Contacts of the helix formed by residues 77 - 96 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A ALA 3.3 6.9 + - - +
74A LEU* 3.1 8.2 + - - +
75A ILE 3.2 0.4 - - - -
76A ALA* 1.3 81.9 - - - +
78A PRO* 1.3 68.4 - - - +
79A LEU 3.4 1.8 - - - -
80A ARG* 3.0 43.9 + - + +
81A ILE* 2.9 23.7 + - - +
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Residues in contact with PRO 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ILE 4.9 1.9 - - - +
76A ALA 3.5 10.1 - - - +
77A ALA* 1.3 81.9 - - - +
79A LEU* 1.3 69.9 + - + +
81A ILE* 3.1 11.2 - - + +
82A PHE* 3.1 24.8 + - - +
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ALA 3.4 0.6 - - - -
78A PRO* 1.3 85.2 - - + +
80A ARG* 1.3 60.1 + - + +
82A PHE* 3.5 15.5 + - + +
83A ASN* 2.9 31.1 + - - +
86A ARG* 5.2 0.3 + - - -
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Residues in contact with ARG 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ILE* 4.5 13.5 - - + +
64A SER* 2.8 28.9 + - - +
65A GLY* 3.7 23.1 + - - -
66A LEU* 4.5 6.5 - - - +
67A ARG* 6.2 0.2 - - - +
74A LEU* 3.7 14.0 - - + +
77A ALA* 3.0 38.0 + - + +
79A LEU* 1.3 76.1 - - + +
81A ILE* 1.3 60.9 + - - +
83A ASN* 3.4 4.9 + - - +
84A ALA* 2.9 29.6 + - - +
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Residues in contact with ILE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ILE* 5.8 1.3 - - + -
74A LEU* 3.1 38.3 - - + +
75A ILE* 4.3 24.0 - - + +
77A ALA 2.9 13.9 + - - +
78A PRO* 3.1 25.8 - - + +
80A ARG* 1.3 73.9 - - - +
82A PHE* 1.3 60.8 + - + +
84A ALA* 3.3 0.4 + - - -
85A TRP* 2.9 29.9 + - + +
109A GLY 5.8 0.7 - - - -
110A PRO* 4.6 17.7 - - + -
113A LEU* 4.5 22.2 - - + -
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Residues in contact with PHE 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A PRO 3.1 19.5 + - - +
79A LEU* 3.6 16.2 - - + +
81A ILE* 1.3 78.4 - - + +
83A ASN* 1.3 56.9 + - - +
85A TRP* 3.6 31.3 - + - +
86A ARG* 3.0 79.3 + - + +
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Residues in contact with ASN 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ARG 4.1 2.4 - - - +
79A LEU 2.9 18.8 + - - +
80A ARG* 3.8 5.8 - - - +
82A PHE* 1.3 75.0 - - - +
84A ALA* 1.3 59.5 + - - +
86A ARG* 3.3 27.2 + - - +
87A GLN* 2.4 65.5 + - - +
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ILE* 4.1 6.0 - - + +
63A ILE* 3.9 23.8 - - + -
74A LEU* 4.6 1.8 - - + -
80A ARG 2.9 18.3 + - - +
81A ILE* 3.8 5.4 - - - +
83A ASN* 1.3 76.4 + - - +
85A TRP* 1.3 62.2 + - - +
87A GLN* 3.3 13.2 + - - +
88A ALA* 3.1 23.6 + - - +
110A PRO* 3.8 28.2 - - + +
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Residues in contact with TRP 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ILE* 2.9 21.4 + - + +
82A PHE* 3.6 36.3 - + - +
84A ALA* 1.3 77.4 - - - +
86A ARG* 1.3 57.1 + - + +
88A ALA* 3.3 2.9 + - - +
89A ARG* 2.9 37.2 + - - +
110A PRO* 4.1 9.6 - - + +
113A LEU* 3.6 36.3 - - + +
114A ALA* 3.5 23.2 - - - +
117A SER* 3.1 36.7 + - - -
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Residues in contact with ARG 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LEU 5.2 0.6 + - - -
82A PHE* 3.0 63.4 + - + +
83A ASN* 3.6 36.8 + - - +
85A TRP* 1.3 76.3 - - + +
87A GLN* 1.3 66.1 + - - +
89A ARG* 3.7 15.6 - - + +
90A ALA* 3.0 24.3 + - - +
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Residues in contact with GLN 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A PHE 4.2 3.1 - - - +
61A ILE* 3.5 13.1 - - + -
62A ARG* 2.7 51.8 + - - +
83A ASN* 2.4 54.8 + - - +
