Contacts of the helix formed by residues 76 - 86 (chain F) in PDB entry 6AHU
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 LYS 76 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A G 3.6 32.7 - - - +
37A C 5.2 6.7 - - - +
39A G 3.8 6.7 + - - -
38F MET* 4.6 18.3 - - + +
40F VAL 4.5 13.5 - - - +
41F LYS* 3.9 3.7 - - + +
42F GLU 2.9 44.3 + - - +
43F GLY* 4.1 0.8 - - - +
46F ILE* 3.9 26.2 - - + +
72F ARG* 4.2 10.8 - - + +
73F ALA* 3.2 8.4 + - - +
75F THR* 1.3 85.6 - - + +
77F THR* 1.3 58.9 + - - +
78F VAL 3.2 1.8 - - - -
79F THR* 2.7 23.3 + - - +
80F CYS* 3.0 15.4 + - - +
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Residues in contact with THR 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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38F MET* 4.9 7.5 - - - +
67F PHE* 3.6 24.3 - - - +
68F SER 3.2 27.8 + - - +
69F GLY* 4.2 5.2 - - - -
73F ALA 3.0 17.3 + - - +
74F THR* 4.0 9.9 - - - +
76F LYS* 1.3 74.0 - - - +
78F VAL* 1.3 65.1 + - - +
80F CYS* 3.8 7.7 - - - +
81F ALA* 3.3 16.8 + - - +
135F LEU* 3.8 25.1 - - + +
137F ILE* 3.7 9.8 - - - +
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Residues in contact with VAL 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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74F THR 3.4 21.3 - - - +
75F THR 4.5 4.0 - - - +
76F LYS 3.2 1.2 - - - +
77F THR* 1.3 75.9 - - - +
79F THR* 1.3 58.9 + - - +
80F CYS 3.2 0.2 - - - -
81F ALA* 3.5 2.8 + - - +
82F GLU* 3.1 28.1 + - - +
135F LEU* 4.0 26.0 - - + -
137F ILE* 4.1 7.4 - - + +
78G ILE* 4.5 11.4 - - + -
102G THR* 3.8 32.5 - - + -
128G SER* 3.8 24.9 - - - +
129G ALA 4.3 5.4 - - - +
130G ILE* 5.2 3.1 - - + -
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Residues in contact with THR 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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37A C 3.7 53.2 + - + +
46F ILE* 5.6 5.9 - - - +
75F THR 3.5 11.9 - - - +
76F LYS* 2.7 26.8 + - - +
78F VAL* 1.3 74.9 - - - +
80F CYS* 1.3 60.4 + - - +
82F GLU* 3.5 6.4 + - - +
83F ILE* 3.3 31.4 + - - +
127G ASN* 5.5 0.4 - - - +
128G SER* 3.4 23.1 - - - +
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Residues in contact with CYS 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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36F VAL* 4.7 2.7 - - - -
38F MET* 5.1 8.5 - - + -
46F ILE* 5.8 9.6 - - + -
49F LEU* 4.5 24.0 - - - -
50F MET* 3.3 42.6 - - - +
53F ALA* 6.1 0.4 - - - -
67F PHE* 3.7 21.8 - - + -
76F LYS 3.0 17.9 + - - +
77F THR* 3.9 10.3 - - - +
78F VAL 3.2 0.6 - - - -
79F THR* 1.3 78.3 - - - +
81F ALA* 1.3 58.3 - - - +
82F GLU 3.5 0.5 + - - -
83F ILE* 5.2 2.0 - - - -
84F LEU* 3.8 7.3 + - - +
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Residues in contact with ALA 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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67F PHE* 3.7 30.0 - - + -
77F THR 3.3 14.1 + - - +
78F VAL 4.2 0.9 - - - +
80F CYS* 1.3 78.6 - - - +
82F GLU* 1.3 63.5 + - - +
84F LEU* 3.8 4.9 + - - +
85F LYS* 3.3 19.6 + - - +
93F GLN* 4.9 5.2 - - - +
137F ILE* 3.8 26.5 - - + -
139F LEU* 4.3 9.1 - - + +
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Residues in contact with GLU 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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37A C 3.4 32.3 - - - +
78F VAL* 3.1 18.4 + - - +
79F THR* 3.9 7.0 - - - +
80F CYS 3.3 0.8 - - - -
81F ALA* 1.3 77.2 - - - +
83F ILE* 1.3 64.1 + - - +
85F LYS* 3.1 41.1 + - - +
86F ARG* 3.4 17.5 + - + +
93F GLN* 5.4 0.7 + - - -
102G THR* 4.0 18.2 + - - -
103G SER* 3.7 17.9 + - - +
104G THR* 2.4 26.9 + - - +
128G SER* 5.5 1.3 - - - -
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Residues in contact with ILE 83 (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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37A C 3.8 39.3 - - + +
38A U 4.5 31.9 - - + +
46F ILE* 5.2 9.2 - - + -
50F MET* 3.8 27.6 - - + -
79F THR* 3.3 19.4 + - - +
80F CYS* 3.9 2.0 + - - +
81F ALA 3.5 0.2 - - - -
82F GLU* 1.3 74.7 - - - +
84F LEU* 1.3 64.5 + - - +
86F ARG* 3.1 24.2 + - + +
87F ARG* 3.6 16.9 + - + +
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Residues in contact with LEU 84 (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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50F MET* 3.5 15.6 - - + +
53F ALA* 3.4 46.4 - - + +
54F THR* 4.4 4.0 - - - +
57F MET* 5.8 2.2 - - + -
65F ILE* 4.5 15.5 - - + -
67F PHE* 4.1 12.1 - - + -
80F CYS 3.8 6.6 + - - +
81F ALA 3.8 8.0 + - - +
82F GLU 3.3 0.4 - - - -
83F ILE* 1.3 78.3 - - - +
85F LYS* 1.3 56.4 + - - +
87F ARG* 3.2 7.8 + - + +
88F LEU* 2.8 51.6 + - + +
139F LEU* 3.8 25.4 - - + -
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Residues in contact with LYS 85 (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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81F ALA 3.3 12.4 + - - +
82F GLU* 3.1 39.9 + - - +
83F ILE 3.2 0.4 - - - -
84F LEU* 1.3 77.0 - - - +
86F ARG* 1.3 72.9 + - - +
87F ARG 3.2 0.2 - - - -
88F LEU* 5.4 0.2 - - - -
89F ALA* 3.3 26.8 + - + +
90F GLY 4.4 21.5 - - - +
93F GLN* 6.0 8.5 - - - +
139F LEU* 5.4 9.3 - - + +
156F PRO* 4.3 26.1 - - + +
102G THR 5.9 2.7 - - - -
103G SER* 5.6 2.2 - - - +
104G THR* 4.1 8.3 + - - +
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Residues in contact with ARG 86 (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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37A C 6.0 2.5 - - - +
537B ARG* 6.0 2.2 - - - +
82F GLU* 3.5 18.6 - - + +
83F ILE* 3.1 16.6 + - + +
85F LYS* 1.3 94.6 - - - +
87F ARG* 1.3 67.9 + - + +
89F ALA* 5.8 0.4 - - - -
104G THR* 5.4 5.4 - - - -
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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