Contacts of the helix formed by residues 71 - 85 (chain C) in PDB entry 4X4P
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 SER 71 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C PHE* 1.3 75.5 - - - +
72C LYS* 1.3 66.7 + - - +
73C GLU* 3.2 18.0 + - - +
74C GLU* 3.3 16.4 + - - +
75C LEU* 3.2 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C SER* 1.3 76.1 - - - +
73C GLU* 1.3 66.8 + - + +
75C LEU* 3.5 22.5 + - + +
76C ARG* 3.7 21.5 + - - +
97C HIS* 3.5 33.3 + - + -
98C PRO* 5.0 9.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C SER* 3.2 11.8 + - - +
72C LYS* 1.3 81.7 - - + +
74C GLU* 1.3 71.3 + - + +
75C LEU 3.5 0.3 + - - -
76C ARG* 3.6 14.4 + - - +
77C GLU* 3.6 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C PHE* 4.8 2.1 - - - -
70C PHE* 4.1 23.9 - - + -
71C SER* 3.3 22.4 + - - +
73C GLU* 1.3 84.8 - - + +
75C LEU* 1.3 65.4 + - - +
77C GLU* 3.4 25.7 - - - +
78C ARG* 3.3 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C PHE* 4.0 36.3 - - + -
67C PRO 5.3 0.9 - - - +
70C PHE* 4.0 19.5 - - + -
71C SER 3.2 23.2 + - - +
72C LYS* 3.5 16.6 - - + +
73C GLU 3.2 0.4 - - - -
74C GLU* 1.3 75.8 - - - +
76C ARG* 1.3 60.5 + - + +
79C GLY* 2.8 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C LYS* 3.7 21.2 + - - +
73C GLU* 3.6 10.1 + - - +
74C GLU 3.4 0.2 - - - -
75C LEU* 1.3 79.6 - - + +
77C GLU* 1.3 55.7 + - - +
79C GLY* 4.9 0.2 - - - -
80C LEU* 2.7 55.6 + - + +
94C TYR* 3.5 30.7 + - - -
98C PRO* 3.4 36.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C GLU 3.6 9.3 + - - +
74C GLU* 3.4 32.4 + - - +
75C LEU 3.3 0.8 - - - -
76C ARG* 1.3 78.2 - - - +
78C ARG* 1.3 72.0 + - + +
80C LEU* 4.3 1.2 - - - +
81C GLU* 2.9 38.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C PHE* 3.5 29.0 - - + -
70C PHE* 5.4 10.5 - - + -
74C GLU* 3.3 14.8 + - + +
77C GLU* 1.3 94.8 + - + +
79C GLY* 1.3 57.9 + - - +
81C GLU* 4.6 7.0 - - - -
82C ILE* 2.9 48.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C LEU* 3.7 21.3 - - - +
66C PHE* 3.9 5.3 - - - -
75C LEU 2.8 19.4 + - - -
76C ARG* 3.7 0.4 - - - -
78C ARG* 1.3 78.9 - - - +
80C LEU* 1.3 66.4 + - - +
83C GLY* 3.4 15.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ARG* 2.7 57.3 + - + +
77C GLU* 4.3 1.3 - - - +
79C GLY* 1.3 76.8 - - - +
81C GLU* 1.3 58.5 + - - +
82C ILE 3.2 0.4 - - - -
83C GLY* 3.7 0.7 - - - -
84C LYS* 2.7 32.0 + - - +
92C ILE* 3.6 49.2 - - + +
94C TYR* 4.8 2.2 - - - +
98C PRO* 4.5 10.5 - - + +
99C TYR* 4.5 20.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C GLU* 2.9 25.3 + - + +
78C ARG* 4.6 7.9 - - - -
80C LEU* 1.3 78.3 - - - +
82C ILE* 1.3 59.7 + - + +
84C LYS* 3.8 24.2 + - - +
85C ALA* 3.1 28.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C LEU* 3.4 30.5 - - + -
38C LEU* 4.3 11.4 - - + -
40C VAL* 3.4 38.4 - - + -
64C LEU* 4.0 16.6 - - + -
66C PHE* 4.8 5.2 - - + -
78C ARG* 2.9 44.0 + - + +
80C LEU 3.2 0.2 - - - -
81C GLU* 1.3 77.6 - - + +
83C GLY* 1.3 64.3 + - - +
85C ALA* 3.1 13.6 + - - +
86C VAL* 3.3 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C LEU* 4.8 2.6 - - - +
79C GLY 3.4 13.5 + - - -
80C LEU* 3.3 5.0 + - - -
82C ILE* 1.3 80.0 - - - +
84C LYS* 1.3 61.2 + - - +
86C VAL* 3.3 1.7 + - - -
87C LEU* 3.2 39.7 + - - +
90C TYR* 5.1 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C LEU 2.7 21.5 + - - +
81C GLU* 3.8 28.8 + - - +
83C GLY* 1.3 73.4 - - - +
85C ALA* 1.3 60.7 + - - +
86C VAL 3.2 1.3 + - - -
87C LEU 3.6 4.5 - - - +
90C TYR* 3.4 68.0 - - + -
92C ILE* 6.3 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ARG* 5.1 4.9 - - - +
38C LEU* 3.7 25.1 - - + +
81C GLU* 3.1 20.6 + - - +
82C ILE 3.4 6.7 - - - +
83C GLY 3.1 0.8 - - - -
84C LYS* 1.3 77.6 - - - +
86C VAL* 1.3 60.0 + - - +
87C LEU 4.9 0.2 - - - -
----------------------------------------------------------
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