Contacts of the helix formed by residues 63 - 76 (chain J) in PDB entry 4DVQ
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 HIS 63 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58J GLU* 5.2 10.2 + - - -
61J TYR* 2.8 9.7 + - + -
62J GLU* 1.3 97.9 + - + +
64J LEU* 1.3 68.1 + - - +
65J HIS* 3.3 6.7 - - - -
66J LEU* 3.1 26.5 + - + +
67J GLU* 3.1 16.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51J ARG* 5.2 6.5 - - - +
61J TYR* 3.5 40.1 + - + +
62J GLU 3.7 1.0 - - - -
63J HIS* 1.3 76.6 - - - +
65J HIS* 1.3 58.6 + - - +
67J GLU* 3.3 4.9 + - - +
68J MET* 2.8 59.9 + - + +
239J PHE* 4.5 16.6 - - + -
380J LEU* 4.4 7.0 - - + -
381J PHE* 4.2 24.5 - - + -
406J PHE* 4.6 5.2 - - + -
485J TYR* 4.1 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 65 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62J GLU 3.7 18.9 + - - -
63J HIS 4.0 2.2 - - - -
64J LEU* 1.3 78.8 - - - +
66J LEU* 1.3 90.9 + - + +
68J MET* 3.5 4.0 + - - +
69J HIS* 2.9 29.7 + - - +
380J LEU* 3.7 33.2 - - + +
406J PHE* 5.8 1.3 - - - -
408J TYR* 3.6 32.0 - + + +
409J SER* 5.1 0.5 + - - -
483J MET* 3.0 44.2 + - + -
485J TYR* 4.1 4.3 - - + -
489J LEU* 3.6 16.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63J HIS* 3.1 18.1 + - + +
65J HIS* 1.3 98.5 - - + +
67J GLU* 1.3 59.4 - - - +
69J HIS* 3.4 9.7 + - + +
70J GLN* 2.9 28.8 + - - +
408J TYR* 3.5 28.5 - - + +
482J LYS* 6.5 1.1 - - + -
483J MET 5.4 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 67 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44J HIS* 3.2 30.1 + - - +
51J ARG* 5.2 1.4 - - - -
61J TYR* 2.8 38.1 + - - -
63J HIS* 3.1 15.2 + - + +
64J LEU* 3.6 10.3 - - - +
66J LEU* 1.3 78.6 - - - +
68J MET* 1.3 63.6 + - + +
70J GLN* 3.1 10.1 + - + +
71J THR* 3.0 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 68 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44J HIS* 4.6 16.4 - - - -
51J ARG* 5.4 7.0 - - - -
64J LEU* 2.8 38.2 + - + +
65J HIS 4.0 2.9 - - - +
67J GLU* 1.3 79.0 - - - +
69J HIS* 1.3 62.7 + - - +
71J THR* 3.3 4.7 + - - -
72J PHE* 3.1 33.0 + - + -
79J PHE* 3.3 33.7 - - + -
81J TYR* 5.9 2.5 - - + -
90J CYS* 3.5 23.3 - - - -
404J GLN* 5.3 0.2 - - - +
406J PHE* 3.5 46.0 - - + -
409J SER* 4.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 69 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65J HIS 2.9 18.5 + - - +
66J LEU* 3.6 14.1 - - + +
67J GLU 3.3 0.2 - - - -
68J MET* 1.3 74.7 - - - +
70J GLN* 1.3 64.2 + - - +
72J PHE* 3.5 8.9 + - - +
73J GLN* 3.2 50.4 + - + +
92J MET* 5.3 4.4 - - + +
408J TYR* 4.0 15.8 - + + -
409J SER* 3.0 43.6 + - - +
412J ARG* 4.2 25.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 70 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66J LEU 2.9 14.5 + - - +
67J GLU* 3.2 13.9 - - + +
69J HIS* 1.3 76.6 - - - +
71J THR* 1.3 55.2 + - - +
73J GLN* 2.8 39.6 + - - +
74J GLU* 3.0 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 71 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44J HIS* 3.6 27.5 + - + -
45J PRO* 4.5 1.9 - - + +
67J GLU* 3.0 16.2 + - - +
68J MET* 3.3 8.1 + - - -
70J GLN* 1.3 78.3 - - - +
72J PHE* 1.3 56.8 + - - +
74J GLU* 3.9 15.7 + - - +
75J LEU* 3.2 50.6 + - + +
79J PHE* 3.5 29.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 72 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68J MET* 3.1 27.5 + - + +
69J HIS 3.9 5.6 - - - +
70J GLN 3.1 0.6 + - - -
71J THR* 1.3 75.3 - - - +
73J GLN* 1.3 59.2 + - - +
76J GLY* 3.0 43.3 + - - -
77J PRO 4.0 6.7 - - - -
79J PHE* 3.4 25.6 - + - -
90J CYS* 3.6 20.9 - - + -
91J VAL* 3.7 26.7 - - - -
92J MET* 3.3 40.5 - - + +
406J PHE* 4.0 26.5 - + + -
409J SER* 3.7 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 73 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69J HIS* 3.2 48.0 + - + +
70J GLN* 2.8 22.1 + - - +
72J PHE* 1.3 77.6 - - + +
74J GLU* 1.3 65.7 + - + +
75J LEU 3.3 0.4 - - - -
76J GLY 4.4 1.8 + - - -
92J MET* 5.7 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 74 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45J PRO* 4.2 23.2 - - - +
70J GLN* 3.0 42.7 + - + +
71J THR* 3.9 16.2 + - - +
73J GLN* 1.3 79.9 - - - +
75J LEU* 1.3 71.5 + - + +
76J GLY 3.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J PRO* 4.0 29.1 - - + +
43J GLN 3.3 32.1 - - - +
44J HIS* 4.3 0.7 - - - -
45J PRO* 4.5 5.6 - - + -
71J THR* 3.2 38.4 + - + +
74J GLU* 1.3 92.8 - - + +
76J GLY* 1.3 63.4 + - - +
78J ILE 3.8 8.5 - - - +
79J PHE* 3.9 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 76 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72J PHE* 3.0 34.0 + - - +
73J GLN 4.4 2.4 + - - -
74J GLU 3.8 1.0 - - - -
75J LEU* 1.3 80.6 - - - +
77J PRO* 1.4 63.5 - - - +
78J ILE* 2.8 19.6 + - - +
79J PHE* 4.4 0.9 - - - -
----------------------------------------------------------
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