Contacts of the helix formed by residues 406 - 422 (chain F) in PDB entry 3SRF
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 406 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404F SER* 3.4 14.7 + - - +
405F THR* 1.3 79.2 - - - +
407F LEU* 1.3 67.0 + - - +
408F MET* 3.3 15.3 + - - +
409F GLU* 3.0 40.1 + - + +
410F ALA* 3.3 19.8 + - - +
439F GLN* 4.9 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 407 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405F THR 4.2 9.9 - - - +
406F ASP* 1.3 75.2 + - - +
408F MET* 1.3 63.2 - - - +
410F ALA* 3.1 18.0 + - - +
411F MET* 3.1 15.2 + - - +
520F PHE* 3.8 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 408 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406F ASP* 3.3 13.6 + - - +
407F LEU* 1.3 77.0 - - - +
409F GLU* 1.3 57.0 + - - +
411F MET* 3.2 5.9 + - + -
412F ALA* 2.9 32.6 + - + +
435F ARG* 4.8 2.2 - - + +
436F SER* 3.3 39.0 - - - +
439F GLN* 3.8 22.7 - - + -
440F VAL* 4.1 11.7 - - + -
511F LEU* 5.6 0.2 - - + -
520F PHE* 3.8 29.6 - - + -
521F THR* 3.6 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 409 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401F SER* 3.9 14.1 - - - +
404F SER* 2.9 31.8 + - - +
406F ASP* 3.0 29.9 + - + +
407F LEU 3.3 0.4 - - - -
408F MET* 1.3 77.2 - - - +
410F ALA* 1.3 55.9 + - - +
412F ALA* 3.5 3.9 - - - +
413F MET* 3.0 35.5 + - - +
439F GLN* 3.4 25.8 + - - +
442F ARG* 3.6 18.4 + - - -
443F TYR* 2.7 26.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 410 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406F ASP 3.3 7.9 + - - +
407F LEU* 3.1 12.6 + - - +
409F GLU* 1.3 76.9 - - - +
411F MET* 1.3 55.9 + - + +
413F MET* 3.0 11.0 + - - +
414F GLY* 2.8 33.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 411 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407F LEU 3.1 15.2 + - - +
408F MET* 3.5 15.0 - - + +
410F ALA* 1.3 74.0 - - - +
412F ALA* 1.3 55.0 + - - +
414F GLY* 3.6 0.8 + - - -
415F SER* 2.6 38.1 + - - -
511F LEU* 3.7 19.5 - - + -
520F PHE* 3.9 16.2 - - + -
521F THR 3.4 27.1 - - - +
522F ASN* 3.4 25.8 - - - +
524F MET* 3.7 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 412 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408F MET* 2.9 21.4 + - + +
409F GLU* 3.5 8.5 - - - +
411F MET* 1.3 77.7 - - - +
413F MET* 1.3 57.4 + - - +
415F SER* 3.6 1.4 + - - -
416F VAL* 3.1 36.0 + - - +
439F GLN 3.4 33.9 - - - +
440F VAL* 3.9 16.2 - - - +
443F TYR* 4.0 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 413 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394F PHE* 3.5 14.2 - - + -
398F VAL* 3.7 43.3 - - + +
401F SER* 5.0 1.6 - - - -
409F GLU* 3.0 20.7 + - - +
410F ALA* 3.0 8.9 + - - +
412F ALA* 1.3 73.8 - - - +
414F GLY* 1.3 60.4 + - - +
417F GLU* 3.0 30.9 + - - +
443F TYR* 3.8 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 414 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410F ALA 2.8 19.4 + - - -
411F MET* 4.0 1.6 - - - -
413F MET* 1.3 72.9 - - - +
415F SER* 1.3 57.8 + - - +
417F GLU* 3.5 5.3 + - - +
418F ALA* 2.9 30.8 + - - +
524F MET* 4.3 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 415 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411F MET 2.6 22.8 + - - -
412F ALA* 3.9 4.0 - - - -
413F MET 3.3 0.2 - - - -
414F GLY* 1.3 77.3 - - - +
416F VAL* 1.3 56.6 + - - +
418F ALA* 3.4 3.3 + - - +
419F SER* 2.9 28.9 + - - -
427F LEU* 3.9 12.9 - - - +
440F VAL* 5.2 0.2 - - - -
509F ILE* 4.1 5.5 - - - +
511F LEU* 3.2 38.3 - - - +
524F MET* 3.4 21.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 416 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394F PHE* 3.7 19.7 - - + -
412F ALA 3.1 19.8 + - - +
415F SER* 1.3 73.3 - - - +
417F GLU* 1.3 63.9 - - - +
419F SER* 2.8 20.0 + - - -
420F TYR* 3.2 40.9 + - + +
427F LEU* 4.6 1.3 - - + -
440F VAL* 3.7 33.7 - - + +
443F TYR* 4.0 6.1 - - + +
445F PRO* 3.8 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 417 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391F ARG* 5.9 2.9 - - - +
394F PHE* 3.4 38.6 - - + -
395F GLU* 6.1 0.3 - - - +
413F MET 3.0 15.8 + - - +
414F GLY* 3.7 6.3 - - - +
416F VAL* 1.3 77.6 - - - +
418F ALA* 1.3 60.8 + - - +
420F TYR* 3.2 25.4 + - - +
421F LYS* 3.3 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 418 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414F GLY 2.9 18.8 + - - +
415F SER* 3.5 10.3 - - - +
417F GLU* 1.3 77.0 - - - +
419F SER* 1.3 58.8 + - - +
421F LYS* 3.5 6.5 + - - +
422F CYS* 3.1 30.3 + - - -
509F ILE* 4.3 13.0 - - + -
524F MET* 4.4 13.9 - - + -
526F VAL* 5.1 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 419 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415F SER 2.9 13.2 + - - -
416F VAL* 2.8 24.4 + - - -
417F GLU 3.2 0.2 - - - -
418F ALA* 1.3 73.7 - - - +
420F TYR* 1.3 67.1 + - - +
423F LEU* 3.4 3.5 - - - +
424F ALA* 3.0 48.0 + - - +
427F LEU* 4.3 12.8 - - - -
445F PRO* 4.1 13.7 - - - +
446F ARG* 5.2 1.0 + - - -
447F ALA* 5.1 4.5 + - - +
509F ILE* 4.1 8.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 420 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390F HIS* 3.6 36.7 + - + +
391F ARG* 5.0 7.9 - - + -
394F PHE* 3.8 21.3 - + + +
416F VAL* 3.2 34.6 + - + +
417F GLU* 3.2 20.8 + - - +
419F SER* 1.3 81.0 - - - +
421F LYS* 1.3 63.8 + - - +
423F LEU* 3.7 18.5 + - - +
443F TYR 3.9 3.5 + - - -
444F ARG 2.7 25.5 + - - -
445F PRO* 4.2 1.6 - - + -
446F ARG* 3.8 42.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 421 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417F GLU 3.3 9.0 + - - +
418F ALA* 3.8 9.6 - - - +
419F SER 3.4 0.4 - - - -
420F TYR* 1.3 78.3 - - - +
422F CYS* 1.3 60.9 + - + +
423F LEU* 3.1 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 422 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418F ALA* 3.1 19.5 - - - +
421F LYS* 1.3 78.2 - - + +
423F LEU* 1.3 69.7 + - - +
424F ALA* 3.1 15.6 + - - -
507F VAL* 4.0 33.2 - - + +
509F ILE* 4.2 7.9 - - - -
526F VAL* 5.0 7.0 - - + -
----------------------------------------------------------
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