Contacts of the helix formed by residues 437 - 452 (chain Z) in PDB entry 5GJQ
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 GLU 437 (chain Z).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434Z TYR* 5.3 0.3 - - - -
435Z SER 3.8 1.9 + - - +
436Z SER* 1.3 85.2 - - - +
438Z ASP* 1.3 53.8 + - - +
439Z TYR* 4.0 9.0 - - + +
440Z ILE* 3.0 18.8 + - + +
441Z LYS* 2.3 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 438 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437Z GLU* 1.3 71.1 - - - +
439Z TYR* 1.3 51.1 + - - +
441Z LYS* 3.1 10.8 - - - +
442Z SER* 2.2 39.0 + - - -
474Z SER* 5.9 2.2 - - - -
475Z ASN* 5.6 1.8 - - + +
476Z THR* 3.5 15.6 - - - +
477Z MET* 3.5 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 439 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404Z ASP* 3.0 36.3 - - - +
405Z HIS* 4.4 3.6 - - + +
407Z MET* 4.7 1.3 - - + -
408Z LEU* 3.4 10.8 - - - +
437Z GLU* 3.2 7.1 - - + +
438Z ASP* 1.3 76.2 - - - +
440Z ILE* 1.3 63.5 + - - +
442Z SER* 3.0 12.0 + - - -
443Z GLY 2.9 17.8 + - - -
476Z THR* 3.4 11.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 440 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407Z MET* 4.7 12.6 - - + +
408Z LEU 5.1 0.4 - - - +
411Z ALA* 5.1 0.5 - - - +
432Z TYR* 2.9 25.1 - - + +
435Z SER* 4.2 13.5 - - - +
436Z SER* 4.3 3.4 - - - +
437Z GLU* 3.0 29.4 + - + +
439Z TYR* 1.3 76.4 - - - +
441Z LYS* 1.3 63.5 + - - +
443Z GLY* 2.9 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 441 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432Z TYR 3.9 0.4 + - - -
433Z LEU* 3.0 27.3 - - - +
434Z TYR* 4.5 5.7 - - + +
437Z GLU 2.3 28.7 + - - +
438Z ASP* 3.1 14.8 - - - +
440Z ILE* 1.3 67.0 - - - +
442Z SER* 1.3 63.4 + - - +
443Z GLY 2.9 1.4 + - - -
444Z ALA 3.5 2.3 + - - -
445Z LEU* 3.4 18.3 + - - +
477Z MET* 4.9 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 442 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405Z HIS* 6.3 0.7 - - - -
408Z LEU* 3.9 10.9 - - - +
438Z ASP 2.2 29.7 + - - -
439Z TYR* 3.0 15.2 + - - -
441Z LYS* 1.3 67.3 - - - +
443Z GLY* 1.3 62.8 + - - +
445Z LEU* 3.4 9.3 - - - +
446Z LEU* 3.0 25.3 + - - +
476Z THR* 3.2 24.5 - - - -
477Z MET* 4.9 1.5 - - - +
479Z LEU* 5.4 0.7 - - - -
480Z GLY* 4.3 8.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 443 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408Z LEU* 3.3 25.8 - - - -
411Z ALA* 3.3 16.8 - - - -
412Z ALA* 3.5 7.3 + - - +
439Z TYR 2.9 4.6 + - - -
440Z ILE 2.9 12.2 + - - -
441Z LYS 2.9 0.2 + - - -
442Z SER* 1.3 77.5 - - - +
444Z ALA* 1.3 56.8 + - - -
447Z ALA* 2.8 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 444 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411Z ALA* 4.0 3.7 - - - +
429Z ILE* 3.1 44.6 - - + +
432Z TYR* 4.5 0.4 - - + -
433Z LEU* 3.4 20.5 - - + +
440Z ILE 4.0 2.6 + - - -
441Z LYS 3.5 2.4 + - - -
443Z GLY* 1.3 72.3 - - - +
445Z LEU* 1.3 60.4 + - - +
447Z ALA* 2.7 9.4 + - - -
448Z CYS* 2.2 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 445 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441Z LYS 3.4 12.9 + - - +
442Z SER* 3.3 12.5 + - - +
444Z ALA* 1.3 78.8 - - - +
