Contacts of the helix formed by residues 53 - 72 (chain G) in PDB entry 3J45
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 THR 53 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G ALA* 5.1 12.1 - - + +
32G ALA* 6.2 0.3 - - - +
51G PHE* 3.0 19.6 - - + +
52G MET* 1.3 84.4 - - + +
54G ARG* 1.3 52.7 + - - +
55G MET 2.9 6.3 - - - -
56G THR* 2.0 51.3 + - + -
57G ALA* 3.5 0.3 + - - +
173y TRP* 5.5 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 54 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G ASN* 2.1 57.7 + - + +
51G PHE* 4.0 18.9 - - + +
52G MET 3.3 2.9 - - - +
53G THR* 1.3 76.4 + - - +
55G MET* 1.3 61.1 + - + +
56G THR 3.0 1.8 - - - -
57G ALA* 3.1 18.6 + - + +
58G LEU* 3.0 47.0 + - + +
25y PHE* 5.6 9.3 - - - -
173y TRP* 5.6 3.4 - - + -
177y GLN* 6.2 2.9 - - - +
181y ARG* 5.9 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 55 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G MET* 4.2 16.2 - - + +
53G THR 2.9 0.4 - - - -
54G ARG* 1.3 79.2 - - - +
56G THR* 1.3 58.7 + - + +
58G LEU* 3.7 18.7 + - + +
59G LEU* 2.5 48.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 56 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G MET* 4.4 2.0 - - - +
24G GLN* 4.7 36.8 - - + +
25G GLY* 5.8 1.3 - - - -
28G ALA* 4.8 9.9 - - + +
53G THR* 2.0 44.5 + - + +
55G MET* 1.3 78.1 - - + +
57G ALA* 1.3 68.0 + - - +
59G LEU* 2.9 15.9 + - + +
60G ALA* 2.9 22.7 + - - +
173y TRP* 5.4 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G ARG* 3.1 28.5 - - + +
56G THR* 1.3 81.9 + - - +
58G LEU* 1.3 58.2 + - + +
60G ALA* 2.9 22.8 + - - +
61G THR* 3.2 20.3 + - + +
170y PHE* 5.7 0.4 - - - -
173y TRP* 3.4 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G ARG* 3.0 41.4 + - + +
55G MET* 4.2 21.1 - - + +
57G ALA* 1.3 77.3 - - + +
59G LEU* 1.3 57.2 + - + +
61G THR* 4.0 9.4 - - - +
62G LEU* 2.6 50.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 59 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G MET* 3.2 20.6 - - + +
24G GLN* 4.7 12.3 - - - +
55G MET* 2.5 42.3 + - + +
56G THR* 2.9 17.1 + - + +
58G LEU* 1.3 78.7 - - + +
60G ALA* 1.3 57.0 + - - +
62G LEU* 4.0 7.3 - - + +
63G PHE* 3.0 27.5 + - - +
66G ILE* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 60 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G MET* 3.9 11.9 - - + +
56G THR 2.9 10.6 + - - +
57G ALA* 2.9 12.0 + - - +
59G LEU* 1.3 73.6 - - - +
61G THR* 1.3 62.0 + - + +
62G LEU 3.0 1.1 - - - -
63G PHE* 2.6 31.0 + - - +
64G PHE* 3.1 22.7 + - + -
169y MET* 5.2 13.0 - - + -
170y PHE* 4.9 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 61 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G ALA* 3.2 10.9 + - + +
58G LEU* 3.7 15.6 + - - +
60G ALA* 1.3 75.1 - - - +
62G LEU* 1.3 67.9 + - - +
64G PHE* 3.4 9.0 + - - +
65G ILE* 3.2 34.4 + - - +
170y PHE* 3.2 41.0 - - + -
173y TRP* 6.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58G LEU* 2.6 39.9 + - + +
59G LEU* 4.1 9.2 - - + +
60G ALA 3.0 0.6 - - - -
61G THR* 1.3 85.1 + - - +
63G PHE* 1.3 55.8 + - - +
65G ILE* 3.9 11.6 - - + +
66G ILE* 2.4 47.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 63 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G ILE* 4.1 23.8 - - + -
17G VAL* 4.5 5.6 - - + -
