Contacts of the helix formed by residues 477 - 495 (chain B) in PDB entry 6CM9
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 SER 477 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B PRO* 4.3 24.3 - - - +
475B ASP 3.9 0.2 - - - -
476B LYS* 1.3 80.8 - - - +
478B THR* 1.3 71.8 + - - +
479B GLN* 3.5 13.6 + - - +
480B VAL* 4.5 8.2 - - - +
481B GLN* 3.1 28.1 + - - +
516B ASN* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 478 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B SER* 1.3 82.7 + - - +
479B GLN* 1.3 65.7 + - - -
480B VAL 3.5 0.2 + - - -
481B GLN* 3.5 3.1 + - - +
482B LEU* 3.0 35.1 + - + +
516B ASN* 3.9 27.7 + - - +
518B ASP* 5.8 5.6 - - + +
521G VAL* 4.0 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 479 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B PRO* 3.4 22.3 - - + +
443B GLU* 4.5 5.0 - - - -
446B ALA* 4.3 16.2 - - + +
477B SER* 3.5 7.0 + - - +
478B THR* 1.3 82.7 - - + +
480B VAL* 1.3 59.7 + - + +
482B LEU* 3.4 5.5 + - - +
483B GLN* 2.9 36.6 + - + +
519G THR 5.6 2.2 + - - -
520G SER* 5.2 7.5 + - - -
521G VAL* 5.4 9.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 480 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B PRO* 4.2 26.9 - - + +
445B ARG* 3.8 37.5 - - + +
446B ALA* 4.3 4.5 - - - +
449B ILE* 4.6 13.9 - - + +
469B PHE* 5.1 0.4 - - + -
476B LYS* 3.7 40.4 - - + +
477B SER* 4.5 6.8 - - - +
479B GLN* 1.3 76.6 - - - +
481B GLN* 1.3 58.7 + - - +
483B GLN* 3.9 4.9 - - - +
484B LEU* 2.9 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 481 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B PHE* 2.5 59.7 + - + +
474B HIS* 3.3 21.6 + - - +
475B ASP* 3.5 3.2 - - - +
476B LYS* 3.6 12.3 - - + +
477B SER 3.1 23.8 + - - +
478B THR 3.5 3.1 + - - +
479B GLN 3.4 0.4 - - - -
480B VAL* 1.3 77.6 - - - +
482B LEU* 1.3 56.4 + - - +
484B LEU* 3.3 1.8 + - - -
485B LEU* 3.0 26.3 + - - +
516B ASN* 4.2 14.1 + - - +
519B LEU* 3.5 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 482 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B THR* 3.0 29.3 + - + +
479B GLN* 3.9 4.5 - - - +
481B GLN* 1.3 76.5 - - - +
483B GLN* 1.3 59.6 + - - +
485B LEU* 3.3 3.4 + - + +
486B THR* 3.0 33.2 + - - +
518B ASP* 3.3 23.1 - - + +
519B LEU* 4.3 15.5 - - + +
522B ARG* 3.7 35.4 - - + +
526B TYR* 6.5 0.2 - - + -
521G VAL* 6.5 0.4 - - + -
558G GLU* 3.5 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 483 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B ALA* 3.8 21.7 + - + +
449B ILE* 3.4 18.6 - - + +
450B TRP* 3.4 43.0 - - - +
479B GLN* 2.9 23.0 + - + +
480B VAL 4.0 2.7 - - - +
482B LEU* 1.3 75.3 - - + +
484B LEU* 1.3 59.3 + - - +
486B THR* 3.8 10.4 + - - +
487B ALA* 2.9 32.1 + - - +
557G VAL* 4.2 8.8 - - - +
558G GLU* 3.6 33.6 - - + +
561G GLN* 5.3 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 484 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B ILE* 3.7 31.2 - - + -
466B LEU* 4.3 7.9 - - + -
469B PHE* 3.3 34.5 - - + +
470B LEU* 3.9 13.9 - - + -
473B PHE* 3.7 26.2 - - + -
476B LYS* 4.0 12.1 - - + +
480B VAL* 2.9 23.4 + - + +
481B GLN* 3.3 5.4 + - - +
483B GLN* 1.3 76.8 - - - +
485B LEU* 1.3 56.0 + - - +
487B ALA* 4.5 0.4 - - - -
488B ILE* 2.9 47.6 + - + +
506B VAL* 5.1 0.9 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
473B PHE* 5.0 3.3 - - + -
481B GLN 3.0 13.6 + - - +
482B LEU* 3.3 10.1 + - + +
484B LEU* 1.3 76.4 - - - +
486B THR* 1.3 61.8 + - - +
488B ILE* 5.2 0.4 - - - -
489B VAL* 3.3 29.0 + - + +
506B VAL* 4.7 14.8 - - + +
507B LEU* 4.4 17.7 - - + -
510B ALA* 4.3 16.2 - - + -
519B LEU* 3.7 21.5 - - + +
522B ARG* 3.7 17.0 - - + -
523B GLY* 3.5 28.7 - - - +
526B TYR* 3.4 18.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 486 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B TRP* 6.0 2.9 - - + -
482B LEU* 3.0 22.5 + - - +
483B GLN* 3.9 15.3 + - - +
484B LEU 3.3 0.2 - - - -
485B LEU* 1.3 77.5 - - - +
487B ALA* 1.3 59.1 + - - +
489B VAL* 3.4 2.9 + - - +
490B LYS* 2.9 48.4 + - - +
522B ARG* 4.3 6.1 + - - -
