Contacts of the helix formed by residues 390 - 409 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B LEU* 3.8 34.8 - - + -
380B ILE* 3.2 40.8 - - + +
381B TYR 5.0 2.9 - - - +
382B ALA* 5.2 1.6 - - + -
387B ILE* 3.1 33.9 - - + +
388B GLY 3.0 4.2 + - - -
389B GLN* 1.3 77.8 - - - +
391B HIS* 1.3 69.8 + - - +
392B TYR 3.4 2.9 - - - -
393B ALA* 3.3 15.2 + - + +
394B LEU* 3.3 10.6 + - - +
444B LEU* 4.5 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B LEU* 3.7 33.7 - - + +
387B ILE 5.0 2.2 - - - -
388B GLY* 3.7 19.7 + - - +
389B GLN 3.7 1.0 - - - -
390B VAL* 1.3 79.4 - - + +
392B TYR* 1.3 67.2 + - - +
394B LEU* 3.2 7.2 + - - +
395B GLU* 3.1 36.0 + - + +
445B TYR 5.4 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B GLN 5.4 0.2 + - - -
390B VAL 3.4 0.4 - - - -
391B HIS* 1.3 77.5 - - - +
393B ALA* 1.3 59.4 + - - +
395B GLU* 3.4 16.1 + - + +
396B THR* 2.6 52.8 + - - -
445B TYR* 3.5 40.8 + + + +
455B ARG* 3.4 49.3 + - + +
458B VAL* 3.9 25.4 - - + -
459B THR* 2.7 33.9 + - - +
502B PHE* 4.1 12.9 - + - -
505B LEU* 4.8 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 393 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B ILE* 3.8 14.8 - - + -
389B GLN 5.7 0.2 + - - -
390B VAL* 3.3 13.3 + - + +
391B HIS 3.2 0.6 - - - -
392B TYR* 1.3 81.7 - - - +
394B LEU* 1.3 57.5 + - - +
396B THR* 3.4 1.4 + - - -
397B THR* 2.8 34.0 + - - -
443B LEU* 3.6 46.2 + - + +
445B TYR 6.0 0.2 - - - +
458B VAL* 4.9 0.2 - - - -
462B ILE* 3.8 10.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B LEU* 3.4 32.5 - - + +
370B SER 4.1 8.3 - - - +
371B GLN* 3.8 31.4 - - + +
378B VAL* 3.7 37.7 - - + +
380B ILE* 3.8 21.4 - - + +
390B VAL 3.3 3.5 + - - +
391B HIS 3.2 9.1 + - - +
393B ALA* 1.3 81.0 - - - +
395B GLU* 1.3 63.4 + - + +
397B THR* 3.9 0.4 - - - -
398B VAL* 3.1 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B GLN* 5.7 1.6 - - - -
391B HIS* 3.1 27.3 + - + +
392B TYR* 3.4 21.9 + - + +
394B LEU* 1.3 77.6 - - + +
396B THR* 1.3 62.3 + - - +
398B VAL* 3.5 5.9 + - - +
399B LYS* 3.2 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B TYR* 2.6 46.7 + - + -
393B ALA 3.7 3.4 - - - -
395B GLU* 1.3 76.1 - - - +
397B THR* 1.3 65.4 + - - +
398B VAL 3.2 0.2 + - - -
399B LYS* 3.3 4.0 + - - +
400B LEU* 3.1 41.7 + - + +
459B THR* 4.0 17.7 - - + -
462B ILE* 4.1 16.4 - - + -
502B PHE* 4.0 21.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B VAL* 3.8 24.9 - - + -
380B ILE* 3.9 2.0 - - - +
393B ALA 2.8 28.5 + - - -
394B LEU* 3.9 4.3 - - - -
396B THR* 1.3 72.7 - - - +
398B VAL* 1.3 57.9 + - - +
400B LEU 3.4 0.2 + - - -
401B LEU* 2.8 29.7 + - + +
417B LEU* 4.4 6.7 - - + -
419B LEU* 3.3 37.4 - - + +
462B ILE* 3.7 12.2 - - - +
466B LEU* 3.7 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B GLN* 3.8 37.9 - - + +
373B VAL* 4.0 21.3 - - + +
378B VAL* 4.7 4.7 - - + -
394B LEU* 3.1 32.0 + - + +
395B GLU* 3.8 6.5 - - - +
396B THR 3.1 0.4 - - - -
397B THR* 1.3 77.6 - - - +
399B LYS* 1.3 65.9 + - + +
401B LEU* 3.3 5.7 + - - +
402B GLU* 3.2 47.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B GLU* 3.2 21.0 + - + +
396B THR* 3.3 4.2 + - - +
398B VAL* 1.3 81.2 - - + +
400B LEU* 1.3 58.1 + - - +
402B GLU* 3.3 12.2 + - - +
403B PHE* 3.0 24.6 + - - +
501B ILE* 4.0 23.9 + - + +
502B PHE* 3.8 35.9 - - + -
504B GLU* 5.5 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B THR* 3.1 25.9 + - + +
399B LYS* 1.3 74.8 - - - +
