Contacts of the helix formed by residues 448 - 473 (chain B) in PDB entry 3RC0
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 448 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B GLU* 4.6 5.7 + - - -
446B LYS 3.7 1.2 + - - -
447B LEU* 1.3 75.5 - - - +
449B TRP* 1.3 66.1 + - - +
450B ARG* 3.8 7.3 + - - +
451B GLU* 2.8 40.9 + - - +
452B GLN* 2.9 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 449 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B GLU* 3.0 24.0 + - - -
447B LEU 3.9 0.2 + - - -
448B SER* 1.3 73.3 - - - +
450B ARG* 1.3 58.5 + - + +
452B GLN* 3.1 22.1 + - - +
453B GLN* 3.0 47.5 + - + +
474B EDO 3.5 37.0 - - - -
477B EDO 3.2 38.6 - - - -
479B EDO 3.3 27.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 450 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B PHE* 4.5 6.7 + - - +
159B TRP* 3.4 45.3 - - + +
160B PRO* 3.4 17.2 - - - +
163B GLU* 2.9 34.3 + - - +
167B LEU* 3.9 9.9 - - + -
448B SER* 3.3 4.7 + - - +
449B TRP* 1.3 76.3 - - + +
451B GLU* 1.3 58.2 + - - +
453B GLN* 3.4 10.0 + - - +
454B ALA* 2.9 30.8 + - - +
479B EDO 2.8 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 451 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B GLU* 5.1 2.3 - - - +
167B LEU* 3.9 31.8 - - + +
447B LEU* 3.5 26.7 - - + +
448B SER* 2.8 39.6 + - - +
450B ARG* 1.3 76.5 - - - +
452B GLN* 1.3 59.6 + - - +
454B ALA* 3.9 2.2 - - - +
455B LEU* 2.9 30.7 + - - +
458B ARG* 4.9 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 452 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B TYR* 3.3 44.1 + - + +
445B ALA* 3.6 14.1 + - - +
447B LEU* 3.2 23.6 + - + -
448B SER 2.9 16.3 + - - +
449B TRP* 3.4 24.4 - - - +
451B GLU* 1.3 74.9 - - - +
453B GLN* 1.3 65.6 + - - +
455B LEU* 3.3 6.8 + - - +
456B GLN* 3.0 26.9 + - - +
474B EDO 3.0 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 453 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B GLU* 3.8 2.0 + - - -
159B TRP* 3.7 10.0 - - - -
294B ILE* 3.9 16.9 - - + +
298B GLY 3.2 25.9 + - - +
299B PHE* 3.9 11.3 - - - +
300B VAL* 3.8 21.0 - - + +
449B TRP* 3.0 49.7 + - + +
450B ARG* 3.7 7.1 - - - +
452B GLN* 1.3 74.1 - - - +
454B ALA* 1.3 64.2 + - - +
456B GLN* 3.2 5.0 + - - +
457B VAL* 3.1 26.2 + - - +
474B EDO 4.0 3.1 - - - -
477B EDO 4.8 0.4 + - - -
479B EDO 2.7 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 454 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B TRP* 4.6 1.8 - - + -
167B LEU* 3.6 35.0 - - + +
168B LEU* 3.8 17.9 - - + -
294B ILE* 4.7 1.5 - - - +
450B ARG 2.9 18.8 + - - +
451B GLU* 3.9 3.1 - - - +
453B GLN* 1.3 76.0 - - - +
455B LEU* 1.3 62.8 + - - +
457B VAL* 3.0 4.9 + - - +
458B ARG* 3.0 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 455 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B ASP* 3.1 49.1 - - + +
437B LEU* 3.5 28.7 - - + -
438B LEU* 4.3 8.3 - - + +
444B TYR* 3.8 23.1 - - + -
447B LEU* 3.7 18.4 - - + -
451B GLU 2.9 19.6 + - - +
452B GLN 3.5 4.5 - - - +
454B ALA* 1.3 76.3 - - - +
456B GLN* 1.3 56.8 + - - +
458B ARG* 3.3 14.6 + - - +
459B TYR* 2.8 38.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 456 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ASN* 4.0 14.6 + - - +
300B VAL* 3.8 14.8 - - + -
301B GLU 4.1 1.1 - - - +
302B PRO* 3.4 23.4 - - - +
303B TYR* 3.0 29.7 + - - +
438B LEU* 3.8 18.5 - - - +
444B TYR* 2.9 29.3 + - + +
452B GLN 3.0 18.8 + - - +
453B GLN 3.2 8.7 + - - +