526B TYR* 3.8 24.1 + - - +
558G GLU* 5.1 4.3 + - - +
561G GLN* 3.9 22.5 - - + +
565G GLU* 4.2 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 487 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B ILE* 3.6 30.1 - - + +
450B TRP* 5.4 1.6 - - - -
453B GLY* 3.7 20.4 - - - +
466B LEU* 5.0 10.2 - - + +
483B GLN 2.9 18.3 + - - +
484B LEU* 4.1 2.0 - - - +
486B THR* 1.3 78.6 - - - +
488B ILE* 1.3 58.6 + - - +
490B LYS* 3.3 5.4 + - - +
491B LEU* 2.8 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 488 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B LEU* 3.8 23.3 - - + -
470B LEU* 3.7 30.3 - - + -
484B LEU* 2.9 27.4 + - + +
485B LEU 4.9 0.2 - - - +
487B ALA* 1.3 73.5 - - + +
489B VAL* 1.3 59.7 + - - +
491B LEU* 3.3 6.4 + - - +
492B PHE* 2.9 28.8 + - + +
499B THR* 5.6 0.6 - - - -
502B LEU* 3.7 35.7 - - + +
503B VAL* 4.1 7.4 - - + +
506B VAL* 3.7 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 489 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B LEU* 3.3 28.2 + - + +
486B THR 3.4 3.5 + - - +
487B ALA 3.3 0.4 - - - -
488B ILE* 1.3 78.1 - - - +
490B LYS* 1.3 56.4 + - - +
492B PHE* 3.4 6.6 + - + +
493B LEU* 2.9 29.8 + - + +
503B VAL* 4.1 21.1 - - + -
506B VAL* 5.2 2.9 - - + -
507B LEU* 5.3 1.6 - - + -
526B TYR* 3.6 44.2 - - + +
529B LEU* 6.0 1.8 - - + -
530B LEU* 5.9 9.4 - - + -
541B VAL* 4.8 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 490 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B TRP* 5.8 1.7 - - - +
453B GLY* 3.3 28.3 - - - +
454B GLU* 3.7 25.8 - - - +
486B THR* 2.9 29.5 + - - +
487B ALA* 3.6 6.3 - - - +
488B ILE 3.3 0.2 - - - -
489B VAL* 1.3 77.7 - - - +
491B LEU* 1.3 56.3 + - - +
493B LEU* 3.4 6.8 + - - +
494B LYS* 2.9 38.2 + - - +
541B VAL* 4.4 17.1 + - + +
542B LEU* 3.7 25.5 - - + +
545B LYS* 4.8 3.4 - - - +
561G GLN* 3.2 29.9 - - - +
565G GLU* 3.9 4.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 491 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B GLY* 5.0 1.3 + - - -
456B ALA* 3.7 30.7 - - + +
462B ALA* 4.2 10.5 - - + -
463B ASP* 4.1 17.0 - - - +
466B LEU* 3.9 25.8 - - + -
487B ALA 2.8 17.2 + - - +
488B ILE 3.6 3.8 - - - +
490B LYS* 1.3 74.4 - - - +
492B PHE* 1.3 60.4 + - - +
494B LYS* 3.3 3.2 + - + +
495B LYS* 2.8 55.5 + - + +
499B THR* 3.7 24.7 - - + -
502B LEU* 4.5 5.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
488B ILE* 2.9 17.9 + - + +
489B VAL* 4.0 4.3 - - + +
491B LEU* 1.3 76.5 - - - +
493B LEU* 1.3 64.9 + - + +
495B LYS 3.3 14.7 - - - -
496B PRO* 3.3 28.2 - - + +
499B THR* 3.2 34.1 + - - +
500B GLN* 3.3 49.4 - - - -
503B VAL* 3.6 22.0 - - + -
530B LEU* 3.6 41.7 - - + -
534B PRO* 5.7 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 493 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B VAL* 2.9 20.3 + - + +
490B LYS* 3.9 4.7 - - - +
492B PHE* 1.3 78.3 - - + +
494B LYS* 1.3 67.3 + - - +
496B PRO* 4.6 3.6 - - - +
530B LEU* 5.2 7.0 - - + -
534B PRO* 3.5 28.7 - - + +
537B ALA* 3.3 37.2 - - + +
538B LYS* 3.6 31.4 - - + +
541B VAL* 3.6 18.8 - - + -
542B LEU* 3.7 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 494 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B GLY 3.7 6.0 + - - +
454B GLU 2.5 31.6 + - - -
455B TYR* 3.9 1.6 - - - +
456B ALA* 3.1 42.5 - - + +
457B GLU* 3.9 28.2 - - + +
490B LYS* 2.9 20.8 + - - +
491B LEU* 3.7 3.8 - - - +
493B LEU* 1.3 79.8 - - - +
495B LYS* 1.3 62.0 + - + +
496B PRO* 3.6 6.2 - - - +
542B LEU* 3.7 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 495 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B ALA 3.9 18.1 + - - -
457B GLU* 5.1 8.6 + - - +
459B ILE 4.5 12.3 + - - -
460B ASP* 4.5 16.0 + - - +
462B ALA 6.0 0.2 - - - +
463B ASP* 5.7 4.6 - - + +
491B LEU* 2.8 38.5 + - + +
492B PHE 3.3 3.6 - - - +
494B LYS* 1.3 74.6 - - + +
496B PRO* 1.3 61.1 - - - +
497B THR* 3.3 13.9 + - - +
498B GLU* 5.0 18.5 + - + +
499B THR* 2.9 30.4 + - + +
----------------------------------------------------------
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