +
400I GLY* 2.9 23.0 + - - -
428I LEU* 6.0 3.6 - - + -
431I CYS* 5.9 5.2 - - - -
435I LEU* 6.3 5.2 - - + -
450I ALA 3.3 25.8 - - - +
451I GLU* 3.7 28.0 - - + +
455I LEU* 5.2 6.3 - - + -
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Residues in contact with GLN 397 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393I LEU 4.9 0.4 + - - -
394I PRO 3.4 5.4 + - - +
396I LEU* 1.3 79.6 - - + +
398I GLN* 1.3 61.5 + - + +
400I GLY* 3.6 0.5 - - - -
401I GLU* 2.9 35.8 + - - +
449I ARG 2.9 28.3 + - - -
450I ALA* 3.1 20.4 + - - +
451I GLU* 3.7 6.7 - - - -
452I PHE* 3.2 33.7 - - + +
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Residues in contact with GLN 398 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363I TRP* 3.2 30.6 - - + -
394I PRO* 3.0 40.2 + - - +
395I ARG* 4.0 6.8 - - - +
397I GLN* 1.3 78.0 - - + +
399I GLU* 1.3 58.5 + - - +
401I GLU* 3.2 23.3 + - - +
402I ARG* 3.0 27.3 + - - +
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Residues in contact with GLU 399 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363I TRP* 2.4 46.9 + - + +
377I ILE* 3.5 21.0 - - + +
392I ILE* 3.5 16.4 - - - +
395I ARG* 2.8 39.1 + - - +
396I LEU 4.2 1.1 - - - +
398I GLN* 1.3 72.9 - - - +
400I GLY* 1.3 59.0 + - - +
402I ARG* 3.1 15.0 + - + +
403I ILE* 2.8 34.1 + - + +
424I GLN* 5.1 0.3 + - - +
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Residues in contact with GLY 400 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396I LEU 2.9 17.0 + - - -
397I GLN* 3.3 6.0 + - - -
398I GLN 3.2 0.4 - - - -
399I GLU* 1.3 73.9 - - - +
401I GLU* 1.3 59.4 + - - +
403I ILE* 3.2 18.3 + - - +
404I ARG* 3.0 32.1 + - - +
451I GLU 5.3 2.0 - - - -
452I PHE* 4.5 13.7 - - - -
454I SER* 4.9 4.7 - - - -
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Residues in contact with GLU 401 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397I GLN* 2.9 22.6 + - + +
398I GLN* 3.2 24.2 - - - +
400I GLY* 1.3 74.4 - - - +
402I ARG* 1.3 59.8 + - + +
404I ARG* 3.7 2.8 - - - +
405I SER* 2.9 28.9 + - - -
452I PHE* 5.7 3.1 - - + -
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Residues in contact with ARG 402 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363I TRP* 2.5 79.2 + - - +
364I VAL* 4.4 5.5 + - - +
365I ASP 5.5 1.4 + - - -
366I GLU* 6.1 0.6 - - - +
370I TRP* 4.5 21.5 - - + -
373I ARG* 4.1 24.5 - - - +
377I ILE* 5.1 1.4 - - - +
398I GLN 3.0 15.6 + - - +
399I GLU* 3.1 20.2 + - + +
401I GLU* 1.3 74.8 - - + +
403I ILE* 1.3 58.6 + - - +
405I SER* 2.4 26.5 + - - +
406I VAL* 2.9 18.0 + - - +
424I GLN* 3.7 4.5 - - - +
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Residues in contact with ILE 403 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399I GLU* 2.8 19.9 + - + +
400I GLY* 3.3 16.8 - - - +
402I ARG* 1.3 75.8 - - - +
404I ARG* 1.3 53.3 + - + +
405I SER 3.2 0.2 - - - -
406I VAL* 2.9 4.2 + - - +
407I LEU* 2.4 56.7 + - + +
424I GLN* 3.4 44.9 - - + +
428I LEU* 5.6 13.0 - - + -
454I SER* 3.7 29.2 - - - -
455I LEU* 5.3 2.2 - - + +
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Residues in contact with ARG 404 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400I GLY 3.0 15.5 + - - +
401I GLU* 3.7 3.4 - - - +
403I ILE* 1.3 77.2 - - + +
405I SER* 1.3 59.5 + - - +
407I LEU* 2.9 24.5 - - + +
408I ASP* 4.3 12.7 + - + +
452I PHE 3.3 17.7 + - - -
453I GLY* 3.2 13.7 + - - -
454I SER* 3.2 40.1 - - - +
456I GLY 5.2 0.8 + - - -
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Residues in contact with SER 405 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370I TRP* 4.8 3.8 - - - -
401I GLU 2.9 16.0 + - - -
402I ARG* 2.4 31.8 + - - +
404I ARG* 1.3 76.5 - - - +
406I VAL* 1.3 65.6 + - - +
409I GLY* 3.3 17.5 - - - -
410I PRO* 4.3 2.3 - - - +
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Residues in contact with VAL 406 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370I TRP* 3.5 31.2 - - + +
402I ARG 3.3 11.9 - - - +
403I ILE 2.9 7.6 + - - +
405I SER* 1.3 81.1 + - - +
407I LEU* 1.3 71.0 + - + +
409I GLY 3.1 12.8 + - - -
410I PRO* 3.3 16.2 - - + +
416I ASP 5.1 0.2 - - - +
417I ARG* 4.7 22.0 + - + +
420I ALA* 4.0 19.1 - - + -
421I ASP 4.8 1.3 - - - +
424I GLN* 3.4 21.5 - - - +
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Residues in contact with LEU 407 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403I ILE* 2.4 49.9 + - + +
404I ARG* 2.9 33.2 - - + +
406I VAL* 1.3 70.8 - - + +
408I ASP* 1.3 72.2 + - - +
417I ARG 5.7 0.2 - - - +
421I ASP* 3.7 39.5 - - + +
424I GLN* 4.4 6.7 - - + +
454I SER* 5.8 1.6 - - - -
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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