Contacts of the helix formed by residues 457 - 472 (chain D) in PDB entry 2GL7
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 ARG 457 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414D ILE* 5.0 9.6 - - - +
415D ASN* 4.6 12.5 + - - -
418D THR* 4.8 1.0 + - - -
454D ALA* 3.2 17.2 + - - +
455D GLY 3.3 0.8 - - - -
456D ASP* 1.3 79.2 + - - +
458D GLU* 1.3 63.9 + - - +
459D ASP* 2.8 46.0 + - - +
460D ILE* 3.2 42.2 + - + +
461D THR* 3.3 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 458 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456D ASP* 3.0 14.6 + - - +
457D ARG* 1.3 67.2 - - - +
459D ASP* 1.3 64.8 + - - +
460D ILE 3.1 2.5 - - - -
461D THR* 3.4 8.3 - - - -
462D GLU* 3.2 30.0 + - + +
501D PRO* 3.1 11.3 - - - +
502D SER* 4.1 2.5 - - - -
503D HIS* 2.5 55.1 + - - +
505D PRO* 5.5 0.3 - - - +
506D LEU* 3.4 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 459 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418D THR* 3.9 20.0 + - + +
457D ARG* 2.8 49.8 + - - +
458D GLU* 1.3 76.8 + - - +
460D ILE* 1.3 58.3 + - - +
462D GLU* 5.2 0.9 - - - -
463D PRO* 3.2 21.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 460 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414D ILE* 3.3 36.6 - - + -
417D VAL* 4.7 0.4 - - + -
418D THR* 3.3 27.6 - - - +
421D ALA* 4.7 1.9 - - + +
450D THR* 3.9 26.0 - - + -
454D ALA* 3.8 17.0 - - + -
457D ARG* 3.2 46.6 + - + +
458D GLU 3.1 0.4 - - - -
459D ASP* 1.3 78.5 - - - +
461D THR* 1.3 63.7 + - - +
462D GLU 3.3 1.8 - - - -
463D PRO* 3.3 13.9 - - - +
464D ALA* 3.3 14.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 461 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451D VAL* 3.9 21.8 - - + +
454D ALA* 3.5 25.1 - - + -
455D GLY 3.8 16.3 + - - +
456D ASP 5.4 0.2 - - - -
457D ARG 3.3 9.5 + - - +
458D GLU* 3.4 11.3 - - - +
460D ILE* 1.3 76.0 - - - +
462D GLU* 1.3 57.8 + - - +
464D ALA* 4.3 5.8 - - - -
465D ILE* 2.9 37.4 + - - +
497D LEU* 4.3 11.0 - - + -
506D LEU* 3.5 20.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 462 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458D GLU* 3.2 21.6 + - - +
459D ASP* 6.1 0.7 - - - -
461D THR* 1.3 77.8 + - - +
463D PRO* 1.3 64.3 - - + +
465D ILE* 3.8 1.3 - - - +
466D CYS* 2.9 44.0 + - - -
505D PRO* 3.1 31.4 - - - +
506D LEU* 4.2 25.3 + - + +
509D ALA* 5.0 1.1 - - + -
19E ILE* 4.0 25.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 463 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418D THR* 4.6 4.9 - - + +
421D ALA* 3.9 10.1 - - + -
422D GLY* 3.6 30.5 - - - +
425D SER* 3.3 10.5 + - - +
459D ASP 3.2 25.6 - - - +
460D ILE* 3.3 10.8 - - - +
462D GLU* 1.3 99.2 - - + +
464D ALA* 1.3 54.8 + - - +
467D ALA* 3.0 25.3 + - - +
19E ILE* 4.1 19.3 - - + -
21E PHE* 4.9 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 464 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421D ALA* 4.2 5.1 - - + +
447D LEU* 4.1 21.0 - - + +
450D THR* 4.2 19.1 - - + -
451D VAL* 3.8 20.9 - - + +
460D ILE 3.3 17.4 + - - +
461D THR* 3.9 1.1 - - - +
462D GLU 3.3 0.4 - - - -
463D PRO* 1.3 78.0 - - - +
465D ILE* 1.3 57.0 + - - +
467D ALA* 3.4 3.8 + - - +
468D LEU* 3.1 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 465 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451D VAL* 3.9 18.2 - - + -
461D THR 2.9 26.2 + - - +
462D GLU 3.9 2.2 - - - +
464D ALA* 1.3 73.2 - - - +
466D CYS* 1.3 62.2 + - - +
468D LEU* 3.3 7.8 + - + +
469D ARG* 2.9 26.9 + - - +
