Contacts of the helix formed by residues 448 - 463 (chain P) in PDB entry 5G04
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 GLN 448 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527J ILE* 4.4 14.5 + - - +
416P PHE* 6.0 1.4 - - - -
443P TYR* 3.0 23.8 + - + +
446P LEU* 3.5 31.4 - - + +
447P ASN* 1.3 77.5 - - - +
449P LEU* 1.3 62.6 + - - +
450P VAL* 3.6 4.5 - - + -
451P GLU* 3.2 38.1 - - + +
452P ALA 3.5 13.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 449 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444P GLU* 4.0 29.6 - - + +
447P ASN* 3.4 27.2 + - - +
448P GLN* 1.3 69.9 - - - +
450P VAL* 1.3 60.7 + - - +
452P ALA* 3.1 3.8 + - - +
453P LYS* 2.8 35.7 + - - +
476P LEU* 3.9 25.6 - - + -
479P GLN* 5.0 16.4 - - + +
480P LEU* 3.9 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 450 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448P GLN* 5.0 0.9 - - - -
449P LEU* 1.3 77.2 - - - +
451P GLU* 1.3 78.1 + - + +
453P LYS* 3.6 19.3 + - - +
454P LYS* 3.3 51.3 + - + +
480P LEU* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 451 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527J ILE 5.7 0.7 - - - +
530J SER 5.5 2.6 - - - +
531J GLU 5.7 2.6 - - - +
443P TYR* 3.8 29.6 + - + -
448P GLN* 3.2 43.2 - - + +
449P LEU 3.3 0.2 - - - -
450P VAL* 1.3 85.7 - - + +
452P ALA* 1.3 63.5 + - - +
454P LYS* 3.4 17.2 + - - +
455P CYS* 3.1 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 452 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440P GLY* 3.6 26.2 - - - +
443P TYR* 3.6 16.5 - - + +
444P GLU 4.0 4.3 - - - +
448P GLN 3.5 4.3 + - - +
449P LEU 3.1 8.2 + - - +
451P GLU* 1.3 75.2 - - - +
453P LYS* 1.3 60.2 + - - +
455P CYS* 3.1 8.2 + - - +
456P TYR* 2.9 38.2 + - + -
476P LEU* 3.8 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 453 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449P LEU* 2.8 19.7 + - + +
450P VAL* 3.8 19.2 - - - +
452P ALA* 1.3 76.9 - - - +
454P LYS* 1.3 58.7 + - + +
456P TYR* 3.3 3.7 + - - -
457P TRP* 2.9 30.0 + - - +
473P LEU* 3.6 18.6 - - + +
476P LEU* 4.1 24.0 - - + -
477P HIS* 3.9 35.8 + - + +
480P LEU* 3.7 35.5 - - + +
482P GLU* 5.3 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 454 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533J TYR 4.8 8.5 - - - +
450P VAL* 3.3 35.7 + - - +
451P GLU* 3.7 15.4 + - - +
452P ALA 3.3 0.2 - - - -
453P LYS* 1.3 79.4 - - + +
455P CYS* 1.3 52.7 + - - +
457P TRP* 3.4 10.7 + - + +
458P ARG* 2.9 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 455 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532J ALA 3.8 22.9 - - - -
533J TYR 4.7 2.9 + - - -
436P LEU* 3.9 34.6 - - - +
439P LEU* 3.9 26.9 - - - -
440P GLY 4.5 4.0 - - - +
443P TYR* 4.9 6.3 - - + -
451P GLU 3.1 12.9 + - - +
452P ALA* 3.1 12.9 + - - +
454P LYS* 1.3 73.4 - - - +
456P TYR* 1.3 60.0 + - - +
458P ARG* 3.3 8.3 + - - +
459P ALA* 2.8 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 456 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437P VAL* 3.5 32.5 - - + -
440P GLY* 3.0 20.0 + - - -
441P GLU* 3.0 18.7 + - - -
444P GLU* 3.8 3.3 + - - -
452P ALA* 2.9 27.3 + - + -
453P LYS* 3.6 6.7 - - - +
455P CYS* 1.3 75.2 - - - +
457P TRP* 1.3 57.2 + - - +
459P ALA* 3.2 7.8 - - - +
460P TYR* 3.0 26.5 + - - +
469P ALA* 4.0 22.5 - - + +
472P LYS* 3.0 42.9 + - + +
473P LEU* 3.7 31.8 - - + +
476P LEU* 3.7 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 457 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453P LYS 2.9 18.4 + - - +
454P LYS* 3.5 10.3 - - + +
456P TYR* 1.3 74.1 - - - +
458P ARG* 1.3 58.0 + - - +
460P TYR* 3.4 32.1 + + + -
461P ALA* 3.1 27.3 + - + +
470P LEU* 4.7 4.5 - - + -
473P LEU* 3.7 26.2 - - + +
489P CYS* 5.7 3.4 - - - -
492P LYS* 3.6 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 458 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533J TYR* 3.4 51.5 - - - +
426P HIS* 3.4 26.1 + - - -
430P PRO* 3.4 22.0 + - - +
436P LEU* 3.6 17.0 - - + +
454P LYS 2.9 17.1 + - - +
455P CYS* 3.3 6.0 + - - +
457P TRP* 1.3 73.2 - - - +
459P ALA* 1.3 55.3 + - - +
461P ALA* 3.2 9.8 + - + +
462P VAL* 2.8 45.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 459 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433P SER 4.3 2.2 - - - +
436P LEU* 3.8 17.9 - - + +
437P VAL* 4.1 10.3 - - + +
455P CYS 2.8 13.6 + - - +
456P TYR* 3.2 14.6 + - - +
458P ARG* 1.3 75.6 - - - +
460P TYR* 1.3 61.2 + - - +
462P VAL* 3.4 11.2 + - - +
463P GLY 3.2 17.7 + - - -
464P ASP* 2.9 22.7 - - - +
469P ALA* 3.8 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 460 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456P TYR 3.0 13.2 + - - +
457P TRP* 3.6 37.5 - + + +
458P ARG 3.3 0.2 - - - -
459P ALA* 1.3 76.5 - - - +
461P ALA* 1.3 65.9 + - - +
462P VAL 3.5 0.3 + - - -
463P GLY 3.7 12.4 + - - +
464P ASP* 3.3 21.2 + - + +
469P ALA* 5.2 0.9 - - + -
470P LEU* 3.4 41.7 - - + +
473P LEU* 5.8 0.2 - - + -
492P LYS* 4.4 27.7 + - + +
496P ASP* 5.3 8.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 461 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457P TRP* 3.1 18.7 + - + +
458P ARG* 3.2 14.6 + - + +
460P TYR* 1.3 80.0 - - - +
462P VAL* 1.3 62.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 462 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430P PRO 3.9 8.1 - - - +
431P ASN* 3.8 38.1 - - + +
432P ASP 4.4 0.4 - - - -
433P SER* 4.0 16.4 - - - +
436P LEU* 3.6 20.9 - - + -
458P ARG* 2.8 27.4 + - + +
459P ALA* 3.4 11.2 - - - +
461P ALA* 1.3 76.6 - - - +
463P GLY* 1.3 60.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 463 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431P ASN 5.5 1.6 - - - -
433P SER* 4.6 2.0 - - - -
459P ALA 3.2 6.8 + - - -
460P TYR* 3.7 10.1 + - - +
461P ALA 3.6 1.0 - - - -
462P VAL* 1.3 82.1 - - - +
464P ASP* 1.3 70.9 + - - +
465P VAL* 6.0 0.9 - - - -
----------------------------------------------------------
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