Contacts of the helix formed by residues 439 - 451 (chain N) in PDB entry 6AH0
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 ALA 439 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434N VAL* 4.9 2.4 + - - +
437N TRP 3.6 2.4 - - - -
438N LEU* 1.3 75.6 - - - +
440N LEU* 1.3 63.1 - - - +
441N ALA 3.3 3.1 - - - +
442N ARG* 3.6 11.7 + - - +
443N LEU* 3.7 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 440 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439N ALA* 1.3 70.3 - - - +
441N ALA* 1.3 59.3 + - - +
442N ARG 3.2 0.7 - - - -
443N LEU* 4.0 1.3 - - - +
444N GLU* 3.0 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 441 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439N ALA* 3.3 1.2 - - - +
440N LEU* 1.3 79.1 - - - +
442N ARG* 1.3 60.3 + - - +
444N GLU* 4.1 1.2 - - - +
445N THR* 3.6 11.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 442 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430N CYS* 5.4 4.8 - - - +
433N SER 5.8 1.1 - - - -
434N VAL* 5.1 13.7 - - - +
439N ALA* 3.6 10.1 + - - +
440N LEU 3.2 0.6 - - - -
441N ALA* 1.3 72.9 - - - +
443N LEU* 1.3 59.4 + - - +
444N GLU 3.1 1.1 - - - -
445N THR* 2.9 21.1 + - - -
446N TYR* 3.0 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 443 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434N VAL* 5.1 6.6 - - - +
439N ALA 3.7 11.3 + - - -
440N LEU* 4.3 2.0 - - - +
442N ARG* 1.3 72.9 - - - +
444N GLU* 1.3 51.7 + - - +
446N TYR* 3.2 4.2 - - - +
447N GLU* 2.4 35.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 444 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440N LEU 3.0 19.0 + - - -
441N ALA* 4.3 2.2 - - - +
442N ARG 3.0 0.6 + - - -
443N LEU* 1.3 76.0 - - - +
445N THR* 1.3 51.2 + - - +
447N GLU* 3.4 2.6 + - - +
448N ASN* 2.7 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 445 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441N ALA 3.6 8.4 + - - -
442N ARG 2.9 8.8 + - - -
444N GLU* 1.3 74.5 - - - +
446N TYR* 1.3 59.9 + - - +
448N ASN* 3.4 9.5 + - - +
449N ALA* 3.4 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 446 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430N CYS* 5.9 9.1 - - - +
442N ARG 3.0 9.1 + - - -
443N LEU* 3.0 9.5 + - - +
445N THR* 1.3 74.5 - - - +
447N GLU* 1.3 58.4 + - - +
448N ASN 3.2 0.2 - - - -
449N ALA* 3.1 17.2 + - - +
450N ARG* 3.2 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 447 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443N LEU 2.4 24.6 + - - -
444N GLU* 3.5 3.1 - - - +
446N TYR* 1.3 65.2 - - - +
448N ASN* 1.3 55.6 + - - +
450N ARG* 3.3 4.9 - - - +
451N LYS* 2.7 33.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 448 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444N GLU 2.7 20.2 + - - -
445N THR* 3.4 6.9 + - - +
446N TYR 3.2 0.8 - - - -
447N GLU* 1.3 74.0 - - - +
449N ALA* 1.3 56.7 + - - +
451N LYS* 3.9 1.7 + - - +
452N VAL* 3.5 15.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 449 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445N THR 3.4 7.4 + - - -
446N TYR 3.1 10.3 + - - -
448N ASN* 1.3 74.5 - - - +
450N ARG* 1.3 60.5 + - - +
452N VAL* 3.5 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 450 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446N TYR 3.2 8.2 + - - -
447N GLU* 2.9 10.5 + - - +
449N ALA* 1.3 76.1 - - - +
451N LYS* 1.3 63.7 + - - +
452N VAL 3.1 6.0 + - - -
456N ALA* 4.5 21.6 + - - +
459N ASN* 6.3 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 451 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447N GLU 2.7 17.5 + - - -
448N ASN* 4.2 3.4 - - - +
450N ARG* 1.3 70.7 - - - +
452N VAL* 1.3 61.8 + - - +
485N LYS 5.7 5.4 - - - -
486N ILE* 6.0 4.0 - - - +
----------------------------------------------------------
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