Contacts of the helix formed by residues 77 - 96 (chain B) in PDB entry 1F0K
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 ALA 77 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B LEU* 4.3 13.5 - - + -
69B LYS* 4.7 4.5 - - - -
73B ALA 3.5 7.4 + - - +
74B LEU 2.9 12.9 + - - +
76B ALA* 1.3 77.6 - - - +
78B PRO* 1.3 61.8 - - - +
80B ARG* 3.3 24.7 + - - +
81B ILE* 2.9 26.5 + - - +
365B SO4 3.4 19.5 - - - +
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Residues in contact with PRO 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ILE 3.9 11.6 - - - +
76B ALA 3.2 10.1 - - - +
77B ALA* 1.3 88.2 - - - +
79B LEU* 1.3 68.0 + - + +
81B ILE* 3.5 8.2 - - + +
82B PHE* 3.1 28.2 + - - +
365B SO4 3.2 13.0 - - - +
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B PRO* 1.3 85.3 - - + +
80B ARG* 1.3 60.3 + - + +
82B PHE* 3.8 4.5 - - + +
83B ASN* 3.0 29.3 + - - +
365B SO4 3.1 25.9 + - - +
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Residues in contact with ARG 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B SER 4.2 13.5 - - - +
65B GLY* 3.8 27.2 + - - -
66B LEU* 3.7 21.4 - - + +
69B LYS* 4.7 7.6 - - - +
77B ALA* 3.7 15.0 - - - +
79B LEU* 1.3 75.7 - - + +
81B ILE* 1.3 65.6 + - - +
83B ASN* 3.4 5.3 + - - +
84B ALA* 3.1 24.1 + - - +
365B SO4 2.9 44.4 + - - +
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Residues in contact with ILE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B LEU* 4.3 7.3 - - + +
74B LEU* 3.5 51.1 - - + +
75B ILE* 4.6 13.9 - - + -
77B ALA 2.9 19.1 + - - +
78B PRO* 3.5 12.3 - - + +
80B ARG* 1.3 77.2 - - - +
82B PHE* 1.3 68.1 + - + +
84B ALA 3.4 0.2 + - - -
85B TRP* 3.0 28.2 + - + +
110B PRO* 4.0 27.4 - - + -
113B LEU* 4.6 19.1 - - + -
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Residues in contact with PHE 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B PRO 3.1 21.1 + - - +
79B LEU* 3.8 5.2 - - + +
81B ILE* 1.3 79.9 - - + +
83B ASN* 1.3 60.4 + - - +
85B TRP* 3.3 35.5 + + - +
86B ARG* 2.8 70.0 + - + +
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Residues in contact with ASN 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ARG* 5.4 3.3 - - - +
79B LEU 3.0 17.9 + - - +
80B ARG* 3.8 6.7 - - - +
82B PHE* 1.3 79.3 - - + +
84B ALA* 1.3 65.3 + - - +
86B ARG* 3.2 8.6 + - - +
87B GLN* 2.9 44.6 + - - +
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Residues in contact with ALA 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ILE* 4.3 4.2 - - + +
62B ARG 3.5 19.7 + - - +
63B ILE* 4.2 5.8 - - + -
66B LEU* 4.2 5.8 - - + -
80B ARG 3.1 16.2 + - - +
81B ILE 4.0 2.2 - - - +
83B ASN* 1.3 76.3 + - - +
85B TRP* 1.3 57.6 + - - +
87B GLN* 3.3 14.8 + - - +
88B ALA* 3.0 29.8 + - - +
110B PRO* 3.8 26.9 - - + +
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Residues in contact with TRP 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ILE* 3.0 21.7 + - + +
82B PHE* 3.4 46.9 - + - +
84B ALA* 1.3 78.8 - - - +
86B ARG* 1.3 62.9 + - + +
88B ALA* 3.4 1.9 + - - +
89B ARG* 2.9 61.1 + - - +
110B PRO* 4.1 11.6 - - + +
113B LEU* 3.2 34.7 + - + +
114B ALA* 3.5 22.8 - - - +
117B SER* 3.4 20.9 + - - -
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Residues in contact with ARG 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B PHE* 2.8 66.8 + - + +
83B ASN* 3.6 11.7 - - - +
85B TRP* 1.3 80.8 - - + +
87B GLN* 1.3 66.9 + - + +
89B ARG* 3.6 15.9 - - - +
90B ALA* 3.0 24.3 + - - +
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Residues in contact with GLN 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B PHE 5.4 0.9 - - - +
61B ILE* 3.6 17.0 - - + +
62B ARG* 2.9 46.2 + - - +
