Contacts of the helix formed by residues 68 - 82 (chain F) in PDB entry 5A31
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 68 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38F GLU* 3.2 27.6 + - + +
39F GLU 5.8 0.9 - - - +
42F PHE* 5.5 0.7 - - - +
66F CYS 3.5 0.5 - - - +
67F THR* 1.3 84.2 + - - +
69F PRO* 1.3 75.6 - - + +
70F GLN* 4.1 14.2 + - - +
71F CYS* 3.5 25.1 + - - +
72F LYS* 3.1 22.4 + - - +
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Residues in contact with PRO 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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67F THR 3.7 2.6 - - - +
68F THR* 1.3 90.0 - - + +
70F GLN* 1.3 71.4 + - + +
72F LYS* 3.2 3.3 + - + -
73F TYR* 2.9 28.3 + - - +
109F GLU* 3.6 25.8 - - + +
110F PHE* 3.5 40.2 - - + +
113F SER* 4.7 4.0 - - - +
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Residues in contact with GLN 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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42F PHE* 3.7 42.1 - - + -
68F THR* 3.3 12.1 - - - +
69F PRO* 1.3 95.4 - - + +
71F CYS* 1.3 58.2 + - - +
73F TYR* 3.3 8.6 + - - +
74F LEU* 2.9 28.6 + - - +
113F SER* 5.6 5.8 - - - +
18H HIS* 5.9 6.1 - - - +
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Residues in contact with CYS 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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38F GLU* 4.3 6.1 - - - -
41F LEU* 4.6 2.5 - - - -
42F PHE* 3.3 45.1 - - - -
61F LEU* 3.8 19.4 - - + +
66F CYS* 3.3 29.6 - - + -
68F THR* 3.5 15.2 + - - +
69F PRO 3.4 0.2 - - - -
70F GLN* 1.3 77.9 - - - +
72F LYS* 1.3 59.8 + - - +
74F LEU* 3.8 4.1 - - - +
75F LEU* 2.8 31.9 + - - +
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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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66F CYS* 3.5 28.4 - - - +
67F THR* 3.3 22.1 + - - +
68F THR 3.1 12.8 + - - +
69F PRO* 3.7 7.6 - - + +
71F CYS* 1.3 76.4 - - - +
73F TYR* 1.3 63.8 + - - +
75F LEU* 3.5 3.8 - - - +
76F ALA* 2.9 25.3 + - - +
91F ILE* 3.5 37.3 - - + +
92F LEU* 4.7 0.9 - - - -
101F LYS* 5.7 2.7 - - - +
109F GLU* 4.7 14.6 + - - +
110F PHE* 3.9 20.2 - - + -
263Y LYS* 6.0 2.8 - - - +
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Residues in contact with TYR 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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69F PRO 2.9 13.6 + - - +
70F GLN* 3.5 10.5 - - - +
72F LYS* 1.3 77.2 - - - +
74F LEU* 1.3 61.7 + - + +
76F ALA* 3.1 3.3 + - - +
77F LYS* 2.8 44.9 + - + +
92F LEU* 4.4 8.5 - - + -
110F PHE* 4.2 1.2 - - + -
113F SER* 5.2 2.7 - - - +
116F PHE* 4.0 9.2 + - + +
117F THR* 3.2 41.1 - - + -
120F LEU* 3.5 27.9 - - + +
18H HIS* 2.7 64.2 + + + +
19H TYR* 4.6 9.0 - + - -
20H ALA* 5.1 2.1 - - - +
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Residues in contact with LEU 74 (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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42F PHE* 3.9 13.5 - - + -
45F ALA* 3.9 12.3 - - + -
46F THR* 3.4 43.1 - - - +
49F TYR* 4.0 34.8 - - + -
57F ALA* 4.8 1.8 - - + -
61F LEU* 4.1 8.1 - - + -
70F GLN 2.9 15.6 + - - +
71F CYS* 3.8 4.7 - - - +
73F TYR* 1.3 79.7 - - + +
75F LEU* 1.3 57.3 + - - +
77F LYS* 3.1 7.7 + - + +
78F CYS* 2.9 33.6 + - - +
19H TYR* 4.5 13.9 - - + +
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Residues in contact with LEU 75 (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 TYR* 3.7 37.5 - - + +
61F LEU* 4.1 30.6 - - + +
