Contacts of the helix formed by residues 399 - 404 (chain A) in PDB entry 6AGF
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 LEU 399 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 3.4 24.0 - - + +
264A PHE* 3.3 48.5 - - + +
265A ALA* 4.0 2.0 - - - +
268A GLY* 4.8 1.3 - - - -
389A TYR* 3.6 33.4 - - + +
395A ALA* 3.3 24.2 + - + +
396A PHE 3.8 3.4 - - - +
397A LEU 3.1 0.6 - - - -
398A ALA* 1.3 78.0 - - - +
400A PHE* 1.3 61.2 + - - +
401A ARG 3.5 0.4 - - - -
402A LEU* 3.7 19.6 + - + +
403A MET* 3.6 10.2 + - - +
426A PHE* 4.2 15.9 - - + -
430A ILE* 4.8 10.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 4.0 14.1 - - + -
396A PHE 3.1 17.2 + - - +
397A LEU* 3.1 9.9 + - + +
399A LEU* 1.3 75.5 - - - +
401A ARG* 1.3 58.2 + - - +
402A LEU 3.1 4.9 - - - -
403A MET* 3.4 30.4 + - + +
404A THR* 3.2 33.9 + - + -
762A TRP* 3.6 24.5 - + - -
783A LEU* 4.5 8.5 - - + -
786A MET* 3.6 33.4 - - + -
787A VAL* 5.9 0.7 - - + -
1908A 6OU 3.9 46.0 - - + -
1911A 6OU 4.3 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ASN* 5.6 0.4 - - - +
386A TYR 5.3 1.0 + - - -
387A THR* 3.8 15.4 - - - +
397A LEU* 3.1 12.6 + - - +
398A ALA* 3.3 26.2 - - - +
400A PHE* 1.3 78.0 - - - +
402A LEU* 1.3 57.5 + - - +
404A THR* 3.8 7.9 - - - -
405A GLN* 3.4 5.8 + - - -
406A ASP* 3.2 39.0 + - + +
407A TYR* 3.2 41.8 + - - +
408A TRP* 3.7 6.8 - - - +
410A ASN* 4.4 2.2 - - - +
411A LEU* 3.7 40.0 - - + +
762A TRP* 4.2 15.9 - - + -
763A ILE* 4.6 13.4 - - + +
767A TRP* 3.7 26.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A TYR* 5.2 0.2 - - - +
398A ALA 3.9 8.5 - - - +
399A LEU* 3.7 27.6 - - + +
400A PHE 3.1 0.8 - - - -
401A ARG* 1.3 79.5 - - - +
403A MET* 1.3 64.6 + - - +
404A THR 3.3 0.4 - - - -
405A GLN* 3.5 10.3 + - - +
408A TRP* 3.7 39.0 - - + -
411A LEU* 4.0 16.6 - - + -
426A PHE* 5.0 3.4 - - + -
427A PHE* 4.1 23.6 - - + -
430A ILE* 3.7 30.1 - - + -
431A ILE* 4.1 12.1 - - + +
435A SER* 3.3 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A THR* 3.6 21.1 - - - +
261A LEU* 4.2 20.6 - - + -
399A LEU 3.6 11.2 + - - +
400A PHE* 3.4 35.2 + - + +
402A LEU* 1.3 79.5 - - - +
404A THR* 1.3 65.3 + - + +
405A GLN* 4.4 0.2 - - - +
430A ILE* 5.7 0.6 - - - +
434A GLY* 3.8 19.5 - - - +
435A SER* 3.4 24.7 + - - +
438A LEU* 4.4 9.6 - - + -
439A ILE* 3.9 28.8 - - + +
442A ILE* 5.4 1.8 - - + -
1911A 6OU 3.9 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A PHE* 3.2 42.4 + - + +
401A ARG* 3.8 0.9 - - - -
403A MET* 1.3 79.4 - - + +
405A GLN* 1.3 69.5 + - - +
406A ASP* 3.4 5.9 + - - +
760A GLY 5.1 3.9 - - - +
762A TRP* 3.3 27.5 + - - +
786A MET* 5.0 2.5 - - - -
1911A 6OU 4.1 38.2 - - + +
----------------------------------------------------------
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