Contacts of the helix formed by residues 56 - 74 (chain C) in PDB entry 3F5O
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 HIS 56 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C HIS 3.0 19.9 + - - +
50C ASN* 3.8 10.4 - - - +
54C THR 3.2 4.2 + - - -
55C LEU* 1.3 72.3 - - - +
57C GLY* 1.3 70.9 + - - +
58C GLY* 2.8 34.4 + - - -
59C LEU* 3.0 14.9 + - + +
60C THR* 3.1 12.0 + - - -
151C CL 3.7 12.7 - - + +
21D PHE* 3.5 31.4 - + + +
22D GLU* 2.9 41.6 + - - -
62D THR* 4.1 8.5 - - + +
65D ASP* 3.8 5.8 + - - -
66D ASN* 3.1 26.9 + - - -
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Residues in contact with GLY 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C LEU 3.4 2.6 + - - -
56C HIS* 1.3 75.9 - - - +
58C GLY* 1.3 57.1 + - - +
60C THR* 3.5 2.0 + - - -
61C ALA* 3.0 19.2 + - - +
90C TYR* 2.8 42.0 + - - -
151C CL 3.3 11.3 - - - +
65D ASP* 3.5 11.9 - - - -
83D SER* 5.3 0.7 - - - -
86D MET* 4.5 1.1 - - - +
150D COA 4.3 6.9 - - - +
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Residues in contact with GLY 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C HIS* 2.8 19.3 - - - -
57C GLY* 1.3 70.3 - - - -
59C LEU* 1.3 58.7 + - - +
61C ALA* 3.4 9.2 + - - +
62C THR* 2.8 30.3 + - - -
21D PHE* 3.8 1.3 - - - -
58D GLY 3.9 0.7 - - - +
61D ALA 4.8 0.9 - - - -
62D THR* 3.3 32.9 + - - -
65D ASP* 3.3 4.6 + - - -
86D MET* 5.3 0.2 - - - -
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Residues in contact with LEU 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C VAL* 4.2 10.8 - - + +
25C LEU* 3.5 28.0 - - + -
42C MET* 4.5 2.0 - - + -
48C HIS* 3.2 58.3 - - + +
55C LEU* 3.7 11.2 - - + -
56C HIS 3.0 9.6 + - - +
58C GLY* 1.3 74.2 - - - +
60C THR* 1.3 59.5 + - - +
62C THR* 3.0 2.9 + - - -
63C LEU* 2.8 33.8 + - + +
21D PHE* 3.5 37.4 - - + -
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Residues in contact with THR 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C LEU* 3.2 26.4 + - - +
56C HIS 3.1 10.6 + - - -
57C GLY 3.5 9.0 - - - -
58C GLY 3.4 0.2 - - - -
59C LEU* 1.3 74.8 - - - +
61C ALA* 1.3 58.3 + - - +
63C LEU* 3.2 13.1 + - - +
64C VAL* 2.9 28.9 + - + +
88C ILE* 4.0 7.4 - - + -
90C TYR* 3.7 24.1 - - + -
120C LEU* 3.9 14.6 - - + -
129C ILE* 5.5 1.5 - - + +
130C ALA* 3.9 23.3 - - + -
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Residues in contact with ALA 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C GLY 3.0 14.7 + - - +
58C GLY* 3.5 6.5 - - - +
59C LEU 3.2 0.2 - - - -
60C THR* 1.3 76.8 - - - +
62C THR* 1.3 57.0 + - - +
64C VAL* 3.3 3.9 + - - +
65C ASP* 2.9 29.6 + - - +
86C MET* 3.7 7.6 - - + +
88C ILE* 3.7 28.7 - - + -
90C TYR* 4.4 0.4 + - - -
58D GLY* 4.8 1.1 - - - -
61D ALA* 3.4 31.9 - - + -
86D MET* 4.3 1.8 - - + -
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Residues in contact with THR 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C PHE* 3.5 16.9 - - + +
22C GLU* 6.4 0.2 - - - -
24C VAL* 3.8 24.0 - - + -
