Contacts of the helix formed by residues 56 - 74 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48G HIS 3.0 19.8 + - - +
49G THR 4.0 4.3 - - - -
50G ASN* 3.9 3.0 - - - +
54G THR 3.2 4.7 + - - -
55G LEU* 1.3 71.9 - - - +
57G GLY* 1.3 70.1 + - - +
58G GLY* 2.8 35.3 + - - -
59G LEU* 3.0 14.4 + - - +
60G THR* 3.0 12.2 + - - -
151G CL 3.7 18.1 - - + +
21H PHE* 3.5 33.6 - + + +
22H GLU* 3.0 32.6 + - - -
62H THR* 3.9 10.1 - - + +
65H ASP* 3.9 3.8 + - - -
66H ASN* 3.0 34.0 + - - -
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Residues in contact with GLY 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G LEU 3.4 2.8 + - - -
56G HIS* 1.3 76.0 - - - +
58G GLY* 1.3 57.2 + - - +
60G THR* 3.4 2.6 + - - -
61G ALA* 3.0 18.5 + - - +
90G TYR* 2.8 40.5 + - - -
151G CL 3.2 10.5 - - - +
65H ASP* 3.5 13.7 - - - -
83H SER* 5.1 0.7 - - - -
86H MET* 5.5 0.4 - - - -
150H COA 4.3 7.3 - - - +
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Residues in contact with GLY 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G HIS* 2.8 14.4 - - - -
57G GLY* 1.3 73.4 - - - +
59G LEU* 1.3 59.9 + - - +
61G ALA* 3.4 8.7 + - - +
62G THR* 2.9 30.3 + - - -
21H PHE* 3.9 1.1 - - - -
58H GLY 3.8 0.7 - - - +
61H ALA 4.8 1.1 - - - -
62H THR* 3.2 34.0 + - - -
65H ASP* 3.4 3.8 + - - -
86H MET* 5.6 0.4 - - - -
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Residues in contact with LEU 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G VAL* 4.1 9.9 - - + +
25G LEU* 3.5 28.5 - - + -
42G MET* 4.6 1.8 - - + -
48G HIS* 3.2 58.1 - - + +
55G LEU* 3.8 10.8 - - + -
56G HIS 3.0 10.3 + - - +
58G GLY* 1.3 75.3 - - - +
60G THR* 1.3 59.0 + - - +
62G THR* 3.0 3.3 + - - -
63G LEU* 2.8 35.7 + - + +
21H PHE* 3.6 39.3 - - + -
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Residues in contact with THR 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G LEU* 3.3 28.3 + - - +
56G HIS 3.0 7.5 + - - -
57G GLY* 3.5 9.2 - - - -
59G LEU* 1.3 73.8 - - - +
61G ALA* 1.3 59.2 + - - +
63G LEU* 3.2 13.7 + - - +
64G VAL* 2.9 28.2 + - + +
88G ILE* 4.1 8.5 - - + -
90G TYR* 3.7 24.4 - - + -
120G LEU* 3.8 19.7 - - + -
129G ILE* 5.4 2.1 - - + +
130G ALA* 4.0 16.6 - - + -
150H COA 5.9 0.3 - - - -
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Residues in contact with ALA 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G GLY 3.0 13.7 + - - +
58G GLY 3.5 6.5 - - - +
59G LEU 3.2 0.2 - - - -
60G THR* 1.3 76.8 - - - +
62G THR* 1.3 56.1 + - - +
64G VAL* 3.2 4.4 + - - +
65G ASP* 3.0 29.5 + - - +
86G MET* 3.8 6.6 - - + +
88G ILE* 3.4 31.4 - - + -
58H GLY* 4.8 0.7 - - - -
61H ALA* 3.5 29.6 - - + -
86H MET* 4.2 1.8 - - + -
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Residues in contact with THR 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G PHE* 3.6 10.9 - - + +
22G GLU* 6.3 0.4 - - - -
24G VAL* 3.9 23.6 - - + -
25G LEU* 4.1 13.2 - - + -
58G GLY 2.9 15.7 + - - -
59G LEU* 3.0 15.0 + - - -