62F LYS* 4.4 7.4 - - + +
66F CYS* 4.3 18.8 - - - -
71F CYS 2.8 19.8 + - - +
72F LYS 3.5 4.7 - - - +
74F LEU* 1.3 77.2 - - - +
76F ALA* 1.3 60.9 + - - +
77F LYS 3.4 0.2 + - - -
78F CYS* 3.4 3.5 + - - +
79F CYS* 2.9 29.5 + - - -
87F GLU* 4.5 3.1 - - - +
91F ILE* 3.4 30.3 - - + -
292Y LEU* 6.2 4.5 - - + -
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Residues in contact with ALA 76 (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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72F LYS 2.9 15.1 + - - +
73F TYR 3.5 3.8 - - - +
75F LEU* 1.3 78.2 - - - +
77F LYS* 1.3 61.9 + - - +
79F CYS* 3.3 9.9 + - - +
80F VAL* 3.1 28.3 + - + +
88F GLY* 3.8 11.1 - - - +
91F ILE* 4.2 5.8 - - + +
92F LEU* 3.4 41.5 - - + -
120F LEU* 4.1 4.4 - - + +
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Residues in contact with LYS 77 (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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49F TYR* 3.6 22.4 - - + +
73F TYR* 2.8 40.3 + - + +
74F LEU* 3.4 15.7 - - + +
76F ALA* 1.3 77.1 - - - +
78F CYS* 1.3 58.1 + - - +
80F VAL* 3.5 7.3 + - - +
81F ASP* 3.0 26.6 + - - +
120F LEU* 4.0 21.0 - - + +
18H HIS 4.2 0.9 - - - +
19H TYR* 3.2 40.2 + - + -
20H ALA* 4.6 5.7 - - - +
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Residues in contact with CYS 78 (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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49F TYR* 3.6 27.4 - - - -
54F ALA* 3.5 25.1 - - - -
57F ALA* 4.0 7.0 - - - -
58F TYR* 3.8 26.9 - - + -
61F LEU* 6.1 0.2 - - - -
74F LEU* 2.9 15.9 + - - +
75F LEU* 3.5 10.1 - - - +
77F LYS* 1.3 76.4 - - - +
79F CYS* 1.3 54.9 + - - +
81F ASP* 3.2 7.9 + - - +
82F LEU* 2.8 38.6 + - + +
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Residues in contact with CYS 79 (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 TYR* 3.6 26.9 - - - -
75F LEU* 2.9 26.6 + - - -
76F ALA 3.3 2.9 + - - +
78F CYS* 1.3 74.4 - - - +
80F VAL* 1.3 59.0 + - - +
82F LEU* 3.2 4.9 + - - +
83F SER 2.9 8.7 + - - -
84F LYS* 2.9 37.3 + - + +
87F GLU* 3.6 15.9 - - - -
88F GLY* 3.4 25.6 - - - +
91F ILE* 3.8 17.9 - - - -
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Residues in contact with VAL 80 (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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76F ALA 3.1 15.5 + - - +
77F LYS* 3.8 7.2 - - - +
79F CYS* 1.3 79.3 - - + +
81F ASP* 1.3 62.8 + - - +
83F SER* 3.0 16.6 + - - +
84F LYS 5.0 1.8 - - - -
85F LEU* 5.0 9.0 - - + +
88F GLY* 5.0 5.6 - - - -
120F LEU* 3.7 24.0 - - + -
123F HIS* 4.2 25.4 - - + +
124F VAL* 3.8 20.2 - - + -
127F LYS* 4.6 12.8 + - + +
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Residues in contact with ASP 81 (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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49F TYR* 3.9 19.5 + - - +
54F ALA* 3.2 27.8 - - - +
77F LYS* 3.0 14.7 + - - +
78F CYS* 3.3 11.7 - - - +
80F VAL* 1.3 78.1 - - - +
82F LEU* 1.3 58.8 + - - +
83F SER* 3.4 7.1 + - - -
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Residues in contact with LEU 82 (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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54F ALA* 3.4 33.0 - - + -
55F TYR* 4.0 15.3 - - + +
58F TYR* 3.3 44.4 - - + -
78F CYS 2.8 20.7 + - - +
79F CYS 3.2 3.8 + - - +
81F ASP* 1.3 73.1 - - - +
83F SER* 1.3 69.5 + - - +
84F LYS* 3.2 31.4 + - + +
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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