25C LEU* 4.2 12.1 - - + -
58C GLY 2.8 15.4 + - - -
59C LEU* 3.0 14.9 + - - -
61C ALA* 1.3 72.5 - - - +
63C LEU* 1.3 56.9 + - - +
65C ASP* 3.3 5.9 + - - +
66C ASN* 2.8 37.7 + - - +
21D PHE* 4.6 0.5 - - - -
56D HIS* 4.0 14.8 - - + +
58D GLY* 3.3 19.6 + - - -
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Residues in contact with LEU 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LEU* 3.5 28.5 - - + -
28C ILE* 3.8 16.8 - - + -
42C MET* 4.2 14.4 - - + -
55C LEU* 4.7 2.5 - - + -
59C LEU* 2.8 21.4 + - + +
60C THR* 3.5 9.6 - - - +
62C THR* 1.3 73.0 - - - +
64C VAL* 1.3 65.4 + - - +
67C ILE* 2.9 52.8 + - + +
100C ILE* 4.0 26.2 - - + -
102C ILE* 4.1 15.3 - - + +
120C LEU* 4.1 13.9 - - + -
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Residues in contact with VAL 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C THR 2.9 20.6 + - - +
61C ALA* 3.3 8.3 + - - +
63C LEU* 1.3 74.1 - - - +
65C ASP* 1.3 55.4 + - - +
68C SER* 2.7 37.9 + - - -
86C MET* 3.8 23.1 - - + -
87C ASN 4.9 0.4 - - - +
88C ILE* 4.5 11.7 - - + -
118C VAL* 3.6 26.9 - - + +
120C LEU* 4.0 20.2 - - + -
132C GLY* 4.2 26.2 - - - +
134C HIS* 4.5 7.6 - - + -
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Residues in contact with ASP 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ALA 2.9 17.4 + - - +
62C THR* 3.4 8.5 - - - +
64C VAL* 1.3 77.3 - - - +
66C ASN* 1.3 67.5 + - - +
68C SER* 3.0 14.0 + - - -
69C THR* 2.8 26.9 + - - -
83C SER* 3.6 9.8 + - - -
86C MET* 4.1 9.7 - - + +
134C HIS* 3.2 24.5 - - - -
136C LYS* 4.7 1.4 + - - -
149C UOC 5.0 1.7 - - - +
150C COA 5.8 0.4 - - - -
56D HIS* 3.7 4.7 + - - +
57D GLY* 3.6 11.3 + - - -
58D GLY 3.4 22.9 + - - -
90D TYR* 5.0 0.5 + - - -
151D CL 4.2 1.2 - - - +
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Residues in contact with ASN 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C MET* 3.7 17.7 - - - +
22C GLU* 2.9 20.7 + - - +
25C LEU* 3.5 24.0 - - + +
62C THR* 2.8 20.4 + - - +
65C ASP* 1.3 79.1 + - - +
67C ILE* 1.3 58.6 + - + +
69C THR* 3.1 8.4 + - - -
70C MET* 2.9 35.5 + - + +
1001C P6G 3.8 11.9 + - - +
56D HIS* 3.1 34.7 + - - -
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Residues in contact with ILE 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ILE* 4.6 8.1 - - + -
38C VAL* 4.0 26.3 - - + +
40C CYS* 3.9 19.7 - - + -
63C LEU* 2.9 39.7 + - + +
66C ASN* 1.3 79.4 - - + +
68C SER* 1.3 63.1 + - - +
70C MET* 3.2 12.9 + - + +
71C ALA 3.1 17.3 + - - -
102C ILE* 3.3 46.2 - - + +
104C ALA* 3.5 20.2 - - + +
118C VAL* 5.2 0.4 - - + -
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Residues in contact with SER 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C VAL 2.7 24.6 + - - -
65C ASP 3.0 3.6 + - - -
67C ILE* 1.3 75.8 - - - +
69C THR* 1.3 60.9 + - - +
71C ALA* 3.1 7.2 + - - +
72C LEU* 3.1 24.9 + - - +
104C ALA* 3.7 11.4 - - - +
116C THR* 3.2 30.1 - - - +
118C VAL* 3.7 13.0 - - - +
134C HIS* 2.7 24.7 + - - -