61G ALA* 1.3 75.7 - - - +
63G LEU* 1.3 58.2 + - - +
65G ASP* 3.4 2.6 + - - +
66G ASN* 2.9 31.8 + - - +
21H PHE* 4.7 0.7 - - - -
56H HIS* 4.0 20.9 - - + +
58H GLY* 3.2 24.8 - - - -
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Residues in contact with LEU 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G LEU* 3.6 29.8 - - + -
28G ILE* 3.9 20.6 - - + -
42G MET* 4.3 12.1 - - + -
55G LEU* 4.6 3.1 - - + -
59G LEU* 2.8 25.9 + - + +
60G THR* 3.4 10.5 - - - +
62G THR* 1.3 69.9 - - - +
64G VAL* 1.3 66.0 + - - +
67G ILE* 2.9 35.5 + - + +
100G ILE* 4.1 16.8 - - + -
102G ILE* 4.0 25.3 - - + +
120G LEU* 4.0 22.2 - - + -
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Residues in contact with VAL 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G THR* 2.9 21.8 + - + +
61G ALA* 3.5 8.1 - - - +
63G LEU* 1.3 74.7 - - - +
65G ASP* 1.3 54.3 + - - +
68G SER* 2.6 38.3 + - - -
86G MET* 3.8 23.3 - - + -
88G ILE* 4.3 15.3 - - + -
118G VAL* 3.7 27.5 - - + +
120G LEU* 4.1 20.2 - - + -
132G GLY* 4.4 20.0 - - - +
134G HIS* 4.5 10.1 - - + -
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Residues in contact with ASP 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G ALA 3.0 17.2 + - - +
62G THR* 3.4 8.3 - - - +
64G VAL* 1.3 76.0 - - - +
66G ASN* 1.3 65.2 + - - +
68G SER* 2.9 14.7 + - - -
69G THR* 2.7 30.1 + - - -
83G SER* 3.6 8.8 + - - -
86G MET* 4.1 9.7 - - - +
134G HIS* 3.2 23.9 - - - -
136G LYS* 4.6 2.1 + - - -
149G UOC 4.9 2.8 - - - +
56H HIS* 3.8 4.1 + - - -
57H GLY* 3.6 11.3 + - - -
58H GLY 3.4 23.8 + - - +
90H TYR* 4.9 0.7 + - - -
151H CL 4.1 3.7 - - - +
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Residues in contact with ASN 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G MET* 3.1 21.6 - - + +
22G GLU* 2.9 18.8 + - - +
25G LEU* 3.5 20.0 - - + -
62G THR* 2.9 20.5 + - - +
65G ASP* 1.3 80.3 + - - +
67G ILE* 1.3 61.7 + - + +
69G THR* 3.1 8.5 + - - -
70G MET* 2.9 30.8 + - + +
1001G P6G 3.8 15.0 - - - +
56H HIS* 3.1 34.7 + - - -
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Residues in contact with ILE 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G LEU* 4.4 4.7 - - + -
28G ILE* 3.8 19.5 - - + -
38G VAL* 3.8 29.5 - - + +
40G CYS* 4.4 7.2 - - + -
63G LEU* 2.9 27.7 + - + +
64G VAL 4.8 0.2 - - - +
66G ASN* 1.3 82.7 - - + +
68G SER* 1.3 62.0 + - - +
70G MET* 3.4 29.2 + - + +
71G ALA 3.1 17.0 + - - -
102G ILE* 3.8 32.8 - - + +
104G ALA* 3.4 18.0 - - + +
118G VAL* 5.1 0.7 - - + -
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Residues in contact with SER 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64G VAL 2.6 24.8 + - - -
65G ASP 2.9 6.9 + - - -
67G ILE* 1.3 75.6 - - - +
69G THR* 1.3 62.2 + - - +
71G ALA* 3.1 6.3 + - - +
72G LEU* 3.1 24.3 + - - +
104G ALA* 3.8 10.8 - - - +
116G THR* 3.2 29.7 - - - +
118G VAL* 3.7 12.8 - - - +
134G HIS* 2.8 25.3 + - - -
