Contacts of the helix formed by residues 405 - 416 (chain C) in PDB entry 3F7F
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 GLU 405 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C ASP* 3.8 16.6 - - - +
404C VAL* 1.3 87.1 - - + +
406C ARG* 1.3 59.0 + - - +
407C GLY 3.2 0.2 - - - -
408C PHE* 3.0 12.3 + - + +
409C CYS* 2.9 35.2 + - - -
437C ASN* 3.1 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 406 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400C LYS* 3.5 46.7 - - - +
401C THR 3.6 23.3 - - - +
403C ASP* 3.4 27.8 + - + +
405C GLU* 1.3 79.7 - - - +
407C GLY* 1.3 56.6 + - - +
408C PHE 3.1 0.2 - - - -
409C CYS* 3.3 21.4 + - - +
410C ASN* 2.9 59.1 + - - +
669C ARG 5.5 4.2 + - - -
670C GLN* 3.8 23.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 407 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C ASP 3.3 6.8 + - - -
404C VAL 3.3 9.2 + - - -
405C GLU 3.2 0.6 - - - -
406C ARG* 1.3 81.0 - - - +
408C PHE* 1.3 55.7 + - - +
410C ASN* 3.8 13.4 - - - +
411C LEU* 2.9 35.8 + - - +
443C LEU* 4.1 12.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 408 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C VAL* 3.2 8.8 + - + -
405C GLU* 3.0 21.7 + - + +
407C GLY* 1.3 77.7 - - - +
409C CYS* 1.3 60.6 + - - +
410C ASN 3.2 0.2 - - - -
411C LEU* 3.4 5.8 + - + +
412C LYS* 2.9 37.7 + - + +
420C PHE* 3.6 25.9 - + - -
424C GLN* 3.3 28.7 - - - -
434C MET* 4.0 29.4 - - + -
442C TYR* 4.3 7.0 - + - -
443C LEU* 5.3 6.7 - - + -
446C LEU* 3.4 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 409 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C GLU* 2.9 18.4 + - - -
406C ARG* 3.7 26.7 - - - +
408C PHE* 1.3 75.5 - - - +
410C ASN* 1.3 60.5 + - - +
412C LYS* 3.9 6.0 - - - +
413C SER* 2.9 34.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 410 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C THR* 3.4 25.3 - - + +
400C LYS 2.9 27.8 + - - +
401C THR* 5.2 0.2 - - - +
406C ARG* 2.9 52.2 + - - +
407C GLY* 3.8 11.4 - - - +
408C PHE 3.2 0.2 - - - -
409C CYS* 1.3 76.5 - - - +
411C LEU* 1.3 56.0 + - + +
413C SER* 3.7 4.1 - - - -
414C ARG* 2.8 37.0 + - - +
669C ARG* 5.7 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 411 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C GLY 2.9 25.9 + - - +
408C PHE* 3.9 7.0 - - + +
409C CYS 3.4 0.6 - - - -
410C ASN* 1.3 74.7 - - + +
412C LYS* 1.3 58.3 + - - +
414C ARG* 4.1 10.1 - - - +
415C TYR* 2.7 49.5 + - + +
420C PHE* 4.2 4.3 - - + -
443C LEU* 4.3 20.6 - - + -
446C LEU* 4.5 16.8 - - + -
447C GLU* 3.8 29.4 - - - +
450C LEU* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 412 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C GLU* 5.4 7.4 - - - +
408C PHE* 2.9 27.3 + - + +
409C CYS* 3.9 5.8 - - - +
411C LEU* 1.3 75.1 - - - +
413C SER* 1.3 58.7 + - - +
416C GLY* 3.0 31.4 + - - -
417C THR* 3.7 23.1 + - - +
420C PHE* 3.7 45.0 - - + -
421C GLU* 5.0 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 413 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C GLN* 3.9 8.3 + - - -
409C CYS 2.9 20.7 + - - -
410C ASN* 3.7 3.4 - - - -
412C LYS* 1.3 78.6 - - - +
414C ARG* 1.3 62.3 + - - +
415C TYR 3.5 0.2 + - - -
416C GLY* 4.0 1.6 + - - -
668C TYR 4.7 0.2 + - - -
669C ARG* 2.8 33.0 + - - +
670C GLN 4.7 5.9 - - - -
671C ASP* 4.9 2.0 + - - -
672C LYS* 3.2 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 414 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C GLN* 3.7 10.0 + - - -
387C VAL* 3.5 29.4 + - + +
388C ASP* 3.2 27.1 + - - +
391C SER* 2.7 42.0 + - - -
410C ASN 2.8 22.7 + - - +
411C LEU* 3.1 10.3 + - - +
413C SER* 1.3 77.2 + - - +
415C TYR* 1.3 102.7 + - + +
447C GLU* 5.3 5.3 + - - -
451C ARG* 6.0 2.0 - - - +
669C ARG* 6.5 0.4 - - - -
672C LYS* 4.2 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 415 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ASN* 5.3 6.2 + - - +
13C GLN* 4.3 5.5 + - - -
388C ASP* 5.5 0.4 - - - -
411C LEU* 2.7 36.8 + - + +
412C LYS 4.5 0.4 - - - +
414C ARG* 1.3 126.0 + - - +
416C GLY* 1.3 63.8 + - - +
419C ILE* 3.6 46.1 - - + +
420C PHE* 4.6 1.6 - - + +
447C GLU* 4.5 4.1 + - - -
450C LEU* 3.7 50.9 - - + +
451C ARG* 3.8 19.8 + - - +
454C LYS* 4.1 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 416 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ASN* 6.1 2.0 - - - -
13C GLN* 4.4 25.4 - - - -
412C LYS 3.0 17.0 + - - -
413C SER 4.0 2.3 + - - -
414C ARG 3.7 1.2 - - - -
415C TYR* 1.3 81.5 - - - +
417C THR* 1.3 60.1 + - - -
418C GLN* 3.4 3.4 - - - -
419C ILE 3.3 1.6 + - - -
420C PHE* 3.0 26.9 + - - +
----------------------------------------------------------
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