18G GLY* 2.8 45.1 - - - -
21G MET* 3.8 23.6 - - + -
59G LEU 3.0 18.3 + - - +
60G ALA* 2.6 20.4 + - - +
62G LEU* 1.3 72.4 - - - +
64G PHE* 1.3 86.0 + + - -
66G ILE* 3.2 17.4 - - + +
67G SER* 3.2 27.0 + - - -
162y VAL* 6.0 1.3 - - + -
166y THR* 4.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 64 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E ARG* 4.2 2.2 + - - -
21G MET* 6.1 0.7 - - + -
60G ALA* 3.1 37.4 + - + -
61G THR* 3.4 7.4 + - - +
63G PHE* 1.3 92.3 - + - +
65G ILE* 1.3 62.8 + - + +
66G ILE 2.9 5.2 - - - -
67G SER* 2.8 24.7 + - - +
68G LEU* 3.3 7.3 + - - +
41y ILE* 6.1 2.2 - - + -
77y ILE* 4.6 24.5 - - + -
163y SER* 4.3 14.4 - - - -
166y THR* 1.7 57.0 - - + -
167y GLY* 4.4 2.0 - - - -
169y MET* 5.7 0.4 - - + -
170y PHE* 4.7 17.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 65 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E ARG* 2.5 57.2 - - + +
61G THR* 3.2 24.7 + - - +
62G LEU* 3.4 12.5 + - + +
64G PHE* 1.3 76.7 - - + +
66G ILE* 1.3 57.9 + - + +
68G LEU* 2.9 22.6 + - + +
69G VAL* 3.6 10.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 66 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G ILE* 6.2 2.7 - - + -
59G LEU 5.4 0.4 - - - +
62G LEU* 2.4 40.4 - - + +
63G PHE* 3.2 18.8 - - + +
65G ILE* 1.3 75.4 - - + +
67G SER* 1.3 61.7 + - - +
68G LEU 2.9 5.8 + - - -
69G VAL* 3.3 9.1 - - + +
70G LEU* 3.2 44.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 67 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G PHE* 3.2 18.5 + - - -
64G PHE* 2.8 31.4 + - - +
66G ILE* 1.3 75.7 - - - +
68G LEU* 1.3 61.0 + - - +
70G LEU* 4.4 8.3 - - - -
71G GLY* 3.1 20.9 + - - -
41y ILE* 5.6 4.3 - - - +
42y PRO* 4.6 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E ARG* 2.3 77.8 - - + +
64G PHE 3.3 7.1 + - - +
65G ILE* 2.9 19.1 - - + +
66G ILE 2.9 1.4 - - - -
67G SER* 1.3 82.5 - - - +
69G VAL* 1.3 67.2 + - + +
72G ASN* 3.4 25.3 + - - +
73G ILE* 4.3 2.4 + - - +
39y ILE* 2.4 43.1 - - + -
40y PRO 4.5 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 69 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E ARG* 5.9 2.2 - - + -
65G ILE* 4.3 9.0 - - + +
66G ILE* 3.3 17.0 - - + +
68G LEU* 1.3 87.5 - - + +
70G LEU* 1.3 74.6 + - + +
73G ILE* 2.7 53.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G LEU* 5.0 18.2 - - + -
11G ILE* 4.5 15.7 - - + +
14G ILE* 4.4 25.8 - - + -
66G ILE* 3.2 40.0 + - + +
67G SER* 4.4 5.6 - - - +
69G VAL* 1.3 89.2 - - + +
71G GLY* 1.3 64.5 + - - +
72G ASN 4.9 1.2 - - - +
73G ILE 5.2 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 71 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G ILE* 4.7 15.7 - - - +
67G SER* 3.1 20.8 + - - +
70G LEU* 1.3 80.1 - - - +
72G ASN* 1.3 67.0 + - - +
42y PRO* 5.1 15.0 - - - -
149y VAL* 5.6 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 72 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E ARG 5.7 1.4 + - - -
127E PHE* 5.5 8.3 + - - +
68G LEU* 3.4 17.2 + - + +
70G LEU 5.0 0.5 - - - +
71G GLY* 1.3 84.4 - - - +
73G ILE* 1.3 70.9 + - + +
40y PRO* 4.5 30.2 + - - +
41y ILE 6.2 0.3 - - - -
45y ASP* 5.4 1.9 - - - +
149y VAL* 5.1 10.2 - - - +
----------------------------------------------------------
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