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Residues in contact with THR 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G ASP* 2.7 24.6 + - - -
66G ASN* 3.1 7.6 + - - -
68G SER* 1.3 79.3 + - - +
70G MET* 1.3 62.7 + - - +
72G LEU* 3.0 11.9 + - - +
73G LEU* 3.0 21.0 + - + +
80G PRO* 3.7 24.7 - - + +
136G LYS* 2.8 36.6 + - - +
149G UOC 4.2 7.4 - - + -
1001G P6G 3.8 17.7 - - - -
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Residues in contact with MET 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G LEU* 3.9 27.2 - - + +
11G VAL* 4.8 4.0 - - + -
12G ILE* 4.4 10.1 - - + -
15G MET* 4.1 21.1 - - - -
28G ILE* 3.9 15.0 - - + -
38G VAL* 3.7 14.4 - - + -
40G CYS* 4.2 15.0 - - - -
66G ASN* 2.9 15.7 + - + +
67G ILE* 3.4 37.5 - - + +
69G THR* 1.3 76.2 - - - +
71G ALA* 1.3 61.8 + - - +
73G LEU* 3.1 21.1 + - - +
74G CYS* 3.2 16.6 + - - -
1001G P6G 3.9 15.7 - - - +
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Residues in contact with ALA 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36G GLY* 3.6 25.1 - - - +
38G VAL* 3.6 13.8 - - + +
67G ILE 3.1 12.7 + - - +
68G SER* 3.1 11.6 + - - +
70G MET* 1.3 76.2 - - - +
72G LEU* 1.3 57.5 + - - +
74G CYS* 3.1 22.0 + - - +
75G THR* 3.7 0.3 - - - +
104G ALA* 4.1 18.4 - - + +
105G HIS 4.8 0.7 - - - -
106G VAL* 3.6 18.3 - - + +
116G THR* 5.3 0.2 - - + -
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Residues in contact with LEU 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G SER 3.1 13.3 + - - +
69G THR* 3.0 9.9 + - - +
71G ALA* 1.3 71.9 - - - +
73G LEU* 1.3 61.5 + - - +
74G CYS 3.1 1.6 - - - -
75G THR* 2.7 25.8 + - + -
78G GLY* 3.5 8.5 - - - -
79G ALA 3.6 17.0 - - - +
80G PRO* 3.8 9.4 - - + +
106G VAL* 3.8 22.4 - - + -
109G GLN* 4.1 14.6 - - + +
114G ALA* 3.5 32.5 - - + -
116G THR* 3.9 17.3 - - + -
136G LYS* 3.7 31.9 - - + -
138G LEU* 5.0 0.7 - - + -
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Residues in contact with LEU 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G MET* 4.0 24.1 - - + +
8G LEU* 4.4 12.1 - - + -
11G VAL* 4.8 3.4 - - + -
69G THR 3.0 15.4 + - - +
70G MET* 3.1 11.6 + - - +
72G LEU* 1.3 77.3 - - - +
74G CYS* 1.3 57.0 + - - +
75G THR 3.3 7.3 + - - +
78G GLY* 3.5 30.9 - - - +
80G PRO* 4.0 25.4 - - + -
149G UOC 3.7 31.0 - - + -
1001G P6G 3.7 25.4 - - - -
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Residues in contact with CYS 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G MET* 3.5 34.3 - - + -
8G LEU* 3.8 22.9 - - - -
33G ALA* 4.1 7.6 - - - -
34G ALA 3.4 16.2 - - - +
35G PRO* 3.1 9.8 - - + +
36G GLY 2.8 19.2 + - - -
38G VAL* 3.8 8.1 - - - -
70G MET 3.2 14.9 + - - -
71G ALA* 3.1 10.4 + - - +
72G LEU 3.1 1.0 - - - -
73G LEU* 1.3 76.5 - - - +
75G THR* 1.3 57.1 + - - -
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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
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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