84A ALA* 3.6 7.9 - - - +
85A TRP 3.3 0.2 - - - -
86A ARG* 1.3 75.2 - - - +
88A ALA* 1.3 63.0 + - - +
90A ALA* 3.4 6.5 + - - +
91A ILE* 3.1 31.1 + - + +
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 4.8 2.2 - - + -
61A ILE* 4.1 11.9 - - + +
84A ALA 3.1 13.1 + - - +
85A TRP 3.6 4.5 - - - +
86A ARG 3.2 0.2 - - - -
87A GLN* 1.3 75.7 - - - +
89A ARG* 1.3 60.2 + - - +
91A ILE* 3.3 10.8 + - - +
92A MET* 2.9 37.6 + - + +
110A PRO 3.7 9.4 - - - +
111A GLY* 4.0 11.0 - - - -
114A ALA* 3.3 22.9 - - + -
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Residues in contact with ARG 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A TRP* 2.9 46.1 + - - +
86A ARG* 3.3 15.7 + - - +
88A ALA* 1.3 78.1 - - - +
90A ALA* 1.3 57.5 + - - +
92A MET* 3.2 1.0 + - - +
93A LYS* 2.8 65.9 + - + +
114A ALA* 3.9 8.7 - - + -
117A SER* 2.8 46.6 + - - +
118A LEU* 3.3 31.1 - - + +
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Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ARG 3.0 16.4 + - - +
87A GLN* 3.6 7.6 - - - +
89A ARG* 1.3 76.5 - - - +
91A ILE* 1.3 63.6 + - + +
93A LYS* 3.4 9.7 + - - +
94A ALA* 3.2 24.1 + - - +
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Residues in contact with ILE 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A MET* 3.6 34.8 - - + -
40A LEU* 3.8 16.4 - - + -
59A ASP* 3.7 31.4 - - + +
60A PHE 3.6 24.0 - - - +
61A ILE* 4.5 2.9 - - + -
87A GLN* 3.1 20.8 + - + +
88A ALA* 3.5 9.0 - - - +
89A ARG 3.2 0.2 - - - -
90A ALA* 1.3 78.7 - - + +
92A MET* 1.3 57.3 + - + +
94A ALA* 3.5 4.1 + - - +
95A TYR* 3.0 26.9 + - - +
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Residues in contact with MET 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A MET* 4.1 23.8 - - - -
12A MET* 4.2 4.7 - - - -
40A LEU* 4.4 4.9 - - + -
88A ALA* 2.9 17.9 + - + +
91A ILE* 1.3 74.6 - - + +
93A LYS* 1.3 59.7 + - - +
94A ALA 3.2 0.4 - - - -
95A TYR* 4.8 0.4 - - - -
96A LYS* 2.7 32.4 + - - +
97A PRO* 3.5 15.6 - - + +
100A VAL* 4.0 22.2 - - + -
111A GLY* 3.2 33.0 - - - +
114A ALA* 4.1 7.4 - - + -
115A ALA* 3.6 31.9 - - - -
118A LEU* 3.7 16.8 - - + -
120A ILE* 4.2 6.2 - - + +
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Residues in contact with LYS 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ARG* 2.8 58.6 + - + +
90A ALA* 3.8 8.5 - - - +
91A ILE 3.4 0.2 - - - -
92A MET* 1.3 73.4 - - - +
94A ALA* 1.3 58.0 + - - +
96A LYS* 3.2 31.2 - - - +
118A LEU* 4.2 18.2 - - + -
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Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ALA 3.2 17.3 + - - +
91A ILE* 3.9 4.3 - - - +
93A LYS* 1.3 78.2 - - - +
95A TYR* 1.3 62.2 + - - +
96A LYS* 4.2 6.3 - - - +
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Residues in contact with TYR 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG* 3.1 47.0 + - + -
9A LEU 3.2 16.5 + - - -
10A MET* 4.1 14.1 - - + -
36A GLN* 3.0 41.7 + - + +
37A VAL 3.3 5.3 + - - -
38A ARG* 3.3 47.6 - - + +
59A ASP* 5.1 2.5 - - - +
91A ILE 3.0 17.3 + - - +
94A ALA* 1.3 76.4 - - - +
96A LYS* 1.3 70.7 + - - +
97A PRO* 3.8 27.6 - - + -
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Residues in contact with LYS 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG* 3.6 10.6 - - - +
92A MET 2.7 18.9 + - - +
93A LYS* 3.2 25.6 - - - +
94A ALA* 4.2 5.6 - - - +
95A TYR* 1.3 78.5 - - - +
97A PRO* 1.3 69.6 - - - +
98A ASP* 3.7 5.0 + - - +
120A ILE* 5.6 1.3 - - - -
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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