Contacts of the helix formed by residues 407 - 421 (chain B) in PDB entry 5FPP
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 VAL 407 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B SER* 3.6 32.3 - - - +
230B GLY* 5.7 1.3 - - - +
236B TRP* 5.0 1.8 - - + +
295B PHE* 3.8 27.6 - - + -
330B VAL* 3.8 10.1 - - + -
334B GLU* 3.5 43.3 - - + +
403B GLY 2.8 16.2 + - - +
405B HIS 3.8 0.2 - - - -
406B ASN* 1.3 80.3 - - - +
408B VAL* 1.3 59.8 + - - +
409B CYS 3.4 2.0 - - - -
410B PRO* 3.3 3.9 - - - +
411B VAL* 2.9 36.5 + - + +
447B HIS* 4.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B VAL* 4.1 26.2 - - + -
331B VAL 5.2 1.3 - - - +
332B LYS 6.1 0.2 - - - +
334B GLU* 4.4 13.0 - - + -
403B GLY 3.0 17.2 + - - +
404B ASP* 3.8 20.4 - - - +
407B VAL* 1.3 72.3 - - - +
409B CYS* 1.3 58.5 + - - +
411B VAL* 3.3 3.3 + - - +
412B ALA* 2.9 26.3 + - - +
524B LEU* 4.2 17.9 - - + +
525B ARG* 3.7 40.4 - - + +
529B CYS* 4.3 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B ASP* 3.0 27.4 + - - +
405B HIS* 5.2 0.4 - - - -
408B VAL* 1.3 74.8 - - - +
410B PRO* 1.3 65.0 - - + +
412B ALA* 3.2 0.7 + - - +
413B GLN* 2.8 26.0 + - - +
528B THR 4.4 0.4 - - - -
529B CYS* 2.0 56.8 - - + -
532B TRP* 3.7 23.8 - - + -
533B ASN* 3.3 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 410 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B THR* 3.4 22.7 - - + +
233B ASN* 2.9 25.9 + - - +
234B GLY* 4.3 2.9 - - - -
235B PRO* 4.3 11.0 - - + -
404B ASP 3.3 13.2 - - - +
405B HIS 3.5 13.7 - - - +
406B ASN 3.5 17.7 - - - +
407B VAL 3.3 10.5 - - - +
409B CYS* 1.3 90.4 - - + +
411B VAL* 1.3 56.8 + - - +
413B GLN* 3.4 2.6 + - + +
414B LEU* 2.9 26.2 + - - +
533B ASN* 5.0 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 411 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B LEU* 5.6 1.3 - - + +
229B SER 5.1 0.4 - - - +
230B GLY 4.4 9.0 - - - +
231B THR* 3.5 23.6 - - + -
328B VAL* 4.1 27.7 - - + +
329B GLY* 4.5 9.0 - - - +
330B VAL* 4.1 21.3 - - + -
407B VAL* 2.9 32.4 + - + +
408B VAL 3.5 4.0 - - - +
410B PRO* 1.3 73.0 - - - +
412B ALA* 1.3 61.5 + - - +
414B LEU* 3.3 1.8 + - - +
415B ALA* 2.8 29.4 + - + +
427B ALA* 6.2 0.2 - - + -
524B LEU* 4.3 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B VAL 2.9 16.7 + - - +
409B CYS* 3.2 7.6 + - - +
411B VAL* 1.3 76.0 - - - +
413B GLN* 1.3 63.5 + - - +
415B ALA* 3.9 5.3 - - - +
416B GLY* 3.0 21.8 + - - -
503B TYR* 4.1 10.8 + - - +
524B LEU* 4.1 33.4 - - + +
529B CYS* 4.5 7.6 - - + -
533B ASN* 4.7 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ASN* 3.6 21.6 + - - +
234B GLY 5.3 1.0 + - - -
313B GLU* 4.3 22.5 + - - +
316B ILE* 4.5 6.8 - - + +
317B ASN* 5.7 1.6 - - - -
409B CYS 2.8 16.9 + - - +
410B PRO* 3.5 6.4 - - + +
412B ALA* 1.3 77.7 - - - +
414B LEU* 1.3 57.1 + - - +