446Z LEU* 1.3 63.9 + - - +
448Z CYS* 4.2 3.3 - - - +
449Z GLY 3.3 6.6 + - - -
466Z LEU* 5.4 5.2 - - - +
469Z TYR* 6.1 6.5 - - + -
477Z MET 4.7 1.1 - - - +
480Z GLY 3.3 3.8 - - - -
481Z SER* 3.4 33.4 - - - +
484Z GLY* 3.1 17.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 446 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408Z LEU* 5.8 0.4 - - + -
412Z ALA* 3.9 15.0 - - + -
442Z SER 3.0 15.3 + - - +
443Z GLY 3.9 2.2 - - - +
445Z LEU* 1.3 74.3 - - - +
447Z ALA* 1.3 59.3 + - - +
448Z CYS 3.1 0.7 + - - -
449Z GLY* 3.1 4.7 + - - -
450Z ILE* 2.8 26.7 + - - +
480Z GLY* 3.1 15.2 + - - +
483Z PHE* 4.3 11.9 - - + -
484Z GLY* 4.0 5.8 - - - +
816Z TYR* 4.9 14.6 - - + +
819Z TYR* 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 447 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411Z ALA 3.4 10.5 - - - +
412Z ALA* 3.2 24.2 - - - +
415Z GLY* 3.3 17.2 - - - +
429Z ILE* 5.1 7.4 - - + -
443Z GLY 2.8 20.9 + - - +
444Z ALA* 2.7 14.4 + - - +
446Z LEU* 1.3 73.0 - - - +
448Z CYS* 1.3 56.6 + - - +
450Z ILE* 3.0 11.0 - - - +
451Z VAL* 2.8 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 448 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429Z ILE* 4.9 12.1 - - + -
444Z ALA* 2.2 34.4 + - + +
445Z LEU* 4.2 3.1 - - - +
447Z ALA* 1.3 64.3 - - - +
449Z GLY* 1.3 60.5 - - - +
450Z ILE 2.9 1.3 - - - -
451Z VAL* 2.8 31.8 + - + +
452Z ASN 3.4 4.2 + - - -
462Z ALA* 4.6 9.0 - - + +
463Z LEU* 4.4 10.4 + - - -
466Z LEU* 4.4 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 449 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445Z LEU 3.3 5.7 + - - -
446Z LEU 3.1 7.7 + - - -
448Z CYS* 1.3 76.6 - - - +
450Z ILE* 1.3 55.8 + - - +
452Z ASN 3.8 1.2 - - - -
453Z SER* 2.9 28.0 + - - -
463Z LEU* 5.4 4.2 - - - +
466Z LEU* 5.1 2.8 - - - +
484Z GLY* 3.7 26.5 - - - -
487Z LEU* 4.4 12.4 - - - +
488Z ALA* 4.4 9.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 450 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412Z ALA* 4.5 3.6 - - + +
415Z GLY 3.9 15.5 - - - -
416Z MET* 4.2 5.8 - - - +
419Z LEU* 3.7 14.9 - - + +
420Z TRP 4.3 0.3 + - - -
446Z LEU 2.8 12.8 + - - +
447Z ALA* 3.0 18.4 - - - +
448Z CYS 2.9 0.2 - - - -
449Z GLY* 1.3 76.3 - - - +
451Z VAL* 1.3 65.9 + - - +
453Z SER* 3.1 21.5 + - - +
819Z TYR* 5.8 7.0 - - + -
822Z VAL* 5.6 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 451 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415Z GLY 4.3 3.4 - - - -
418Z LEU* 3.7 20.0 - - + +
420Z TRP* 3.0 29.5 + - - -
421Z ASP 4.9 0.5 + - - -
447Z ALA 2.8 13.4 + - - +
448Z CYS* 2.8 19.1 + - - +
450Z ILE* 1.3 72.7 - - - +
452Z ASN* 1.3 58.4 + - - +
462Z ALA* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 452 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420Z TRP* 5.8 0.4 - - - +
448Z CYS 3.4 3.4 + - - -
449Z GLY 3.8 1.8 - - - -
451Z VAL* 1.3 77.9 - - + +
453Z SER* 1.3 65.4 + - - +
455Z VAL* 3.2 27.4 + - + +
456Z ARG 4.2 10.8 - - - +
457Z ASN* 4.6 10.3 - - - -
462Z ALA* 5.1 3.1 - - + +
463Z LEU* 3.3 37.2 - - + +
487Z LEU 5.4 1.1 - - - +
----------------------------------------------------------
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