Contacts of the helix formed by residues 390 - 409 (chain A) in PDB entry 5MJ6
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 VAL 390 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A LEU* 3.6 35.2 - - + -
380A ILE* 3.6 29.5 - - + +
382A ALA* 4.1 17.0 - - + -
387A ILE* 3.3 27.1 - - + +
388A GLY 3.4 0.8 - - - -
389A GLN* 1.3 77.2 - - - +
391A HIS* 1.3 65.2 + - - +
392A TYR 3.4 2.7 - - - -
393A ALA* 3.5 8.0 + - - +
394A LEU* 3.2 21.0 + - - +
443A LEU 5.3 0.2 - - - -
444A LEU* 3.6 22.2 - - + -
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Residues in contact with HIS 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A LEU* 3.7 33.5 - - + +
387A ILE 4.9 4.0 + - - -
388A GLY* 3.6 22.7 + - - +
389A GLN 3.6 2.6 - - - -
390A VAL* 1.3 77.6 - - - +
392A TYR* 1.3 62.4 + - - +
394A LEU* 3.4 2.3 + - - +
395A GLU* 2.9 44.9 + - - +
445A TYR 5.5 0.2 + - - -
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Residues in contact with TYR 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A GLN 5.0 0.8 + - - -
390A VAL 3.4 0.6 - - - -
391A HIS* 1.3 74.9 - - - +
393A ALA* 1.3 62.0 + - - +
395A GLU* 3.2 15.0 + - + +
396A THR* 2.9 52.4 + - - -
445A TYR* 3.7 36.7 + + + +
455A ARG* 3.3 57.1 + - + +
458A VAL* 4.0 18.8 - - + -
459A THR* 2.6 33.2 + - - +
502A PHE* 4.3 12.2 - + - -
505A LEU* 4.8 1.2 - - - +
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Residues in contact with ALA 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ILE* 4.2 11.0 - - + -
389A GLN 5.5 0.4 + - - -
390A VAL* 3.5 9.8 + - - +
391A HIS 3.4 0.2 - - - -
392A TYR* 1.3 81.8 - - - +
394A LEU* 1.3 61.4 + - - +
396A THR* 3.8 1.0 - - - -
397A THR* 2.8 31.7 + - - -
443A LEU* 3.6 47.3 + - + +
445A TYR* 5.6 0.4 - - - +
458A VAL* 4.7 0.4 - - + -
462A ILE* 3.9 12.3 - - + +
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Residues in contact with LEU 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A LEU* 3.8 36.6 - - + +
370A SER 4.0 15.0 - - - +
371A GLN* 4.0 18.8 - - + +
378A VAL* 3.6 40.4 - - + +
380A ILE* 3.8 19.4 - - + +
390A VAL 3.2 17.4 + - - +
391A HIS 3.8 4.3 - - - +
393A ALA* 1.3 74.7 - - - +
395A GLU* 1.3 66.1 + - + +
397A THR* 3.3 1.1 + - - -
398A VAL* 3.1 32.4 + - + +
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Residues in contact with GLU 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A GLN* 6.1 1.1 - - - +
391A HIS* 2.9 41.0 + - - +
392A TYR* 3.2 17.9 + - + +
394A LEU* 1.3 79.8 - - + +
396A THR* 1.3 60.8 + - - +
398A VAL* 3.5 7.2 + - - +
399A LYS* 3.2 32.2 + - - +
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Residues in contact with THR 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A TYR* 2.9 44.0 + - - -
393A ALA 3.8 3.4 - - - -
395A GLU* 1.3 74.2 - - - +
397A THR* 1.3 65.8 + - - +
399A LYS* 3.1 9.7 + - - +
400A LEU* 2.9 43.6 + - + +
459A THR* 4.1 13.0 - - + -
462A ILE* 4.2 18.2 - - + -
502A PHE* 4.0 17.9 - - + -
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Residues in contact with THR 397 (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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378A VAL* 3.6 28.5 - - + -
380A ILE* 4.2 0.6 - - - +
393A ALA 2.8 27.5 + - - -
394A LEU* 3.6 4.7 - - - -
396A THR* 1.3 73.8 - - - +
398A VAL* 1.3 57.0 + - - +
401A LEU* 2.9 29.4 + - + +
417A LEU* 4.3 12.6 - - + -
419A LEU* 3.2 36.8 - - + +
462A ILE* 3.7 14.4 - - - +
466A LEU* 3.7 11.6 - - + +
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Residues in contact with VAL 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A GLN* 3.9 29.4 - - + +
373A VAL* 3.6 32.5 - - + +
378A VAL* 4.7 5.4 - - + -
394A LEU* 3.1 26.5 + - + +
395A GLU* 3.7 8.7 - - - +
396A THR 3.2 0.2 - - - -
397A THR* 1.3 77.8 - - - +
399A LYS* 1.3 63.0 + - + +
401A LEU* 3.7 6.3 - - - +
402A GLU* 3.3 38.2 + - - +
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Residues in contact with LYS 399 (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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395A GLU* 3.2 19.2 + - - +
396A THR* 3.1 9.2 + - - +
398A VAL* 1.3 80.2 - - + +
400A LEU* 1.3 61.4 + - - +
402A GLU* 3.3 13.0 + - - +
403A PHE* 3.1 22.3 + - - +
501A ILE* 4.2 18.1 + - + +
502A PHE* 4.0 29.9 - - + -
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Residues in contact with LEU 400 (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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396A THR* 2.9 34.8 + - + +
399A LYS* 1.3 74.5 - - - +
401A LEU* 1.3 61.5 + - - +
403A PHE* 3.4 3.7 + - + +
404A PHE* 2.9 43.2 + - + -