416B GLY* 3.9 0.7 - - - -
417B ARG* 2.9 46.8 + - + +
533B ASN* 3.8 41.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 414 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ILE* 6.0 1.8 - - + -
227B LEU* 3.7 30.3 - - + -
231B THR* 4.0 14.6 - - + -
232B PRO* 4.1 10.3 - - + -
233B ASN* 3.6 11.6 - - - +
316B ILE* 3.8 33.4 - - + -
328B VAL* 4.7 10.5 - - + -
410B PRO 2.9 16.6 + - - +
411B VAL* 3.3 4.9 + - + +
413B GLN* 1.3 72.6 - - - +
415B ALA* 1.3 58.6 + - - +
417B ARG* 3.1 1.4 + - - -
418B LEU* 2.8 65.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B VAL* 4.2 20.8 - - + +
411B VAL* 2.8 21.4 + - + +
412B ALA* 3.9 4.0 - - - +
414B LEU* 1.3 72.6 - - - +
416B GLY* 1.3 58.1 + - - +
418B LEU* 3.9 3.8 - - - +
419B ALA* 2.9 31.7 + - - +
425B VAL* 4.1 12.2 - - + +
427B ALA* 5.2 1.8 - - + -
503B TYR* 3.6 29.5 - - + -
524B LEU* 6.1 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B ALA 3.0 16.3 + - - -
413B GLN 3.9 0.7 - - - -
415B ALA* 1.3 77.8 - - - +
417B ARG* 1.3 63.6 + - - +
420B ALA* 3.0 21.1 + - - +
503B TYR* 3.6 15.1 - - - -
505B THR* 3.2 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ILE* 4.0 30.5 - - + +
317B ASN* 3.2 47.2 + - - +
321B PHE* 5.4 0.2 - - - -
413B GLN* 2.9 30.3 + - + +
414B LEU 3.9 2.0 - - - +
416B GLY* 1.3 76.0 - - - +
418B LEU* 1.3 63.6 + - - +
420B ALA* 3.4 16.4 + - - +
421B GLN* 3.2 54.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ILE* 5.0 9.0 - - + -
316B ILE* 5.3 2.0 - - + -
321B PHE* 3.5 47.0 - - + +
324B LEU* 4.9 4.3 - - + -
326B VAL* 3.9 34.5 - - + -
328B VAL* 5.4 1.6 - - + -
414B LEU* 2.8 53.2 + - + +
415B ALA* 3.9 4.0 - - - +
417B ARG* 1.3 72.8 - - - +
419B ALA* 1.3 64.0 + - - +
421B GLN 3.0 12.6 + - - -
422B GLY 3.4 0.2 + - - -
423B ALA* 3.1 29.3 + - + +
425B VAL* 4.0 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B ALA 2.9 19.2 + - - +
416B GLY 3.9 3.1 - - - +
418B LEU* 1.3 76.9 - - - +
420B ALA* 1.3 63.4 + - - +
421B GLN 3.2 0.7 + - - -
422B GLY* 3.4 8.8 + - - -
423B ALA 3.8 15.1 - - - +
425B VAL* 3.7 6.6 - - + +
503B TYR* 3.8 25.6 - - + +
504B THR* 4.2 13.0 - - + -
505B THR* 4.4 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B GLY 3.0 17.5 + - - +
417B ARG* 3.8 22.4 - - - +
419B ALA* 1.3 77.5 - - - +
421B GLN* 1.3 63.8 + - - +
422B GLY 3.5 0.9 + - - -
505B THR* 4.0 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ILE 2.8 25.2 + - - -
317B ASN 3.4 16.3 + - - -
318B THR 3.8 1.4 - - - -
319B GLY* 3.1 27.9 + - - +
320B ASP* 3.9 5.0 - - - +
321B PHE* 3.1 31.8 + - + -
322B GLN* 3.7 2.4 + - - +
417B ARG* 3.2 48.2 + - - +
418B LEU 3.0 6.2 + - - +
420B ALA* 1.3 82.8 - - - +
422B GLY* 1.3 56.0 + - - +
423B ALA 3.5 2.7 - - - -
----------------------------------------------------------
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