Contacts of the helix formed by residues 416 - 425 (chain g) in PDB entry 5M32
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 THR 416 (chain g).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376g SER* 4.5 13.7 - - - +
379g VAL* 5.3 2.9 - - - -
410g ARG* 4.1 11.6 + - - +
414g GLU* 4.1 11.2 - - - +
415g LEU* 1.3 81.3 - - - +
417g HIS* 1.3 63.2 + - - +
418g GLU* 3.1 31.2 + - - +
419g ASP* 2.7 31.3 + - - +
420g TYR* 3.4 19.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 417 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164E ARG* 5.6 3.1 + - - -
167E SER* 5.6 2.7 - - - -
378g ASP 4.0 18.2 + - - +
379g VAL* 4.4 4.5 - - + +
380g ASN* 3.6 28.8 + - + -
383g GLU* 2.7 44.2 + - + +
384g LEU* 3.7 13.4 - - + +
416g THR* 1.3 73.8 - - - +
418g GLU* 1.3 59.7 + - - +
419g ASP 3.1 1.6 - - - -
420g TYR* 2.9 12.6 + - - +
421g MET* 2.6 64.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 418 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164E ARG* 5.6 6.7 - - - +
410g ARG* 5.0 4.9 + - - +
416g THR* 3.1 28.6 + - - +
417g HIS* 1.3 77.9 + - - +
419g ASP* 1.3 58.0 + - - +
420g TYR 3.2 0.2 - - - -
421g MET* 3.7 11.9 - - + -
422g GLU* 2.5 53.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 419 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403g ALA* 3.6 21.5 - - + +
406g ILE* 3.4 19.8 - - + +
407g ALA* 3.5 12.2 - - + +
410g ARG* 2.5 37.1 + - - -
415g LEU* 3.3 7.9 - - + -
416g THR* 2.7 37.9 + - - +
417g HIS 3.1 0.6 - - - -
418g GLU* 1.3 80.0 - - - +
420g TYR* 1.3 54.7 + - + +
422g GLU* 4.9 2.8 - - - +
423g GLY* 2.7 29.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 420 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366g MET* 5.2 2.0 - - + -
370g SER* 2.8 33.8 + - - -
373g MET* 5.1 0.5 - - - -
375g VAL* 4.2 5.4 - - + +
379g VAL* 4.4 17.3 - - + -
381g TYR* 4.0 11.7 + + - -
384g LEU* 3.6 31.9 - - + -
399g VAL* 4.2 14.2 - - + +
400g CYS* 3.8 31.4 - - - +
403g ALA* 3.9 14.4 - - + -
415g LEU* 3.4 28.6 - - + +
416g THR 3.4 18.2 - - - -
417g HIS 2.9 7.7 + - - +
419g ASP* 1.3 78.0 - - + +
421g MET* 1.3 58.2 + - - +
423g GLY* 2.8 18.7 + - - -
424g ILE* 2.8 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 421 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164E ARG* 4.2 46.0 - - + +
166E GLN* 5.1 1.8 - - + -
167E SER* 4.4 21.8 - - - +
383g GLU* 5.4 4.3 - - + +
384g LEU* 4.0 11.7 - - + -
387g CYS* 4.8 23.3 - - + -
388g THR* 6.1 1.1 - - - -
417g HIS* 2.6 46.4 + - + +
418g GLU* 3.7 9.9 - - + -
420g TYR* 1.3 75.0 - - - +
422g GLU* 1.3 59.3 - - - +
424g ILE* 3.5 19.5 + - - +
425g LEU* 3.8 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 422 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406g ILE* 4.1 16.0 - - + +
409g ARG* 3.8 21.1 + - - +
410g ARG* 5.9 0.2 + - - -
418g GLU* 2.5 42.8 + - + +
419g ASP* 4.9 2.6 - - - +
421g MET* 1.3 70.0 - - - +
423g GLY* 1.3 63.0 + - - +
424g ILE 3.2 1.1 + - - -
425g LEU* 3.8 21.3 + - - +
426g GLU* 4.4 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 423 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399g VAL* 5.4 2.7 - - - -
402g GLU* 2.6 34.0 - - - +
403g ALA* 4.6 4.3 - - - -
406g ILE* 4.5 8.1 - - - -
419g ASP 2.7 26.2 + - - -
420g TYR* 2.8 3.9 + - - -
422g GLU* 1.3 73.5 - - - +
424g ILE* 1.3 66.3 + - - +
426g GLU* 3.1 8.7 - - - +
427g VAL 3.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 424 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366g MET* 4.6 6.5 - - + -
384g LEU* 5.2 6.1 - - + +
387g CYS* 6.3 0.2 - - - -
388g THR* 4.0 35.2 - - + -
391g PHE* 4.7 6.7 - - + -
399g VAL* 3.3 41.1 - - + -
420g TYR 2.8 19.9 + - - +
421g MET* 3.6 13.5 - - - +
422g GLU 3.2 0.4 - - - -
423g GLY* 1.3 73.1 - - - +
425g LEU* 1.3 51.3 - - - +
426g GLU 1.7 29.2 + - - -
427g VAL* 2.4 20.5 + - + +
428g GLN* 3.2 20.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 425 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164E ARG* 6.2 5.6 - - + -
421g MET 3.8 7.8 + - - +
422g GLU* 3.8 16.0 + - + +
424g ILE* 1.3 75.3 - - + +
426g GLU* 1.3 58.0 + - - +
428g GLN* 4.2 8.5 - - - +
429g ALA* 4.2 19.8 - - - +
----------------------------------------------------------
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