Contacts of the helix formed by residues 443 - 457 (chain B) in PDB entry 5C16
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 ASP 443 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B ILE* 4.2 14.5 - - + +
438B SER* 4.7 1.0 + - - +
441B GLY 3.8 0.4 - - - -
442B TRP* 1.3 94.7 + - - +
444B ARG* 1.3 74.9 + - + +
445B THR 3.1 0.4 - - - +
446B ALA* 2.9 15.1 + - - +
447B GLN* 3.0 14.2 + - - +
479B HIS* 3.2 16.6 + - - -
480B ARG 5.5 0.2 + - - -
484B ARG* 2.8 45.7 + - - -
500B ILE* 3.9 23.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ALA* 3.9 16.8 - - + -
343B ARG* 3.6 28.3 - - - +
344B GLN* 5.7 0.8 + - - -
347B VAL* 4.8 8.5 - - - +
374B ILE* 3.3 44.6 + - + -
375B HIS 3.5 25.0 + - - +
376B ASN* 4.0 13.0 - - - +
377B ILE* 5.8 4.6 - - + +
380B MET* 6.3 0.2 - - + -
438B SER* 3.9 9.1 + - - -
439B SER* 3.7 24.7 + - - +
443B ASP* 1.3 82.7 - - + +
445B THR* 1.3 56.8 + - - +
447B GLN* 3.3 16.2 + - - +
448B LEU* 3.0 36.9 + - + +
500B ILE* 5.7 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ARG* 3.7 40.6 - - + +
305B CYS 4.3 2.7 - - - +
342B ALA* 5.4 0.2 - - - -
436B VAL* 4.1 15.7 - - + +
437B HIS* 3.4 5.0 - - - -
438B SER* 2.8 39.0 + - - -
441B GLY* 3.3 18.5 - - - +
443B ASP 3.1 0.6 - - - -
444B ARG* 1.3 78.6 - - - +
446B ALA* 1.3 57.6 + - - +
448B LEU* 3.5 1.0 + - - +
449B THR* 3.0 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ARG* 4.2 10.4 - - - +
442B TRP 3.9 16.2 - - - +
443B ASP 2.9 10.2 + - - +
445B THR* 1.3 75.7 - - - +
447B GLN* 1.3 58.0 + - - +
449B THR* 3.6 5.6 + - - -
450B SER* 2.8 37.1 + - - -
473B GLU* 3.8 19.6 - - - +
474B TRP* 3.8 24.6 + - + -
479B HIS* 5.0 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ILE* 4.7 1.6 - - - +
416B LEU* 3.3 29.9 - - + +
443B ASP 3.0 10.1 + - - +
444B ARG* 3.6 25.9 - - - +
446B ALA* 1.3 75.1 - - - +
448B LEU* 1.3 63.6 + - - +
450B SER* 3.5 1.4 + - - -
451B LEU* 3.2 33.8 + - + +
474B TRP* 3.5 25.8 - - + -
500B ILE* 2.9 37.4 + - + +
503B GLN* 2.9 30.6 + - - +
504B PHE* 4.1 6.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 448 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ALA* 3.5 32.3 - - + -
372B LEU* 3.7 20.2 - - + -
374B ILE* 4.6 9.6 - - + -
416B LEU* 3.9 23.8 - - + +
419B GLY* 3.8 12.6 - - - -
420B ALA* 3.7 30.0 - - - +
423B ILE* 3.8 11.6 - - + +
436B VAL* 4.4 12.1 - - + -
444B ARG 3.0 17.3 + - - +
445B THR 4.0 2.2 - - - +
447B GLN* 1.3 76.2 - - - +
449B THR* 1.3 66.5 + - - +
451B LEU* 3.5 0.5 + - - -
452B ALA* 3.1 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 449 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B SER* 4.4 4.0 - - - +
302B ILE* 4.2 14.5 - - + +
304B ARG* 4.0 22.1 + - + -
423B ILE* 5.4 0.7 - - - -
436B VAL* 3.9 31.6 - - + -
445B THR* 3.0 23.6 + - + +
446B ALA 3.6 3.6 + - - -
448B LEU* 1.3 76.1 - - - +
450B SER* 1.3 61.0 + - - +
452B ALA* 3.4 4.5 + - - +
453B MET* 2.8 38.9 + - - +
473B GLU* 2.8 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 450 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B ALA 2.8 20.7 + - - -
447B GLN 3.5 0.3 + - - -
449B THR* 1.3 79.9 + - - +
451B LEU* 1.3 59.1 + - - +
453B MET* 3.4 7.0 + - - +
454B LEU* 2.9 27.9 + - - +
469B LEU* 3.6 20.2 - - - +
