Contacts of the helix formed by residues 405 - 416 (chain A) in PDB entry 6XYU
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 405 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A LYS 4.0 0.6 + - - -
404A ALA* 1.3 78.3 - - - +
406A GLN* 1.3 59.0 + - - +
407A ALA* 3.3 10.5 + - - +
408A GLU* 3.0 37.6 + - - +
409A ARG* 2.8 25.6 + - - +
570A VAL* 4.9 2.4 + - - +
571A ARG* 5.3 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A ASN* 5.7 0.6 + - - +
405A THR* 1.3 72.4 - - - +
407A ALA* 1.3 57.6 + - - +
409A ARG* 3.1 39.2 - - + +
410A GLU* 2.7 62.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A THR* 3.3 7.2 + - - +
406A GLN* 1.3 78.6 - - - +
408A GLU* 1.3 59.0 + - - +
410A GLU* 4.2 11.6 - - - +
411A ALA* 3.3 22.2 + - - +
570A VAL* 3.3 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A ALA* 3.6 22.5 - - + +
405A THR* 3.0 42.8 + - - +
407A ALA* 1.3 77.1 - - - +
409A ARG* 1.3 55.0 + - - +
411A ALA* 3.0 3.9 + - - +
412A ILE* 2.6 48.2 + - + +
567A LEU* 4.1 12.7 - - + +
570A VAL* 4.1 12.6 - - + -
571A ARG* 2.9 52.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A MET 4.8 0.9 - - - +
398A ASN* 3.2 42.6 + - - +
401A PHE* 3.5 30.6 + - + +
402A GLY* 4.1 10.1 + - - -
404A ALA* 3.2 19.0 + - + +
405A THR* 2.8 8.6 + - - +
406A GLN* 3.1 64.6 + - + +
408A GLU* 1.3 75.4 - - - +
410A GLU* 1.3 52.9 + - - +
412A ILE* 3.2 8.4 + - - +
413A ILE* 2.7 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A GLN* 2.7 47.4 + - + +
407A ALA* 4.2 10.4 - - - +
409A ARG* 1.3 71.6 - - - +
411A ALA* 1.3 57.0 + - - +
413A ILE* 3.9 8.2 - - + +
414A PHE* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ALA 3.3 18.3 + - - +
408A GLU 3.0 5.4 + - - +
410A GLU* 1.3 80.1 - - - +
412A ILE* 1.3 58.1 + - - +
414A PHE* 3.4 5.6 + - - +
415A GLN* 2.9 28.9 + - - +
562A PHE* 3.6 10.1 - - + -
566A TYR* 4.3 15.3 - - + +
567A LEU* 3.8 18.8 - - + -
570A VAL* 4.5 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A MET* 3.4 23.6 - - + -
401A PHE* 3.8 34.3 - - + -
404A ALA* 4.8 3.8 - - + -
408A GLU* 2.6 33.7 + - + +
409A ARG* 3.7 4.7 - - - +
411A ALA* 1.3 69.5 - - - +
413A ILE* 1.3 66.8 + - + +
415A GLN 2.9 10.7 + - - -
416A TYR* 3.0 21.4 + - + +
562A PHE* 3.5 22.4 - - + -
563A TRP* 3.8 21.3 - - + -
567A LEU* 3.7 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ARG* 3.9 21.1 - - - +
393A TYR* 3.1 33.6 + - + -
394A LEU* 4.0 12.3 - - + -
397A MET* 3.8 25.8 - - + -
398A ASN* 3.5 38.8 - - - +
401A PHE* 6.1 0.7 - - + -
409A ARG* 2.7 30.6 + - + +
410A GLU* 4.0 6.1 - - - +
412A ILE* 1.3 72.7 - - + +
414A PHE* 1.3 56.3 + - - +
417A THR* 2.7 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A GLU 2.9 20.2 + - - +
411A ALA* 3.8 5.4 - - - +
413A ILE* 1.3 78.3 - - - +
415A GLN* 1.3 65.9 + - - +
416A TYR 3.3 0.3 + - - -
417A THR* 3.4 15.4 + - + -
419A TRP* 3.5 39.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A ALA 2.9 17.7 + - - +
412A ILE 2.9 5.4 + - - +
414A PHE* 1.3 80.6 - - - +
416A TYR* 1.3 82.7 + - + +
417A THR 3.9 1.7 + - - +
430A GLN* 4.6 1.9 - - - +
558A ALA 5.0 4.4 + - - -
559A ARG* 4.8 6.9 + - - +
562A PHE* 3.7 44.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A TYR* 2.8 25.3 + - - +
397A MET* 4.1 6.5 - - + -
412A ILE* 3.0 21.2 + - + +
414A PHE 3.2 0.2 - - - -
415A GLN* 1.3 99.5 - - + +
417A THR* 1.3 60.4 + - - +
418A SER 3.4 0.9 + - - -
430A GLN* 3.1 59.0 - - + +
433A ARG* 3.8 9.9 - - + -
434A ALA* 3.5 29.2 - - + -
437A ASP* 2.9 23.6 + - - +
559A ARG* 4.5 4.2 + - - -
562A PHE* 4.3 1.9 - + - -
563A TRP* 2.9 42.1 + + - -
----------------------------------------------------------
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