455B LEU* 1.3 76.6 - - - +
457B VAL* 1.3 62.1 + - - +
459B TYR* 4.1 3.6 - - - +
460B GLY* 3.3 17.7 + - - -
474B EDO 3.9 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 457 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LEU* 4.2 8.1 - - + -
171B THR* 3.7 27.8 - - + +
173B VAL* 4.9 0.9 - - + -
290B ASN* 4.2 11.5 - - + +
291B TRP* 4.0 23.8 - - + +
294B ILE* 4.1 18.4 - - + -
300B VAL* 3.6 21.3 - - + -
309B ASP* 5.0 1.0 - - - +
453B GLN 3.1 16.5 + - - +
454B ALA 3.0 7.7 + - - +
456B GLN* 1.3 76.6 - - - +
458B ARG* 1.3 65.7 + - - +
460B GLY* 3.5 1.0 + - - -
461B GLN* 3.4 23.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 458 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B CYS 5.7 0.7 - - - -
167B LEU* 2.9 36.9 + - - +
169B GLN 4.7 9.4 - - - +
171B THR* 3.8 22.9 - - + -
427B TYR* 4.7 7.6 - - + -
428B ALA* 6.1 3.4 - - - +
429B THR* 5.2 1.6 + - - -
434B ASP* 3.0 38.0 + - - +
437B LEU* 4.4 7.5 - - - +
451B GLU 4.9 1.6 + - - -
454B ALA* 3.0 31.4 + - - +
455B LEU* 3.5 23.2 - - - +
457B VAL* 1.3 73.9 - - - +
459B TYR* 1.3 58.8 + - - +
461B GLN* 3.2 6.1 + - - +
462B LYS* 2.9 46.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 459 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B TYR* 3.5 38.8 - + + -
431B LEU* 3.9 15.3 - - + -
434B ASP* 4.2 8.2 + - + -
435B GLN* 2.6 56.5 + - - -
438B LEU* 3.4 32.1 - - + -
455B LEU* 2.8 28.0 + - + +
456B GLN* 4.1 4.0 - - - +
458B ARG* 1.3 73.8 - - - +
460B GLY* 1.3 58.9 + - - +
462B LYS* 3.9 4.4 - - - +
463B MET* 2.9 66.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 460 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ASN* 5.8 0.2 - - - -
303B TYR* 4.6 10.9 - - - -
309B ASP* 3.5 22.4 - - - +
456B GLN 3.3 13.5 + - - -
457B VAL 4.1 0.2 - - - -
459B TYR* 1.3 85.0 - - - +
461B GLN* 1.3 59.8 + - - +
463B MET* 3.8 5.1 - - - +
464B ILE* 3.3 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 461 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B GLY 3.7 0.2 - - - +
171B THR* 3.1 42.8 + - - +
291B TRP* 3.6 28.7 - - - +
309B ASP* 5.3 2.7 - - - +
310B THR 3.6 17.0 + - - +
311B ALA* 3.6 15.0 - - + +
312B ASP 5.5 2.1 - - - +
427B TYR* 2.5 35.7 + - - +
457B VAL* 3.4 14.6 + - + +
458B ARG 3.2 7.5 + - - +
459B TYR 3.2 0.4 - - - -
460B GLY* 1.3 75.0 - - - +
462B LYS* 1.3 65.2 + - - +
464B ILE* 3.2 5.4 + - - +
465B LEU* 3.1 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 462 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B LEU* 4.1 22.7 - - + -
427B TYR* 3.7 33.7 - - + +
429B THR* 2.9 40.1 + - - +
430B ASP 3.4 3.8 + - - -
431B LEU* 3.7 37.7 - - + +
434B ASP* 2.5 29.7 + - - +
458B ARG* 2.9 25.2 + - - +
459B TYR 3.9 0.4 - - - +
461B GLN* 1.3 76.6 - - - +
463B MET* 1.3 56.4 + - - +
465B LEU* 3.1 2.2 + - - -
466B HIS* 2.8 36.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 463 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B TYR* 3.2 32.8 - - + +
431B LEU* 3.9 22.2 - - + -
435B GLN* 4.3 4.9 - - - +
459B TYR* 2.9 60.7 + - + +
460B GLY 3.8 4.9 - - - +
462B LYS* 1.3 77.7 - - - +
464B ILE* 1.3 63.1 + - + +
466B HIS* 3.5 1.8 + - - +
467B GLN* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 464 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B ASP* 3.6 6.7 - - + +
310B THR* 3.5 35.9 - - - +
311B ALA* 4.2 5.8 - - + -
356B ILE* 3.6 25.5 - - + +
357B GLY 3.6 18.8 - - - +
358B ARG* 3.6 35.7 - - + +
460B GLY 3.3 15.0 + - - +
