Contacts of the helix formed by residues 50 - 64 (chain C) in PDB entry 3G03
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 MET 50 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C THR 3.8 11.7 + - - +
28C VAL* 4.5 13.9 - - + -
49C THR* 1.3 73.6 - - - +
51C LYS* 1.3 64.6 + - + +
53C VAL* 3.3 5.4 + - + -
54C LEU* 3.0 46.4 + - + +
100C TYR* 4.3 14.1 - - + -
103C ILE* 3.7 26.0 - - + -
104C TYR* 3.9 24.5 - - + +
107C LEU* 3.7 29.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A PHE* 3.7 7.8 - - + -
59A GLN* 3.7 36.8 - - - +
62A MET* 5.6 7.7 - - - +
20B GLU* 5.9 0.2 + - - -
49C THR* 3.2 8.5 + - - +
50C MET* 1.3 79.5 - - + +
52C GLU* 1.3 57.5 + - - +
54C LEU* 3.4 9.8 + - + +
55C PHE* 2.8 28.9 + - - +
100C TYR* 5.6 1.3 - - - -
26D LEU 5.5 0.4 - - - -
27D THR* 2.4 50.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL 4.4 7.3 - - - +
42A GLY* 3.9 3.9 - - - +
55A PHE* 3.9 20.0 - - + -
56A TYR* 2.4 39.2 + - + +
59A GLN* 6.0 0.7 - - + -
27C LEU* 5.4 0.5 - - - +
45C LYS* 2.8 31.3 + - - -
48C TYR* 3.4 11.2 - - + -
49C THR* 2.9 47.6 + - + +
51C LYS* 1.3 74.1 - - - +
53C VAL* 1.3 64.9 + - - +
55C PHE* 3.2 1.8 + - - +
56C TYR* 2.9 35.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C VAL* 4.0 15.5 - - + -
30C PRO* 4.7 4.5 - - + -
34C LEU* 4.4 11.9 - - + -
38C LEU* 3.9 23.8 - - + +
48C TYR* 3.6 24.0 - - + -
49C THR 3.1 14.7 + - - +
50C MET* 3.6 11.9 - - + +
52C GLU* 1.3 76.0 - - - +
54C LEU* 1.3 57.9 + - - +
57C LEU* 2.9 31.0 + - + +
103C ILE* 4.2 29.6 - - + -
107C LEU* 4.9 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C MET* 3.0 32.8 + - + +
51C LYS* 3.7 10.8 - - + +
53C VAL* 1.3 71.5 - - - +
55C PHE* 1.3 67.9 + - - +
57C LEU* 4.4 2.7 - - - -
58C GLY 3.0 9.0 + - - -
99C ILE* 4.6 4.0 - - + -
100C TYR* 3.3 42.0 - - + +
103C ILE* 3.8 24.5 - - + -
23D TRP* 2.8 32.4 + - + +
26D LEU* 4.2 28.0 - - + +
27D THR* 4.9 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LYS* 3.9 9.4 - - + -
52A GLU* 3.5 44.4 - - + -
55A PHE* 3.7 46.0 - + + -
56A TYR* 5.6 0.2 - + - -
51C LYS 2.8 21.3 + - - +
52C GLU 3.2 3.6 + - - +
54C LEU* 1.3 75.8 - - - +
56C TYR* 1.3 83.8 + + - +
58C GLY* 3.2 1.6 + - - -
59C GLN* 2.9 66.8 + - + +
23D TRP* 4.6 4.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LYS* 4.2 4.7 + - - +
48A TYR* 5.4 0.5 - - - -
52A GLU* 2.8 34.4 + - - +
56A TYR* 3.8 29.1 + + - -
38C LEU* 3.8 20.6 - - + -
41C VAL* 3.5 33.7 - - + +
43C ALA* 3.8 38.8 + - + -
45C LYS* 5.0 2.5 - - - -
48C TYR* 4.3 7.4 - + - -
52C GLU* 2.9 32.0 + - + +
55C PHE* 1.3 99.5 - + - +
57C LEU* 1.3 60.8 + - - +
59C GLN* 3.2 4.6 + - + -
