Contacts of the helix formed by residues 72 - 81 (chain C) in PDB entry 1AXC
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 72 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 3.4 16.2 - - + +
19C LEU* 4.2 14.1 - - + -
20C LYS* 4.1 8.4 - - - +
23C ILE* 3.0 53.2 - - + +
24C ASN 2.8 9.5 + - - +
26C ALA* 3.9 21.1 - - + +
28C TRP* 3.3 44.2 - - + +
37C LEU* 4.5 1.6 - - + -
70C VAL* 3.5 5.4 + - + -
71C ASN* 1.3 68.8 - - - +
73C THR* 1.3 60.2 + - - +
75C MET* 4.3 1.1 - - - -
76C SER* 2.8 30.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LYS* 4.6 11.3 + - - +
24C ASN* 3.7 21.2 + - - +
71C ASN* 2.9 13.5 + - - -
72C LEU* 1.3 77.0 - - - +
74C SER* 1.3 59.7 + - - +
76C SER* 3.1 8.8 + - - -
77C LYS* 3.0 45.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ASN* 3.1 29.5 + - - +
73C THR* 1.3 77.9 - - - +
75C MET* 1.3 65.2 + - - +
77C LYS* 3.1 11.7 + - - +
78C ILE* 3.1 25.6 + - - +
116C MET* 4.5 10.1 - - - -
117C LYS 5.9 0.7 - - - -
175E LEU* 3.8 33.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 5.0 5.2 - - + -
16C LEU* 3.6 28.9 - - + -
28C TRP* 3.8 37.9 - - + -
70C VAL* 3.9 16.2 - - + -
71C ASN 2.9 13.6 + - - +
74C SER* 1.3 75.6 - - - +
76C SER* 1.3 57.3 + - - +
78C ILE* 3.2 6.2 + - - +
79C LEU* 2.9 32.0 + - + +
90C LEU* 4.7 10.5 - - + -
99C LEU* 4.1 20.0 - - + -
101C LEU* 4.3 17.0 - - + -
116C MET* 3.5 25.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 3.7 15.9 - - - +
17C GLU* 3.3 12.0 + - - +
20C LYS* 3.1 36.9 + - - +
72C LEU 2.8 18.2 + - - -
73C THR* 3.2 7.4 - - - -
75C MET* 1.3 76.1 - - - +
77C LYS* 1.3 61.9 + - - +
79C LEU* 3.4 3.3 + - - +
80C LYS* 3.0 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C THR* 3.0 33.0 + - + +
74C SER* 3.1 10.2 + - - +
76C SER* 1.3 76.7 - - - +
78C ILE* 1.3 60.6 + - - +
80C LYS* 3.7 25.9 + - - +
81C CYS* 3.6 16.8 - - - -
153E HIS* 4.1 31.8 + - + +
154E ILE* 4.9 1.3 - - + +
175E LEU* 3.9 27.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C SER 3.1 9.6 + - - +
75C MET* 3.4 8.1 - - - +
76C SER 3.1 0.2 - - - -
77C LYS* 1.3 75.8 - - - +
79C LEU* 1.3 65.4 + - - +
81C CYS* 3.1 24.7 + - - +
101C LEU* 3.7 28.0 - - + -
103C PHE* 3.4 10.3 - - + -
114C TYR* 4.0 24.2 - - + -
115C GLU 5.0 0.7 - - - -
116C MET* 3.4 43.5 - - + +
154E ILE* 4.0 20.4 - - + -
175E LEU* 3.9 16.4 - - + -
177E ASN 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 3.2 30.5 - - + +
13C LYS* 3.5 21.8 + - + +
16C LEU* 3.1 38.6 - - + -
75C MET* 2.9 19.2 + - + +
76C SER* 3.4 6.2 + - - +
78C ILE* 1.3 72.4 - - - +
80C LYS* 1.3 56.7 + - - +
81C CYS 2.9 5.4 - - - -
82C ALA* 2.9 23.7 + - - +
88C ILE* 3.8 29.8 - - + -
101C LEU* 4.2 13.5 - - + -
103C PHE* 4.1 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LYS* 4.4 7.9 + - - +
17C GLU* 4.3 22.2 - - - +
20C LYS* 5.0 5.9 - - - +
76C SER* 3.0 25.7 + - - +
77C LYS* 3.9 29.5 - - - +
78C ILE 3.2 0.8 - - - -
79C LEU* 1.3 75.3 - - - +
81C CYS* 1.3 58.5 + - - +
82C ALA 3.3 1.1 - - - -
146E ARG* 3.1 17.3 + - - -
149E ARG* 3.8 5.7 + - - +
150E ASP* 3.7 8.1 - - - +
153E HIS* 4.3 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LYS 3.6 18.2 - - - -
78C ILE* 3.1 13.0 + - - +
79C LEU 2.9 0.6 - - - -
80C LYS* 1.3 80.3 - - - +
82C ALA* 1.3 59.8 + - - +
83C GLY 4.0 0.7 + - - -
86C ASP* 4.6 1.7 - - - +
103C PHE* 3.9 8.7 - - + -
110C LYS* 5.1 6.6 + - - -
112C SER* 5.2 2.9 + - - -
114C TYR* 3.2 40.1 + - + +
146E ARG* 3.5 6.5 + - - -
150E ASP* 3.6 42.3 - - - +
153E HIS* 4.5 2.0 - - - -
154E ILE* 4.7 3.4 - - - -
180E ILE* 6.1 0.3 - - - +
----------------------------------------------------------
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