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Residues in contact with THR 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C ASP* 2.8 23.2 + - - -
66C ASN* 3.1 8.8 + - - -
68C SER* 1.3 77.7 + - - +
70C MET* 1.3 63.3 + - - +
72C LEU* 3.0 11.5 + - - +
73C LEU* 3.0 20.7 + - + +
80C PRO* 3.5 24.5 - - + +
136C LYS* 2.8 36.7 + - - +
149C UOC 4.2 7.6 - - + +
1001C P6G 3.7 19.5 - - - +
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Residues in contact with MET 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 4.2 26.5 - - + +
11C VAL* 4.7 4.7 - - + -
12C ILE* 4.2 9.2 - - + -
15C MET* 3.6 37.7 - - + -
28C ILE* 3.8 13.5 - - + -
38C VAL* 3.9 11.0 - - + -
40C CYS* 4.3 20.2 - - - -
66C ASN* 2.9 22.8 + - + +
67C ILE* 3.2 16.6 + - + +
69C THR* 1.3 77.0 - - - +
71C ALA* 1.3 61.6 + - - +
73C LEU* 3.1 21.7 + - - +
74C CYS* 3.2 15.9 + - - -
1001C P6G 3.8 13.9 - - - +
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Residues in contact with ALA 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C GLY* 3.6 18.7 - - - +
38C VAL* 3.7 14.3 - - + +
67C ILE 3.1 12.2 + - - +
68C SER* 3.1 10.0 + - - +
70C MET* 1.3 75.2 - - - +
72C LEU* 1.3 58.1 + - - +
74C CYS* 3.1 24.9 + - - +
75C THR* 3.5 6.8 - - - +
104C ALA* 4.1 20.4 - - + +
105C HIS 4.7 0.4 - - - -
106C VAL* 3.9 17.9 - - + +
116C THR* 5.3 0.2 - - + -
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Residues in contact with LEU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C SER 3.1 16.2 + - - +
69C THR* 3.0 9.4 + - - +
71C ALA* 1.3 73.1 - - - +
73C LEU* 1.3 61.0 + - - +
74C CYS 3.0 1.8 - - - -
75C THR* 2.6 27.6 + - + -
78C GLY* 3.5 7.3 - - - -
79C ALA 3.7 16.6 + - - +
80C PRO* 3.7 11.2 - - + +
106C VAL* 3.8 22.9 - - + -
109C GLN* 4.3 12.8 - - + +
114C ALA* 3.5 30.3 - - + -
116C THR* 3.9 16.2 - - + -
136C LYS* 3.6 33.9 - - + -
138C LEU* 5.1 0.4 - - + -
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Residues in contact with LEU 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C MET* 5.2 1.0 - - - +
8C LEU* 4.4 17.7 - - + -
11C VAL* 4.9 2.7 - - + -
69C THR 3.0 15.1 + - - +
70C MET* 3.3 12.6 - - - +
72C LEU* 1.3 75.3 - - - +
74C CYS* 1.3 58.3 + - - +
75C THR 3.2 6.9 + - - +
78C GLY* 3.5 31.2 - - - +
80C PRO* 3.8 27.8 - - + -
149C UOC 3.9 31.0 - - + -
1001C P6G 3.9 26.0 - - - -
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Residues in contact with CYS 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C MET* 3.8 40.2 - - + +
8C LEU* 3.7 27.8 - - - -
33C ALA* 4.1 2.0 - - - -
34C ALA 3.5 15.3 - - - +
35C PRO* 3.1 8.7 - - - +
36C GLY 2.8 18.8 + - - +
38C VAL* 3.8 8.7 - - + -
70C MET 3.2 14.9 + - - +
71C ALA* 3.1 14.7 + - - +
72C LEU 3.0 1.4 - - - -
73C LEU* 1.3 76.4 - - - +
75C THR* 1.3 57.8 + - - +
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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) + - + + + + + -
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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