494D VAL* 4.2 13.7 - - + -
497D LEU* 3.9 29.6 - - + -
506D LEU* 4.4 2.9 - - + -
509D ALA* 3.8 10.1 - - + +
510D THR* 3.7 37.9 - - - +
513D LEU* 3.9 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 466 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425D SER* 3.2 17.9 - - - +
462D GLU* 2.9 30.8 + - - +
463D PRO* 3.7 2.0 - - + +
465D ILE* 1.3 77.3 - - - +
467D ALA* 1.3 59.7 + - - +
469D ARG* 3.1 33.4 - - - +
470D HIS* 2.9 31.1 + - + -
509D ALA* 3.5 19.7 - - - -
17E GLU 5.5 0.2 - - - +
19E ILE* 4.0 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 467 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421D ALA 4.5 1.3 - - - +
424D LEU* 4.5 3.4 - - + -
425D SER* 3.5 27.3 + - - +
428D THR* 4.2 9.3 + - + +
447D LEU* 3.9 21.8 - - + -
463D PRO 3.0 16.8 + - - +
464D ALA 3.7 5.2 - - - +
465D ILE 3.2 0.2 - - - -
466D CYS* 1.3 72.7 - - - +
468D LEU* 1.3 64.3 + - - +
470D HIS* 3.2 3.7 + - - +
471D LEU* 3.0 30.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 468 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444D ILE* 3.7 34.3 - - + +
447D LEU* 3.8 39.5 - - + +
448D VAL* 4.3 10.3 - - + +
451D VAL* 4.4 11.9 - - + -
464D ALA 3.1 20.1 + - - +
465D ILE* 3.6 15.3 - - + +
467D ALA* 1.3 71.9 - - - +
469D ARG* 1.3 64.4 + - - +
471D LEU* 3.3 4.1 + - - +
472D THR* 2.9 32.2 + - - +
485D VAL* 4.2 13.0 - - + -
494D VAL* 5.6 3.1 - - + -
513D LEU* 3.8 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 469 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465D ILE 2.9 13.6 + - - +
466D CYS* 3.1 33.8 + - - +
468D LEU* 1.3 76.2 - - - +
470D HIS* 1.3 86.7 + - - +
472D THR* 2.9 19.8 + - - -
473D SER* 3.0 13.9 + - - -
508D LYS* 4.7 10.5 + - - +
509D ALA* 3.7 26.2 - - - +
512D GLY* 4.2 24.6 - - - -
513D LEU* 3.8 13.2 - - + +
516D ASN* 3.0 13.4 - - - +
14E ALA* 4.3 4.9 - - + +
15E ASN 4.0 20.5 + - - -
16E ASP* 4.7 3.6 - - - +
17E GLU* 3.7 27.0 + - - +
19E ILE* 5.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 470 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425D SER* 2.8 33.0 + - - -
428D THR* 3.2 26.5 - - - +
429D CYS* 3.2 17.1 - - - +
435D LYS* 2.8 28.9 + - - +
466D CYS* 2.9 21.9 + - + -
467D ALA 3.2 5.6 + - - +
469D ARG* 1.3 104.9 + - - +
471D LEU* 1.3 60.8 + - - +
472D THR 3.2 0.7 + - - -
473D SER* 3.3 7.4 + - - +
16E ASP* 3.5 20.4 + - - -
17E GLU 3.3 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 471 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428D THR* 4.0 13.2 - - + -
435D LYS* 3.4 39.9 - - + +
438D VAL* 3.7 24.9 - - + -
439D CYS* 3.8 6.7 - - - -
443D GLY 4.9 1.3 - - - -
444D ILE* 4.0 23.6 - - + -
447D LEU* 3.6 31.2 - - + -
467D ALA* 3.0 17.0 + - + +
468D LEU* 3.3 4.7 + - - +
469D ARG 3.3 0.2 - - - -
470D HIS* 1.3 76.6 - - - +
472D THR* 1.3 57.4 + - - +
473D SER 3.4 1.8 - - - -
475D HIS* 2.8 24.2 + - - -
478D ALA* 4.1 0.2 - - - -
481D ALA* 3.3 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 472 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444D ILE* 4.8 2.0 - - + -
468D LEU 2.9 18.6 + - - +
469D ARG 2.9 10.7 + - - -
470D HIS 3.2 0.6 - - - -
471D LEU* 1.3 82.0 - - - +
473D SER* 1.3 58.4 + - - +
478D ALA* 4.1 8.7 - - - -
481D ALA* 4.1 25.8 - - + +
482D GLN* 2.9 30.1 - - - +
485D VAL* 4.3 6.1 - - + -
513D LEU* 3.6 14.7 - - + +
516D ASN* 3.3 25.4 - - - +
517D LEU* 4.2 9.9 - - + -
519D LEU* 4.5 1.6 - - - +
----------------------------------------------------------
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