Contacts of the helix formed by residues 412 - 421 (chain B) in PDB entry 4P3N
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 ASN 412 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B THR* 4.0 1.6 + - - +
409B LYS* 2.2 42.7 + - - -
411B MET* 1.3 73.2 - - - +
413B CYS* 1.3 64.1 + - - +
414B PRO* 3.6 1.8 - - - -
415B GLY* 3.4 5.9 + - - -
416B HIS* 3.2 34.4 + - + +
436B ASP* 3.9 18.9 + - - +
437B PHE 5.0 0.2 - - - -
438B GLY 4.1 8.5 + - - -
440B LEU* 3.7 19.3 - - - +
460B GLN* 4.9 1.2 - - - +
462B ASP* 3.2 37.1 + - - +
464B HIS* 4.3 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B HIS* 5.7 1.3 - - + -
411B MET* 4.0 32.1 - - - -
412B ASN* 1.3 79.5 - - - +
414B PRO* 1.3 71.1 - - + +
416B HIS* 3.0 6.6 + - - +
417B CYS* 2.9 25.0 + - - -
462B ASP* 4.9 2.0 - - - -
464B HIS* 3.1 36.1 - - + +
567B LEU* 3.9 10.5 - - + -
590B HIS* 3.4 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 414 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B LEU* 4.0 16.4 - - + -
383B TRP* 4.0 9.0 - - + -
386B SER* 3.6 24.9 - - - -
388B HIS* 3.8 18.2 - - + -
411B MET 4.2 8.5 - - - +
412B ASN 3.7 1.8 - - - -
413B CYS* 1.3 95.9 - - + +
415B GLY* 1.3 57.1 + - - +
417B CYS* 3.0 5.4 + - + +
418B LEU* 2.9 32.9 + - - +
567B LEU* 5.4 2.2 - - + -
571B PHE* 3.5 30.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A PHE* 3.8 17.4 - - - -
374B THR* 4.8 4.7 - - - -
378B PHE* 4.4 17.8 - - - -
382B LEU* 4.6 2.4 - - - +
383B TRP* 6.3 0.2 - - - -
412B ASN 3.4 7.9 + - - -
413B CYS 3.3 0.8 - - - -
414B PRO* 1.3 79.1 - - - +
416B HIS* 1.3 63.7 + - - +
418B LEU* 3.5 9.1 + - - +
419B MET* 3.2 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B VAL* 3.6 13.6 - - + +
374B THR* 3.9 18.4 - - + -
412B ASN* 3.2 18.7 + - + +
413B CYS 3.0 9.3 + - - +
415B GLY* 1.3 73.0 - - - +
417B CYS* 1.3 60.0 + - - +
419B MET* 3.1 10.3 + - - +
420B PHE* 2.9 28.2 + - - +
434B LEU* 3.7 31.3 + - + +
436B ASP* 3.1 41.7 + - + +
462B ASP* 4.6 2.7 - - - -
464B HIS* 3.1 27.6 + - + +
466B PHE* 3.9 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B CYS 2.9 18.3 + - - -
414B PRO* 3.3 8.3 - - - +
416B HIS* 1.3 76.7 - - - +
418B LEU* 1.3 57.5 + - - +
420B PHE* 3.2 4.1 + - - +
421B ASP* 2.9 29.3 + - - +
466B PHE* 4.5 5.6 - - - -
567B LEU* 3.6 31.9 - - - -
571B PHE* 3.8 25.4 - - + -
573B LEU* 3.7 16.2 - - + +
588B ILE* 3.7 19.3 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
334A PHE* 4.2 4.8 - - + -
336A HIS* 3.6 49.3 - - + +
338A LEU* 4.2 6.3 - - + -
344A PHE* 4.2 20.2 - - + -
378B PHE* 5.0 0.4 - - + -
382B LEU* 3.8 26.5 - - + -
414B PRO 2.9 15.1 + - - +
415B GLY* 3.6 9.0 - - - +
416B HIS 3.3 0.2 - - - -
417B CYS* 1.3 75.0 - - - +
419B MET* 1.3 57.1 + - - +
421B ASP* 3.2 10.4 + - + +
422B HIS* 2.9 27.7 + - - +
571B PHE* 4.1 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A PHE* 3.9 23.1 - - + -
344A PHE* 3.9 10.1 - - + -
345A PHE 4.2 6.1 - - - +
346A LEU* 3.6 27.9 - - + +
347A PRO* 4.6 1.6 - - + -
372B VAL* 3.5 35.9 - - + -
374B THR* 3.8 25.6 - - - -
415B GLY 3.2 13.7 + - - +
416B HIS* 3.1 14.2 + - - +
418B LEU* 1.3 74.7 - - - +
420B PHE* 1.3 62.7 + - - +
422B HIS* 3.2 11.6 - - - +
425B ARG* 3.0 20.8 + - - -
434B LEU* 4.0 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B HIS 2.9 12.4 + - - +
417B CYS* 3.6 7.2 - - - +
419B MET* 1.3 76.1 - - - +
421B ASP* 1.3 61.8 + - - +
422B HIS 3.2 1.1 + - - -
423B ARG 3.5 5.9 - - - +
425B ARG* 2.8 55.2 + - + +
430B LEU* 4.1 17.3 - - + -
432B LEU* 4.0 8.7 - - + -
434B LEU* 4.9 1.7 - - - +
466B PHE* 3.5 50.0 - + + -
573B LEU* 4.2 17.3 - - + -
574B THR 3.6 26.5 - - - -
575B TYR* 4.6 5.4 - - + -
586B PRO* 4.1 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B CYS 2.9 16.7 + - - +
418B LEU* 3.5 11.8 - - + +
419B MET 3.2 0.4 - - - -
420B PHE* 1.3 75.9 - - - +
422B HIS* 1.3 63.9 + - - +
423B ARG* 3.3 7.2 + - - +
571B PHE* 4.0 11.7 - - + +
572B ASN 3.9 11.0 - - - +
573B LEU* 3.6 19.5 - - + +
574B THR* 5.1 1.9 + - - -
----------------------------------------------------------
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