Contacts of the helix formed by residues 483 - 502 (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 LEU 483 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLU* 4.3 2.9 - - - +
477B MET* 3.9 13.7 - - + -
479B TRP 4.2 0.2 + - - -
480B TRP* 3.2 36.2 + - + +
481B ASN 3.5 1.2 + - - -
482B ASP* 1.3 76.3 - - - +
484B TRP* 1.3 62.5 + - - +
486B ASN* 3.0 22.4 + - + +
487B GLU* 3.1 25.2 + - + +
543B MET* 3.4 40.5 - - + +
544B PHE* 3.6 47.8 - - + -
548B SER* 4.4 6.3 - - - +
549B TYR* 5.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 484 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B ASN 5.3 0.2 + - - -
482B ASP* 3.0 16.4 + - - -
483B LEU* 1.3 78.4 - - - +
485B LEU* 1.3 84.9 + - + +
486B ASN 3.2 0.2 - - - -
487B GLU 4.2 0.2 - - - +
488B GLY* 2.6 31.2 + - - +
489B PHE* 3.8 1.4 + + - -
530B ILE* 3.7 42.0 + - + +
531B SER* 4.4 2.0 - - - -
543B MET* 5.9 0.4 - - - +
548B SER* 3.5 30.0 + - - +
552B GLY* 3.7 31.0 - - - -
555B LEU* 4.1 9.0 - - + -
556B LEU* 4.5 15.5 - - + -
586B SER* 3.3 21.5 + - - -
589B LEU* 4.0 4.9 - - + -
590B TRP* 3.5 39.7 - + - -
611B THR* 3.8 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 485 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B PHE* 4.4 5.4 - - - +
477B MET* 5.0 0.9 - - + -
482B ASP* 3.0 24.5 + - + +
484B TRP* 1.3 113.2 - - + +
486B ASN* 1.3 59.2 + - - +
489B PHE* 3.4 27.2 - - + +
575B TYR* 4.6 5.1 + - - +
584B ILE* 3.6 35.3 - - + +
585B GLN 3.6 28.3 - - - +
586B SER* 3.7 9.2 - - - +
589B LEU* 3.9 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 486 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLU* 6.1 0.4 - - - +
357B TYR* 3.9 6.8 + - - +
431B GLU* 5.5 0.9 - - - +
468B HIS* 3.5 12.5 - - + -
471B PHE 3.7 15.3 - - - +
472B GLY* 3.0 32.5 + - - +
475B VAL 4.1 0.6 + - - -
476B THR* 4.0 1.4 - - - +
477B MET* 3.0 54.1 - - - +
483B LEU* 3.0 10.2 + - + +
485B LEU* 1.3 77.7 - - - +
487B GLU* 1.3 63.8 + - + +
488B GLY 3.5 0.4 - - - -
489B PHE* 3.6 0.5 + - - +
490B ALA* 2.9 30.7 + - - +
584B ILE* 5.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 487 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLU* 4.6 2.3 - - - +
431B GLU* 4.5 1.4 - - - +
464B HIS* 3.4 0.7 + - - -
468B HIS* 2.9 13.7 + - - -
483B LEU* 3.1 33.6 + - + +
484B TRP* 4.6 0.2 - - - -
486B ASN* 1.3 76.2 - - + +
488B GLY* 1.3 65.4 + - - +
491B THR* 2.8 31.4 + - - -
544B PHE* 4.0 6.8 - - - -
548B SER* 3.9 8.7 - - - +
549B TYR* 3.2 39.8 + - + -
1126B ZN 2.0 37.5 - - - -
1127B 7O2 3.2 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 488 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B TRP* 2.6 22.8 + - - -
487B GLU* 1.3 74.9 - - - +
489B PHE* 1.3 54.7 + - - -
491B THR 3.2 0.2 + - - -
492B PHE* 2.9 24.9 + - - +
548B SER 3.4 14.5 + - - -
549B TYR 3.7 8.3 - - - -
552B GLY 3.8 4.5 - - - -
553B SER* 3.3 19.1 - - - -