401B LEU* 1.3 60.9 + - - +
402B GLU 3.1 2.0 - - - -
403B PHE* 3.6 4.4 - - + +
404B PHE* 2.9 41.0 + - + -
459B THR 4.2 2.7 - - - +
462B ILE* 3.9 13.5 - - + -
463B ALA* 3.6 35.4 - - + +
466B LEU* 3.7 13.2 - - + -
497B SER* 3.5 29.6 - - - +
498B LEU* 4.6 3.1 - - + -
501B ILE* 3.8 17.9 - - + -
502B PHE* 4.1 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B VAL* 3.8 20.9 - - + -
376B THR* 4.8 9.9 - - + -
378B VAL* 3.7 29.8 - - + -
397B THR 2.8 20.0 + - - +
398B VAL 3.8 2.9 - - - +
400B LEU* 1.3 76.0 - - - +
402B GLU* 1.3 60.5 + - - +
404B PHE* 4.4 2.8 - - - +
405B GLN* 3.4 29.6 + - - +
412B TYR* 4.1 27.1 - - + -
417B LEU* 4.1 19.3 - - + -
466B LEU* 3.8 12.7 - - + +
470B TRP* 4.4 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B VAL* 4.2 21.5 - - + +
398B VAL* 3.2 32.2 + - - +
399B LYS* 3.4 11.2 - - - +
400B LEU 3.1 0.4 - - - -
401B LEU* 1.3 76.8 - - - +
403B PHE* 1.3 67.2 + - - +
405B GLN* 3.2 9.8 + - - +
406B ASN* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B LYS 3.0 14.2 + - - +
400B LEU* 3.2 6.9 + - + +
402B GLU* 1.3 76.8 - - - +
404B PHE* 1.3 74.7 + + - +
406B ASN* 3.3 7.9 + - + +
407B TYR* 2.9 42.5 + + + +
493B MET* 4.8 0.2 - - + -
496B PHE* 4.0 27.4 - + - -
497B SER* 3.4 31.2 - - - -
500B LYS* 3.9 25.4 - - + -
501B ILE* 3.7 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B LEU* 2.9 38.4 + - + +
401B LEU 4.4 0.9 - - - +
403B PHE* 1.3 81.3 - + - +
405B GLN* 1.3 61.2 + - - +
407B TYR* 4.4 1.6 - - + +
408B PHE* 2.9 56.9 + + + +
463B ALA 3.6 24.2 - - - -
466B LEU* 3.9 20.2 - - + -
467B ALA* 3.9 14.1 - - + -
470B TRP* 3.6 21.7 - + + -
493B MET* 3.8 32.1 - - + -
497B SER* 3.6 28.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B VAL* 5.2 7.5 - - - +
374B ASN* 5.8 3.0 - - - +
376B THR* 5.1 3.6 + - - -
401B LEU* 3.4 30.0 + - + +
402B GLU* 3.2 9.1 + - - +
404B PHE* 1.3 77.0 - - - +
406B ASN* 1.3 65.4 + - - +
409B GLU* 3.1 21.0 + - - -
410B ILE 3.7 13.4 + - - +
411B GLN* 3.4 32.9 + - - +
412B TYR* 2.8 41.9 + - - +
470B TRP* 3.8 11.9 - - + -
1Q NAG 4.7 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B GLU 3.0 15.9 + - - +
403B PHE* 3.7 9.4 - - + +
405B GLN* 1.3 80.5 - - - +
407B TYR* 1.3 63.0 + - - +
409B GLU* 3.5 14.9 + - - +
569B GLN* 4.6 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B PHE* 2.9 35.1 + + + +
404B PHE* 4.1 3.1 - - - +
406B ASN* 1.3 76.5 - - - +
408B PHE* 1.3 84.6 + + - +
409B GLU* 3.1 8.0 + - - +
492B PHE* 5.7 0.2 - - - -
493B MET* 3.8 24.2 - - + -
496B PHE* 3.6 32.2 - + - -
560B LYS* 5.9 0.2 - - - +
565B GLU* 4.3 6.2 + - + +
568B PHE* 3.8 20.6 - + - -
569B GLN* 3.0 67.2 + - + +
572B VAL* 4.7 8.7 - - + -
573B VAL* 4.0 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B PHE* 2.9 44.4 + + - +
407B TYR* 1.3 81.1 - + - +
409B GLU* 1.3 70.8 + - - +
410B ILE* 3.0 12.7 + - - +
467B ALA* 4.7 3.6 - - - -
470B TRP* 3.4 48.7 - + + +
471B PHE* 3.4 28.7 - + - -
493B MET* 3.5 40.2 - - + -
572B VAL* 3.9 8.5 - - + -
573B VAL* 3.9 13.9 - - - +
576B LEU* 3.7 24.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B GLN 3.1 14.1 + - - -
406B ASN 3.6 13.5 - - - +
407B TYR 3.1 8.5 - - - +
408B PHE* 1.3 77.8 - - - +
410B ILE* 1.3 61.5 - - - +
569B GLN* 3.6 18.1 + - - +
570B HIS* 5.7 2.3 - - - +
573B VAL* 4.0 25.5 - - + +
577B HIS* 4.0 8.9 + - + -
2Q NAG 4.2 12.8 + - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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