Contacts of the helix formed by residues 64 - 76 (chain C) in PDB entry 3I5G
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 LYS 64 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C PHE* 3.6 2.4 - - - -
26C GLY 3.5 13.0 - - - +
27C ASP* 4.5 10.5 + - - +
63C TYR* 1.3 78.0 - - - +
65C LEU* 1.3 66.1 + - - +
66C GLU* 3.2 20.9 - - + +
67C GLU* 3.1 38.2 + - + +
68C ILE* 3.3 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 5.2 2.9 - - + +
11C VAL* 4.1 19.7 - - + -
12C ARG* 2.7 62.1 - - + +
15C PHE* 3.3 35.8 - - + -
16C ASP* 6.0 0.2 - - - +
26C GLY 4.2 0.6 + - - -
64C LYS* 1.3 74.0 - - - +
66C GLU* 1.3 80.2 + - + +
68C ILE* 3.2 3.2 + - - +
69C LEU* 3.1 37.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ARG* 4.9 3.1 + - - -
64C LYS* 3.2 23.2 - - + +
65C LEU* 1.3 100.1 + - + +
67C GLU* 1.3 57.8 + - + +
69C LEU* 4.1 12.3 - - + +
70C PRO* 3.0 20.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ALA 3.8 3.8 - - - +
63C TYR* 3.5 32.8 - - + -
64C LYS* 3.1 53.2 + - + +
66C GLU* 1.3 77.7 - - + +
68C ILE* 1.3 62.1 + - - +
69C LEU 3.3 0.2 - - - -
70C PRO* 2.8 23.5 - - - +
71C ILE* 3.6 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C VAL* 4.0 22.4 - - + -
15C PHE* 3.5 27.8 - - + -
28C VAL* 4.4 6.5 - - + -
33C VAL* 5.1 10.3 - - + -
36C LEU* 3.3 36.3 - - + -
37C LEU* 5.7 3.6 - - + -
40C LEU* 5.6 2.0 - - + -
63C TYR* 3.8 32.1 - - + -
64C LYS 3.3 1.3 + - - +
65C LEU* 3.2 8.2 + - - +
67C GLU* 1.3 77.2 - - - +
69C LEU* 1.3 66.0 - - - +
71C ILE* 3.0 10.1 + - + +
72C TYR* 2.8 24.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C LEU* 3.7 29.9 - - + +
8C ILE* 4.1 33.2 - - + -
11C VAL* 3.7 33.4 - - + -
65C LEU* 3.1 28.2 + - + +
66C GLU* 4.1 13.0 - - + +
68C ILE* 1.3 79.5 - - - +
70C PRO* 1.3 71.0 - - + +
72C TYR* 3.1 12.7 + - - +
73C GLU* 3.1 11.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C GLU 3.0 18.8 - - - +
67C GLU* 2.8 23.1 - - - +
69C LEU* 1.3 91.8 - - + +
71C ILE* 1.3 53.6 + - + +
73C GLU* 3.7 13.6 - - + +
74C GLU* 2.7 47.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C VAL* 4.2 22.2 - - + -
37C LEU* 4.5 9.9 - - + -
52C HIS* 3.1 41.8 - - + +
63C TYR* 4.1 34.1 - - + +
67C GLU 3.6 14.4 - - - +
68C ILE* 3.0 12.4 + - + +
70C PRO* 1.3 76.1 - - + +
72C TYR* 1.3 66.3 + - - +
74C GLU* 4.0 6.3 - - - +
75C MET* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C LEU* 3.8 35.7 - - + -
7C GLU* 4.5 17.5 + - + +
10C GLU* 5.6 2.3 + - - -
11C VAL* 3.9 20.2 - - + -
37C LEU* 4.0 15.9 - - + +
40C LEU* 3.5 41.5 + - + +
42C MET* 3.7 26.2 - - + -
68C ILE* 2.8 14.0 + - + +
69C LEU* 3.3 8.3 - - - +
71C ILE* 1.3 79.3 - - - +
73C GLU* 1.3 49.7 + - - +
75C MET* 3.4 2.6 - - - +
76C SER* 2.6 42.6 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
1C SER* 4.7 1.9 - - - -
2C GLN* 3.2 43.4 + - - +
3C LEU* 3.5 38.3 + - + +
69C LEU* 3.1 10.5 + - - +
70C PRO* 3.7 19.5 - - + +
72C TYR* 1.3 76.3 - - - +
74C GLU* 1.3 77.9 + - - +
76C SER* 3.0 17.4 + - - +
77C SER* 3.4 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
----------------------------------------------------------
52C HIS* 4.0 18.0 + - + +
70C PRO* 2.7 38.5 + - + +
71C ILE* 4.0 5.8 - - - +
73C GLU* 1.3 84.4 - - - +
75C MET* 1.3 56.9 + - - +
77C SER* 2.7 40.2 + - - -
78C LYS 4.1 0.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
33C VAL* 6.0 0.2 - - + -
37C LEU* 3.5 27.1 - - + -
42C MET* 3.3 24.0 - - + +
44C PRO* 4.3 11.9 - - + -
48C GLN* 3.6 40.6 + - + +
49C VAL* 4.2 5.8 - - - +
52C HIS* 3.6 41.0 + - + -
71C ILE* 3.0 18.3 + - + +
72C TYR* 3.4 6.5 - - - +
74C GLU* 1.3 79.3 - - - +
76C SER* 1.3 57.7 + - - +
77C SER 2.9 6.2 + - - -
78C LYS* 3.4 18.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
3C LEU* 5.6 0.3 - - - +
42C MET* 3.3 23.1 - - - -
72C TYR* 2.6 31.1 + - - -
73C GLU* 3.0 19.2 + - - +
75C MET* 1.3 72.2 - - - +
77C SER* 1.3 59.9 + - - +
78C LYS 3.4 6.7 - - - +
79C ASP* 5.0 2.3 - - - +
----------------------------------------------------------
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