60C TYR* 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 5.4 4.0 - - + -
37C LEU* 4.2 15.7 - - + -
38C LEU* 3.9 8.6 - - + +
53C VAL* 2.9 20.2 + - + +
54C LEU* 3.8 4.0 - - + +
56C TYR* 1.3 77.0 - - - +
58C GLY* 1.3 60.8 + - - +
60C TYR* 3.2 6.7 + - + +
61C ILE* 3.1 28.2 + - + +
82C LEU* 3.7 29.8 - - + -
86C PHE* 5.3 2.2 - - + -
99C ILE* 4.5 4.3 - - + -
102C MET* 3.7 26.7 - - + -
103C ILE* 4.1 21.1 - - + -
23D TRP* 3.6 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C LEU 3.0 11.3 + - - -
55C PHE 3.7 2.0 - - - -
57C LEU* 1.3 75.2 - - - +
59C GLN* 1.3 61.7 + - - +
61C ILE 3.3 1.2 + - - -
62C MET* 2.9 25.3 + - - +
19D PHE* 3.6 17.3 - - - -
23D TRP* 3.3 35.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLU* 3.4 23.6 - - - +
49A THR* 5.3 1.0 + - - -
51A LYS* 4.5 9.0 - - - +
41C VAL* 4.1 12.1 - - + +
55C PHE* 2.9 59.4 + - + +
56C TYR* 3.2 11.6 + - + +
58C GLY* 1.3 78.2 - - - +
60C TYR* 1.3 53.4 + - - +
62C MET* 3.7 25.4 - - - +
63C THR* 2.8 43.7 + - - +
20D GLU* 6.0 0.6 - - - +
23D TRP* 6.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 3.3 45.8 - - + -
40C SER* 3.4 26.0 - - - -
41C VAL* 3.5 14.5 - - + +
56C TYR 3.0 8.5 + - - +
57C LEU 3.3 9.0 - - - +
59C GLN* 1.3 77.3 - - - +
61C ILE* 1.3 66.8 + - + +
63C THR* 3.7 0.2 - - - -
64C LYS* 3.0 57.4 + - + +
66C LEU* 4.0 10.5 - - + -
80C ASP* 2.8 28.8 + - - -
81C LEU* 3.8 15.2 - - + +
82C LEU* 3.9 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C LEU* 3.1 18.7 + - + +
58C GLY 3.3 5.4 + - - +
60C TYR* 1.3 83.1 - - + +
62C MET* 1.3 61.1 + - - +
65C ARG* 3.1 2.8 + - - -
66C LEU* 3.1 37.4 + - + -
67C TYR* 4.0 8.1 - - + +
75C VAL* 4.1 18.6 - - + -
82C LEU* 3.5 30.7 - - + -
91C PHE* 4.2 13.2 - - + -
19D PHE* 3.5 25.6 - - + -
23D TRP* 3.6 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLU* 4.7 10.5 - - + -
51A LYS* 5.7 4.0 - - + -
58C GLY 2.9 12.3 + - - +
59C GLN* 3.7 33.9 - - - +
61C ILE* 1.3 74.2 - - - +
63C THR* 1.3 60.9 + - - +
65C ARG* 2.9 30.3 + - - -
67C TYR* 3.9 16.0 - - + -
19D PHE* 3.1 31.9 - - + -
20D GLU* 3.6 41.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLU* 4.5 11.6 + - - +
41C VAL* 4.2 16.8 - - + +
59C GLN* 2.8 29.0 + - - +
60C TYR 3.7 2.7 - - - -
62C MET* 1.3 75.1 - - - +
64C LYS* 1.3 71.9 + - + +
65C ARG* 3.5 8.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C TYR* 3.0 50.6 + - + +
63C THR* 1.3 87.6 - - + +
65C ARG* 1.3 72.1 + - - +
66C LEU* 3.2 22.2 + - + +
80C ASP* 2.9 25.6 + - - -
----------------------------------------------------------
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