83B ASN* 2.9 30.4 + - - +
84B ALA* 3.3 12.2 + - - +
86B ARG* 1.3 78.3 - - + +
88B ALA* 1.3 62.2 + - - +
90B ALA* 3.3 7.8 + - - +
91B ILE* 3.1 26.1 + - + +
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Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B LEU* 4.9 3.8 - - + -
61B ILE* 3.9 16.5 - - + +
84B ALA 3.0 16.5 + - - +
85B TRP 3.8 0.9 - - - +
87B GLN* 1.3 76.9 - - - +
89B ARG* 1.3 64.3 + - - +
91B ILE* 3.2 5.6 + - - +
92B MET* 3.0 32.5 + - + +
110B PRO 3.9 10.8 - - - +
111B GLY* 4.0 11.9 - - - -
114B ALA* 3.5 20.4 - - + -
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Residues in contact with ARG 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B TRP* 2.9 56.9 + - - +
86B ARG* 3.6 17.7 - - - +
88B ALA* 1.3 77.3 - - - +
90B ALA* 1.3 56.6 + - - +
92B MET* 3.3 1.6 + - - +
93B LYS* 2.9 51.4 + - + +
114B ALA* 3.8 18.6 - - + +
117B SER* 2.8 41.2 + - - +
118B LEU* 3.3 34.0 - - + +
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Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ARG 3.0 16.7 + - - +
87B GLN* 3.6 6.7 - - - +
88B ALA 3.3 0.4 - - - -
89B ARG* 1.3 76.2 - - - +
91B ILE* 1.3 63.4 + - + +
93B LYS* 3.4 10.0 + - - +
94B ALA* 3.1 25.3 + - - +
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Residues in contact with ILE 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B MET* 3.6 23.8 - - + -
40B LEU* 4.0 7.4 - - + -
59B ASP* 3.5 45.1 - - + +
60B PHE 3.7 10.5 - - - +
61B ILE* 3.5 32.8 - - + -
87B GLN* 3.1 10.2 + - + +
88B ALA* 3.5 7.9 - - - +
90B ALA* 1.3 78.7 - - + +
92B MET* 1.3 57.1 + - - +
94B ALA* 3.5 4.4 + - - +
95B TYR* 2.9 27.7 + - - +
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Residues in contact with MET 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B MET* 4.1 23.8 - - - -
12B MET* 4.3 2.9 - - - -
40B LEU* 4.8 4.5 - - + -
88B ALA* 3.0 17.2 + - + +
91B ILE* 1.3 75.0 - - + +
93B LYS* 1.3 61.4 + - - +
94B ALA 3.2 0.4 - - - -
95B TYR* 4.7 0.4 - - - -
96B LYS* 2.8 28.3 + - - +
97B PRO* 3.3 16.5 - - + +
100B VAL* 3.9 26.9 - - + -
111B GLY* 3.3 31.6 - - - +
114B ALA* 4.1 5.4 - - + -
115B ALA* 3.6 31.6 - - + -
118B LEU* 3.7 15.3 - - + -
120B ILE* 4.2 5.6 - - + +
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Residues in contact with LYS 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ARG* 2.9 41.8 + - + +
90B ALA* 3.8 8.3 - - - +
91B ILE 3.3 0.2 - - - -
92B MET* 1.3 76.9 - - - +
94B ALA* 1.3 58.3 + - - +
96B LYS* 3.2 29.5 - - - +
118B LEU* 4.0 26.7 - - + -
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Residues in contact with ALA 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ARG* 5.7 0.9 + - - -
90B ALA 3.1 17.4 + - - +
91B ILE* 3.8 4.9 - - - +
93B LYS* 1.3 78.1 - - - +
95B TYR* 1.3 63.1 + - - +
96B LYS* 4.2 6.9 - - - +
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Residues in contact with TYR 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ARG* 2.8 66.8 + - + +
9B LEU 3.2 18.7 + - - -
10B MET* 3.8 18.8 - - + -
36B GLN* 3.0 35.4 + - + +
37B VAL 3.6 1.0 - - - -
38B ARG* 3.3 46.7 + - + +
57B GLU* 5.6 1.6 - - - -
59B ASP* 4.9 2.2 - - - +
91B ILE 2.9 19.2 + - - +
94B ALA* 1.3 75.6 - - - +
96B LYS* 1.3 69.1 + - - +
97B PRO* 3.7 28.7 - - + -
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Residues in contact with LYS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ARG* 3.1 17.2 - - - +
92B MET 2.8 15.6 + - - +
93B LYS* 3.2 24.5 - - - +
94B ALA 4.2 5.2 - - - +
95B TYR* 1.3 81.4 - - - +
97B PRO* 1.3 68.7 - - - +
98B ASP* 3.8 4.2 + - - +
120B ILE* 5.6 0.7 - - - -
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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