459A THR* 4.1 3.8 - - + +
462A ILE* 3.9 5.6 - - + -
463A ALA* 3.6 33.4 - - + +
466A LEU* 3.5 15.7 - - + -
497A SER* 3.6 28.9 - - - +
498A LEU* 5.0 0.2 - - + -
501A ILE* 3.9 19.3 - - + -
502A PHE* 4.1 15.9 - - + -
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Residues in contact with LEU 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A VAL* 4.8 11.9 - - + -
376A THR* 4.8 12.3 - - + -
378A VAL* 3.9 21.1 - - + -
397A THR* 2.9 17.9 + - + +
398A VAL* 3.7 5.4 - - - +
400A LEU* 1.3 78.3 - - - +
402A GLU* 1.3 63.3 + - + +
404A PHE* 3.3 2.5 + - - -
405A GLN* 3.0 43.7 + - - +
412A TYR* 4.2 10.8 - - + -
417A LEU* 3.9 27.8 - - + -
466A LEU* 3.8 10.2 - - + +
470A TRP* 4.0 24.2 - - + -
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Residues in contact with GLU 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A VAL* 3.9 21.5 - - + +
398A VAL* 3.3 31.1 + - - +
399A LYS* 3.3 11.5 + - - +
401A LEU* 1.3 76.9 - - - +
403A PHE* 1.3 64.0 + - - +
405A GLN* 3.4 10.4 + - - +
406A ASN* 3.1 24.1 + - - +
1I NAG 5.5 10.0 - - + +
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Residues in contact with PHE 403 (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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399A LYS 3.1 11.6 + - - +
400A LEU* 3.5 8.1 - - + +
402A GLU* 1.3 80.3 - - - +
404A PHE* 1.3 77.3 + + - +
406A ASN* 3.3 6.7 + - + +
407A TYR* 3.0 38.9 + + + +
496A PHE* 4.5 14.4 - + - -
497A SER* 3.5 28.9 - - - -
500A LYS* 3.7 37.9 - - + -
501A ILE* 3.9 28.0 - - + -
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Residues in contact with PHE 404 (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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400A LEU* 2.9 36.4 + - + +
401A LEU 4.0 1.1 - - - +
403A PHE* 1.3 87.7 - + - +
405A GLN* 1.3 58.4 + - - +
407A TYR* 4.5 2.2 - + + +
408A PHE* 2.9 60.0 + + + +
463A ALA 3.6 23.8 - - - -
466A LEU* 3.8 24.2 - - + -
467A ALA* 3.9 9.9 - - + -
470A TRP* 3.8 20.4 - + + -
493A MET* 3.9 24.7 - - + -
497A SER* 3.6 33.2 - - - -
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Residues in contact with GLN 405 (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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373A VAL* 5.2 6.1 + - - +
376A THR* 5.0 5.2 + - - -
401A LEU* 3.0 37.6 + - - +
402A GLU* 3.8 9.5 - - - +
404A PHE* 1.3 77.7 - - - +
406A ASN* 1.3 54.7 + - - +
409A GLU* 3.1 25.5 + - - -
410A ILE 3.7 11.1 + - - +
411A GLN* 3.6 26.9 + - - +
412A TYR* 3.0 39.8 + - - +
470A TRP* 3.8 9.6 - - + -
1I NAG 3.5 22.0 - - + +
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Residues in contact with ASN 406 (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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402A GLU 3.1 17.2 + - - +
403A PHE* 3.8 7.3 - - + +
405A GLN* 1.3 76.6 - - - +
407A TYR* 1.3 68.9 + - - +
409A GLU* 3.8 15.3 + - - +
569A GLN* 4.5 4.5 + - - -
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Residues in contact with TYR 407 (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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403A PHE* 3.0 34.6 + + + +
404A PHE* 3.9 5.8 - + + +
406A ASN* 1.3 82.6 + - - +
408A PHE* 1.3 81.7 + + + +
409A GLU* 3.5 1.4 + - - +
493A MET* 4.0 23.6 - - + -
496A PHE* 3.6 36.3 - + - -
565A GLU* 4.4 5.5 + - + +
568A PHE* 3.7 15.8 - - - -
569A GLN* 3.2 68.6 + - + +
572A VAL* 4.7 7.2 - - + -
573A VAL* 3.8 8.1 - - - +
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Residues in contact with PHE 408 (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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404A PHE* 2.9 46.9 + + - +
407A TYR* 1.3 95.7 - + - +
409A GLU* 1.3 71.0 + - - +
410A ILE* 3.3 12.7 + - + +
467A ALA* 4.8 3.6 - - - -
470A TRP* 3.3 54.1 - + + +
471A PHE* 3.4 29.8 - + - -
493A MET* 3.9 17.9 - - + -
572A VAL* 4.1 4.9 - - + -
573A VAL* 3.6 17.8 - - - +
576A LEU* 3.8 22.6 - - + +
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Residues in contact with GLU 409 (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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405A GLN 3.1 16.8 + - - -
406A ASN* 3.9 11.9 - - - +
407A TYR 3.2 2.4 - - - -
408A PHE* 1.3 79.4 - - - +
410A ILE* 1.3 61.2 + - - +
411A GLN* 4.3 1.8 - - - -
569A GLN* 4.0 16.5 + - - -
570A HIS* 6.0 0.9 + - - -
573A VAL* 3.3 28.7 - - + +
577A HIS* 4.1 9.6 + - + -
2I NAG 5.1 9.8 + - - -
4I MAN 5.2 0.7 + - - -
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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