Contacts of the helix formed by residues 56 - 73 (chain F) in PDB entry 5M64
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 GLU 56 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55F PRO* 1.3 80.8 - - + +
57F ASP* 1.3 69.9 + - - +
59F GLN* 3.0 13.3 + - + +
60F GLN* 3.0 24.8 + - - +
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Residues in contact with ASP 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F PRO* 3.7 15.6 - - - +
56F GLU* 1.3 81.6 + - - +
58F PHE* 1.3 62.7 + - - +
60F GLN* 3.1 8.6 + - - +
61F HIS* 2.9 44.4 + - + +
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Residues in contact with PHE 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1203B LYS* 5.1 9.2 - - + -
23D HIS* 4.6 15.0 - + + -
24D ALA 3.4 11.7 - - - +
25D THR* 3.4 41.7 - - + -
55F PRO* 3.4 11.4 - - + +
56F GLU 3.2 0.4 - - - -
57F ASP* 1.3 85.8 + - - +
59F GLN* 1.3 64.0 + - - +
61F HIS* 3.4 11.0 + - + +
62F GLU* 2.8 49.2 + - + +
44G ALA* 3.5 24.9 - - + -
46G TYR* 3.2 23.1 - - - -
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Residues in contact with GLN 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D THR* 2.5 46.8 + - - +
26D GLN* 3.9 13.0 + - + +
55F PRO 3.0 18.5 + - - +
56F GLU* 3.0 15.0 + - + +
58F PHE* 1.3 78.3 - - - +
60F GLN* 1.3 60.1 + - - +
62F GLU* 3.6 11.2 - - - +
63F GLN* 2.8 43.7 + - + +
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Residues in contact with GLN 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F GLU* 3.0 19.7 + - - +
57F ASP* 3.1 11.4 + - - +
59F GLN* 1.3 74.1 - - - +
61F HIS* 1.3 84.6 + - - +
63F GLN* 3.2 6.1 + - - +
64F ILE* 2.9 45.2 + - - +
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Residues in contact with HIS 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1203B LYS* 5.5 20.4 - - + +
57F ASP* 2.9 38.2 + - + +
58F PHE* 3.8 13.7 - - + +
60F GLN* 1.3 88.8 + - - +
62F GLU* 1.3 61.7 + - - +
64F ILE* 3.2 11.0 - - - +
65F ARG* 3.1 27.1 + - - +
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Residues in contact with GLU 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F PHE* 2.8 42.7 + - + +
59F GLN* 3.6 17.5 - - - +
60F GLN 3.2 0.2 - - - -
61F HIS* 1.3 77.5 - - - +
63F GLN* 1.3 63.1 + - - +
65F ARG* 3.2 15.1 + - - +
66F ARG* 2.8 72.5 + - - +
46G TYR* 4.8 3.3 + - - -
90G LEU* 5.8 0.2 - - - +
119G HIS* 6.0 0.2 + - - -
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Residues in contact with GLN 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F GLN* 2.8 29.8 + - + +
60F GLN* 3.2 6.5 + - - +
62F GLU* 1.3 80.2 - - - +
64F ILE* 1.3 59.2 + - - +
66F ARG* 3.3 10.8 + - - +
67F LYS* 3.0 32.4 + - - +
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Residues in contact with ILE 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F GLN* 2.9 35.3 + - - +
61F HIS* 3.2 23.3 - - - +
63F GLN* 1.3 76.1 - - - +
65F ARG* 1.3 55.6 + - + +
67F LYS* 3.4 25.1 - - - +
68F THR* 2.4 48.7 + - + +
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Residues in contact with ARG 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F HIS 3.1 26.4 + - - +
62F GLU* 3.2 20.8 + - - +
64F ILE* 1.3 77.1 - - + +
66F ARG* 1.3 91.9 + - - +
68F THR* 3.2 7.3 + - - -
69F LEU* 3.0 50.0 + - - +
46G TYR* 5.4 3.4 + - - -
117G TRP* 3.2 44.6 - - - +
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Residues in contact with ARG 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F GLU* 2.8 54.3 + - - +
63F GLN* 3.6 14.4 - - - +
64F ILE 3.3 0.2 - - - -
65F ARG* 1.3 99.6 - - - +
67F LYS* 1.3 57.5 + - - +
69F LEU* 3.2 12.8 + - - +
70F LYS* 3.0 50.7 + - + +
90G LEU* 3.4 41.0 - - - +
91G ASP 5.0 7.5 + - - -
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Residues in contact with LYS 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F GLN* 3.0 21.4 + - - +
64F ILE* 3.4 23.0 - - - +
66F ARG* 1.3 78.0 - - - +
68F THR* 1.3 80.1 + - + +
70F LYS* 4.3 4.5 - - - +
71F GLU* 3.1 31.3 + - + +
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Residues in contact with THR 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F ILE* 2.4 32.8 + - + +
65F ARG* 3.2 13.5 + - - -
67F LYS* 1.3 99.9 - - + +
69F LEU* 1.3 57.2 + - - +
71F GLU* 4.3 7.3 - - - +
72F LYS* 2.9 30.2 + - - +
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Residues in contact with LEU 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F ARG* 3.0 48.0 + - - +
66F ARG* 3.7 12.8 - - - +
68F THR* 1.3 77.0 + - - +
70F LYS* 1.3 83.6 + - - +
72F LYS* 3.3 7.9 + - + +
73F ALA* 3.0 24.8 + - - +
143F PHE* 4.0 15.0 - - + -
91G ASP 5.3 1.8 - - - +
92G ALA* 3.5 33.4 - - + +
93G ASP* 4.3 1.1 - - - +
94G PRO* 4.8 0.2 - - + -
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Residues in contact with LYS 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F ARG* 3.0 33.9 + - + +
67F LYS* 4.3 4.3 - - - +
69F LEU* 1.3 93.4 - - - +
71F GLU* 1.3 61.6 + - - +
73F ALA* 3.4 19.8 + - - +
91G ASP 5.0 4.6 + - - -
93G ASP 3.3 10.7 + - - +
94G PRO* 3.2 47.8 - - + +
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Residues in contact with GLU 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169E ARG* 5.0 10.2 + - - -
67F LYS* 3.1 20.9 + - + +
68F THR* 4.3 6.5 - - - +
70F LYS* 1.3 74.5 - - - +
72F LYS* 1.3 68.7 + - - +
73F ALA 3.4 7.1 + - - +
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Residues in contact with LYS 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169E ARG* 4.8 2.8 + - - +
68F THR 2.9 22.1 + - - +
69F LEU* 3.3 8.9 + - + +
71F GLU* 1.3 80.0 + - - +
73F ALA* 1.3 64.1 + - - +
74F ILE* 3.8 1.9 + - - +
137F TYR* 4.7 16.0 + - - -
141F GLY* 3.2 38.5 - - - +
142F SER* 3.6 22.9 - - - +
143F PHE* 3.5 33.4 + - + +
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Residues in contact with ALA 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169E ARG* 5.6 0.5 + - - -
69F LEU 3.0 6.8 + - - +
70F LYS 3.5 15.0 - - - +
71F GLU 3.2 9.2 - - - +
72F LYS* 1.3 82.7 - - - +
74F ILE* 1.3 64.3 + - - +
75F PRO* 4.4 3.2 - - - +
143F PHE* 3.6 27.8 - - + -
94G PRO* 3.6 29.2 - - + -
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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
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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