556B LEU* 4.1 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 489 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B PHE* 3.4 51.8 - + + -
484B TRP* 3.8 4.3 + + - -
485B LEU* 3.4 28.9 - - + +
486B ASN 3.6 1.2 + - - +
488B GLY* 1.3 72.6 - - - +
490B ALA* 1.3 67.3 + - - +
492B PHE* 3.1 1.5 + + - +
493B MET* 2.8 37.0 + - + +
556B LEU* 3.5 34.6 - - + +
568B PHE* 4.2 10.3 - + - -
572B VAL* 3.9 21.8 - - + -
575B TYR* 4.9 3.1 - + - -
589B LEU* 3.6 42.4 - - + -
593B PHE* 5.2 1.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 490 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B HIS* 3.5 18.9 + - + +
467B ALA* 3.9 17.2 - - + +
468B HIS* 3.4 37.0 - - + +
471B PHE* 4.6 2.1 - - - +
486B ASN 2.9 20.0 + - - +
487B GLU 4.2 0.9 - - - +
489B PHE* 1.3 76.9 - - - +
491B THR* 1.3 57.6 + - - +
493B MET 3.9 0.3 - - - -
494B GLU* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 491 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B HIS* 3.4 17.8 - - - -
487B GLU 2.8 22.3 + - - -
488B GLY 3.5 3.4 - - - -
490B ALA* 1.3 78.5 - - - +
492B PHE* 1.3 61.9 + - - +
494B GLU* 3.2 8.1 - - - +
495B TYR* 3.2 33.0 + - + -
511B PHE* 4.7 0.4 - - + -
549B TYR* 3.5 24.7 - - - +
550B PHE* 3.8 26.5 - - + -
553B SER* 3.5 17.3 - - - +
1127B 7O2 3.9 1.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 492 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B TYR* 5.7 0.2 - - - -
488B GLY 2.9 16.5 + - - +
489B PHE* 3.1 4.0 + + - +
491B THR* 1.3 78.1 - - - +
493B MET* 1.3 72.1 + - + +
495B TYR* 3.2 5.2 + - + +
496B PHE* 2.8 51.0 + + + +
511B PHE* 5.1 7.2 - + - -
553B SER* 3.6 28.2 - - - -
556B LEU* 4.0 12.8 - - + -
557B LEU* 3.6 33.9 - - + -
560B LYS* 3.4 31.2 - - + -
568B PHE* 3.6 30.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 493 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B PHE* 4.8 0.7 - - + -
404B PHE* 3.8 17.2 - - + -
407B TYR* 3.8 22.4 - - + -
408B PHE* 3.5 40.2 - - + -
467B ALA* 3.8 17.0 - - + -
471B PHE* 4.3 11.0 - - + -
489B PHE* 2.8 30.4 + - + +
492B PHE* 1.3 89.2 - - + +
494B GLU* 1.3 67.3 + - - +
496B PHE* 3.8 17.0 - - + -
497B SER* 2.9 29.2 + - - -
568B PHE* 5.2 3.6 - - - -
572B VAL* 5.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 494 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B LYS* 3.3 59.0 - - + +
463B ALA* 4.2 9.4 - - - +
464B HIS* 2.8 32.1 + - - +
467B ALA* 4.7 0.6 - - - +
490B ALA 2.9 14.4 + - - +
491B THR* 3.2 9.5 - - - +
492B PHE 3.2 0.2 - - - -
493B MET* 1.3 79.1 - - - +
495B TYR* 1.3 76.2 + - + +
497B SER* 3.2 7.1 + - - -
498B LEU* 3.2 25.5 - - - +
1127B 7O2 3.6 18.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 495 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B LYS* 3.2 29.0 + - + -
491B THR* 3.2 31.0 + - + +
492B PHE* 4.0 4.3 - - + +
494B GLU* 1.3 97.8 + - + +
496B PHE* 1.3 63.5 - - - +
498B LEU* 3.6 4.3 + - + +
499B GLU* 3.2 22.9 + - - +