461B GLN 3.2 7.5 + - - +
463B MET* 1.3 76.7 - - + +
465B LEU* 1.3 65.0 + - - +
467B GLN* 3.2 11.8 + - - +
468B LEU* 3.0 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 465 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ALA* 3.8 18.8 - - + -
312B ASP 4.7 0.7 - - - +
313B ILE* 4.1 28.3 - - + -
356B ILE* 5.0 4.5 - - + -
420B VAL* 3.4 25.5 - - + +
423B THR* 3.7 24.7 - - + -
424B LEU* 3.9 17.9 - - + -
427B TYR* 4.0 25.6 - - + +
461B GLN 3.1 18.6 + - - +
462B LYS 3.6 5.4 - - - +
464B ILE* 1.3 76.8 - - - +
466B HIS* 1.3 56.7 + - - +
468B LEU* 2.9 11.7 + - + +
469B LEU 2.9 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 466 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B LEU* 3.4 33.9 - - + +
430B ASP* 5.6 3.2 - - + +
431B LEU* 3.5 46.9 + - + +
462B LYS 2.8 28.8 + - - +
463B MET 4.1 2.9 - - - +
465B LEU* 1.3 69.5 - - - +
467B GLN* 1.3 65.1 + - - +
469B LEU* 3.3 19.0 + - + +
470B GLU* 3.0 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 467 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B GLY 4.8 2.4 + - - -
358B ARG* 2.8 33.2 + - - +
402B ILE* 3.7 23.4 - - + +
463B MET 3.1 14.5 + - - +
464B ILE* 3.4 13.0 + - - +
465B LEU 3.2 0.2 - - - -
466B HIS* 1.3 76.9 - - - +
468B LEU* 1.3 63.2 + - - +
470B GLU* 3.4 17.5 + - - +
471B LEU* 3.1 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 468 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ILE* 4.0 16.4 - - + -
356B ILE* 4.2 29.2 - - + -
361B VAL* 5.5 2.2 - - + -
405B ILE* 3.7 29.8 - - + -
416B LEU* 4.3 20.9 - - + -
420B VAL* 3.5 25.8 - - + -
464B ILE 3.0 11.5 + - - +
465B LEU* 2.9 14.7 + - + +
467B GLN* 1.3 78.5 - - - +
469B LEU* 1.3 61.3 + - - +
471B LEU* 3.2 8.3 + - + +
472B THR* 3.0 32.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 469 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B GLN* 3.6 42.0 - - + +
420B VAL* 3.8 13.0 - - + -
421B LEU* 3.9 21.8 - - + -
424B LEU* 3.5 29.8 - - + -
465B LEU 2.9 7.7 + - - +
466B HIS* 3.3 26.5 - - + +
468B LEU* 1.3 75.4 - - - +
470B GLU* 1.3 58.0 + - + +
472B THR* 3.2 5.2 + - - -
473B SER* 2.7 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 470 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B HIS* 3.0 19.9 + - + +
467B GLN* 3.6 18.7 - - - +
468B LEU 3.3 0.2 - - - -
469B LEU* 1.3 77.7 - - + +
471B LEU* 1.3 63.8 + - + +
473B SER* 3.3 21.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 471 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B ILE* 3.8 51.1 - - + +
405B ILE* 3.9 26.6 - - + +
406B PRO* 3.7 37.6 - - + +
413B ARG* 4.3 1.6 - - - -
467B GLN* 3.1 32.8 + - + +
468B LEU* 3.2 10.3 + - + +
470B GLU* 1.3 80.4 - - + +
472B THR* 1.3 60.6 + - - +
473B SER 3.2 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 472 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B ILE* 3.7 21.3 - - + -
413B ARG* 3.6 45.4 + - - +
416B LEU* 4.0 27.6 - - + -
417B GLN* 3.3 27.6 + - - +
420B VAL* 5.6 0.4 - - + +
468B LEU* 3.0 19.7 + - + +
469B LEU* 3.2 8.7 + - - -
471B LEU* 1.3 74.6 - - - +
473B SER* 1.3 64.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 473 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B ARG* 4.2 12.7 + - - -
417B GLN* 3.5 21.5 + - - +
469B LEU* 2.7 24.1 + - - +
470B GLU* 3.5 16.9 - - - -
471B LEU 3.2 4.3 - - - -
472B THR* 1.3 82.5 - - - +
----------------------------------------------------------
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