473B GLU* 4.1 13.9 - - - -
474B TRP* 3.0 17.2 + - - -
504B PHE* 3.0 31.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 451 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B LEU* 4.6 16.6 - - + +
417B LEU* 4.5 5.6 - - + -
420B ALA* 3.6 20.2 - - + -
447B GLN* 3.2 26.1 + - + +
450B SER* 1.3 72.6 - - - +
452B ALA* 1.3 67.7 + - - +
454B LEU* 3.2 5.2 + - + +
455B MET* 3.0 29.4 + - + +
504B PHE* 3.7 24.5 - - + -
507B CYS* 3.8 36.1 - - + -
508B VAL* 4.0 3.6 - - + -
511B MET* 3.5 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 452 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ILE* 4.3 7.0 - - + -
420B ALA* 3.7 19.6 - - + +
423B ILE* 3.7 29.6 - - + -
424B ALA* 4.3 4.5 - - + +
448B LEU 3.1 19.4 + - - +
449B THR 3.8 3.1 - - - +
451B LEU* 1.3 76.9 - - - +
453B MET* 1.3 57.8 + - - +
455B MET* 3.2 7.3 + - - +
456B LEU* 2.9 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 453 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B SER* 3.9 19.7 - - - +
293B TRP* 4.0 19.5 - - + -
302B ILE* 4.4 7.9 - - + -
449B THR* 2.8 22.8 + - - +
450B SER 3.7 4.3 - - - +
452B ALA* 1.3 78.5 - - - +
454B LEU* 1.3 56.9 + - - +
456B LEU* 4.4 5.4 - - - +
457B ASP* 3.0 27.5 + - - +
460B TYR* 3.5 45.8 - - + +
469B LEU* 3.6 20.4 - - + -
472B LYS* 4.0 7.9 - - - -
473B GLU* 3.7 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 454 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B SER 2.9 13.9 + - - +
451B LEU* 3.2 9.4 + - + +
453B MET* 1.3 75.7 - - - +
455B MET* 1.3 58.2 + - - +
457B ASP 4.0 1.6 - - - +
460B TYR* 3.2 42.1 - - + +
461B ARG* 3.0 39.2 + - + +
466B PHE* 4.0 11.7 - - + -
469B LEU* 3.9 13.7 - - + -
504B PHE* 5.4 0.2 - - + -
508B VAL* 3.9 20.2 - - + -
511B MET* 3.6 28.9 - - + -
519B PHE* 3.6 17.9 - - + -
585B LEU* 5.3 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 455 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B LEU* 3.9 10.3 - - + +
420B ALA* 3.5 30.5 - - + +
421B VAL* 3.8 27.6 - - + +
424B ALA* 4.2 11.4 - - + -
451B LEU* 3.0 18.6 + - + +
452B ALA* 3.2 7.4 + - - +
454B LEU* 1.3 76.7 - - - +
456B LEU* 1.3 57.0 + - - +
461B ARG* 2.9 16.4 + - - +
511B MET* 4.2 15.0 - - - -
584B VAL* 3.3 4.5 - - + -
585B LEU* 2.9 42.0 + - + +
586B TYR* 5.1 0.2 - - - -
587B PRO* 3.4 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 456 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B TRP* 3.8 41.2 - - + -
302B ILE* 4.0 18.6 - - + -
424B ALA* 3.6 38.6 - - + +
427B ILE* 3.9 17.0 - - + -
428B GLU* 4.1 8.5 - - + +
452B ALA 2.9 20.3 + - - +
453B MET* 4.1 4.3 - - - +
455B MET* 1.3 79.5 - - - +
457B ASP* 1.3 59.1 + - - +
458B SER 4.1 0.9 + - - -
461B ARG* 4.3 1.6 - - - -
582B ASN 5.5 1.6 - - - +
583B HIS 5.4 0.7 - - - -
584B VAL* 3.9 34.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 457 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ARG* 3.0 28.5 + - - -
293B TRP* 2.9 37.9 + - + +
453B MET 3.0 12.1 + - - +
454B LEU 4.0 3.6 - - - +
455B MET 3.6 0.8 - - - -
456B LEU* 1.3 79.2 - - - +
458B SER* 1.3 63.1 + - - +
459B TYR* 3.0 20.3 + - - +
460B TYR* 3.1 28.6 + - + +
461B ARG* 4.0 4.1 + - - -
----------------------------------------------------------
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