507B SER* 3.4 39.0 - - - -
508B TYR* 4.6 1.6 - - - -
510B ASP* 3.6 11.4 + - + +
511B PHE* 3.4 59.9 + + + -
514B ALA* 5.4 0.3 - - - +
550B PHE* 4.4 12.7 - + - -
1127B 7O2 5.9 0.2 - + - -
1129B BR 4.7 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 496 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B PHE* 4.0 16.2 - + - -
407B TYR* 3.6 39.3 - + - -
492B PHE* 2.8 37.7 + + + +
493B MET* 3.8 24.5 - - + +
495B TYR* 1.3 73.4 - - - +
497B SER* 1.3 63.1 + - - +
499B GLU* 3.3 4.6 + - + +
500B LYS* 3.1 51.0 + - + +
560B LYS* 3.8 17.9 - - + -
565B GLU* 3.5 30.5 - - + -
1129B BR 4.2 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 497 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B LEU* 3.5 18.1 - - - +
403B PHE* 3.4 35.7 - - - -
404B PHE* 3.6 13.7 - - - -
463B ALA* 3.8 4.9 - - - +
493B MET 2.9 23.4 + - - -
494B GLU 3.2 4.7 + - - -
496B PHE* 1.3 77.7 - - - +
498B LEU* 1.3 60.8 + - - +
500B LYS* 3.4 0.7 + - - +
501B ILE* 3.0 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 498 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B LEU* 4.6 1.3 - - + -
459B THR* 3.7 27.8 - - + -
460B LYS* 3.5 36.6 - - + +
463B ALA* 4.1 15.0 - - + -
494B GLU* 3.2 19.8 + - + +
495B TYR* 4.0 3.6 - - + +
496B PHE 3.2 1.0 - - - -
497B SER* 1.3 75.8 + - - +
499B GLU* 1.3 61.0 + - - +
502B PHE* 2.9 54.0 + - + +
505B LEU* 5.2 1.6 - - + -
507B SER* 3.3 35.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 499 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B TYR 3.2 17.2 + - - +
496B PHE* 3.3 6.3 + - + +
498B LEU* 1.3 77.0 - - - +
500B LYS* 1.3 70.6 - - + +
503B LYS* 3.1 66.8 + - - +
507B SER* 4.7 6.0 + - - -
508B TYR* 4.0 35.5 + - + +
1132B BR 4.5 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 500 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B PHE* 3.9 22.9 - - + -
496B PHE* 3.1 39.0 + - + +
497B SER 3.8 4.0 - - - +
499B GLU* 1.3 85.9 - - + +
501B ILE* 1.3 71.4 + - + +
502B PHE 3.7 0.2 - - - -
503B LYS* 4.9 3.3 + - - +
565B GLU* 3.1 33.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 501 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B LYS* 4.0 30.9 + - + +
400B LEU* 3.8 19.1 - - + -
403B PHE* 3.7 42.0 - - + -
497B SER 3.0 16.8 + - - +
500B LYS* 1.3 84.2 - - + +
502B PHE* 1.3 91.0 + - + +
503B LYS 3.8 1.1 - - - -
504B GLU* 4.3 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 502 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B TYR* 4.1 13.5 - + - -
396B THR* 4.0 20.2 - - + -
399B LYS* 3.8 33.2 - - + -
400B LEU* 4.1 11.9 - - + -
459B THR* 4.0 13.9 - - + -
498B LEU* 2.9 34.7 + - + +
501B ILE* 1.3 114.3 - - + +
503B LYS* 1.3 64.4 + - - +
504B GLU* 3.1 19.1 - - - -
505B LEU* 3.0 42.7 + - + +
506B SER 4.4 0.7 + - - -
507B SER* 5.1 1.0 + - - -
----------------------------------------------------------
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