Contacts of the helix formed by residues 67 - 93 (chain A) in PDB entry 2DF9
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 ARG 67 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LEU* 3.6 18.2 + - - +
66A GLY* 1.3 83.8 + - - +
68A PHE* 1.3 56.0 + - + +
70A ILE* 2.7 35.6 - - - +
71A PHE* 2.7 21.2 - - + -
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Residues in contact with PHE 68 (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 ILE* 4.8 22.4 - - + -
65A LEU 5.6 0.2 - - - +
66A GLY* 4.3 0.2 - - - -
67A ARG* 1.3 80.0 - - + +
69A LEU* 1.3 71.0 + - + +
70A ILE 3.1 0.4 - - - -
71A PHE* 2.7 46.3 + + + +
72A VAL* 2.8 31.8 + - + -
75A VAL* 6.4 0.4 - - + -
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Residues in contact with LEU 69 (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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55A ILE* 6.1 5.6 - - + -
59A SER* 4.7 19.5 - - - -
64A LEU* 4.8 8.7 - - + -
65A LEU 2.7 31.2 - - - +
66A GLY* 3.6 12.3 - - - -
67A ARG 3.3 0.8 - - - -
68A PHE* 1.3 88.6 - - + +
70A ILE* 1.3 60.2 + - + +
72A VAL* 2.7 32.3 - - + +
73A MET* 3.1 8.1 + - - +
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Residues in contact with ILE 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLY 4.0 15.7 - - - +
67A ARG* 2.7 23.1 + - - +
69A LEU* 1.3 77.0 - - + +
71A PHE* 1.3 71.4 + - + +
73A MET* 3.1 6.3 + - - +
74A VAL* 2.7 49.2 + - + +
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Residues in contact with PHE 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ARG* 2.7 42.8 - - + -
68A PHE* 2.7 40.0 + + + +
70A ILE* 1.3 95.1 - - + +
72A VAL* 1.3 60.0 + - - +
74A VAL* 3.9 4.8 - - - +
75A VAL* 2.9 29.8 + - - +
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Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 4.7 19.1 - - + -
51A ILE* 5.8 6.1 - - + -
55A ILE* 4.7 21.8 - - + -
68A PHE* 2.8 26.0 + - + +
69A LEU* 2.7 35.7 - - + +
71A PHE* 1.3 76.6 - - - +
73A MET* 1.3 66.4 + - + +
75A VAL* 3.0 10.2 - - + +
76A ALA* 2.8 38.8 + - + +
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Residues in contact with MET 73 (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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52A ALA* 6.1 4.0 - - + -
55A ILE* 5.3 10.8 - - + -
69A LEU 3.1 7.4 + - - +
70A ILE* 3.7 8.3 - - - +
72A VAL* 1.3 87.6 - - + +
74A VAL* 1.3 53.4 + - + +
76A ALA* 3.7 6.1 - - - +
77A THR* 2.6 51.5 + - - +
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Residues in contact with VAL 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 2.7 43.2 + - + +
71A PHE* 3.9 4.3 - - - +
73A MET* 1.3 73.9 - - + +
75A VAL* 1.3 57.4 + - - +
77A THR* 3.1 6.9 + - - -
78A LEU* 2.8 55.9 + - + +
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Residues in contact with VAL 75 (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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12A CYS* 5.0 19.5 - - - -
68A PHE* 6.4 0.7 - - + -
71A PHE 2.9 22.6 + - - +
72A VAL* 3.0 15.3 - - + +
74A VAL* 1.3 77.8 - - - +
76A ALA* 1.3 70.7 + - + +
78A LEU* 3.1 9.7 + - + +
79A ILE* 2.8 47.8 + - + +
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Residues in contact with ALA 76 (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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48A LEU* 4.2 20.2 - - + +
72A VAL* 2.8 21.0 + - + +
73A MET* 3.7 8.7 - - - +
75A VAL* 1.3 84.2 - - + +
77A THR* 1.3 58.5 + - - +
79A ILE* 2.7 30.8 - - - +
80A VAL* 2.8 14.9 + - - +
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Residues in contact with THR 77 (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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73A MET* 2.6 41.5 + - - +
74A VAL* 3.4 7.1 - - - -
76A ALA* 1.3 73.9 - - - +
78A LEU* 1.3 57.0 + - + +
80A VAL* 2.7 15.3 - - + +
81A MET* 2.6 49.3 + - + +
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Residues in contact with LEU 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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74A VAL* 2.8 39.5 + - + +
75A VAL* 3.1 8.9 + - + +
77A THR* 1.3 79.8 - - + +
79A ILE* 1.3 58.7 + - + +
81A MET* 3.7 8.5 - - + +
82A ASN* 2.6 49.5 + - - +
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Residues in contact with ILE 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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12A CYS* 6.3 1.6 - - - -
15A ILE* 4.1 26.7 - - + -
16A SER* 5.7 5.6 - - - +
19A VAL* 5.0 15.9 - - + +
44A GLN* 4.4 4.1 + - - +
48A LEU* 3.0 39.3 - - + -
75A VAL* 2.8 31.1 + - + +
76A ALA* 2.7 28.7 - - - +
78A LEU* 1.3 75.5 - - + +
80A VAL* 1.4 56.8 - - - +
82A ASN* 3.2 11.6 + - - +
83A CYS* 2.6 38.2 + - - +
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Residues in contact with VAL 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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45A THR* 4.7 16.8 - - + +
48A LEU* 4.9 10.3 - - + -
76A ALA 2.8 14.0 + - - +
77A THR* 2.7 31.2 - - + +
79A ILE* 1.4 80.4 - - + +
81A MET* 1.3 72.2 + - + +
83A CYS* 2.8 29.4 - - - -
84A VAL* 2.9 26.7 + - + +
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Residues in contact with MET 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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77A THR* 2.6 42.5 + - + +
78A LEU* 3.7 12.3 - - + +
80A VAL* 1.3 86.5 - - + +
82A ASN* 1.3 62.7 + - - +
84A VAL* 2.7 24.3 - - + +
85A ILE* 2.7 40.7 + - + +
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Residues in contact with ASN 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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19A VAL* 5.1 3.6 - - + +
23A TYR* 2.6 28.6 + - + +
78A LEU* 2.6 40.8 + - - +
79A ILE* 3.4 11.0 - - - +
81A MET* 1.3 74.6 - - - +
83A CYS* 1.3 50.8 + - - +
85A ILE* 3.0 15.3 + - - +
86A VAL 2.6 33.4 + - - -
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Residues in contact with CYS 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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19A VAL* 5.3 3.6 - - + -
23A TYR* 4.3 1.8 - - - -
41A LEU* 3.1 19.7 - - + +
44A GLN* 2.9 37.7 - - - +
45A THR* 5.0 3.6 - - - -
48A LEU* 6.1 0.7 - - - -
79A ILE* 2.6 22.4 + - - +
80A VAL* 2.8 44.2 - - - -
81A MET 3.2 0.2 - - - -
82A ASN* 1.3 74.9 - - - +
84A VAL* 1.3 59.0 + - - +
86A VAL* 2.7 27.5 - - + +
87A LEU* 2.7 13.7 + - - +
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Residues in contact with VAL 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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41A LEU* 5.0 1.1 - - + -
80A VAL* 2.9 23.4 + - + +
81A MET* 2.7 46.7 - - + +
83A CYS* 1.3 77.9 - - - +
85A ILE* 1.3 58.1 + - + +
87A LEU* 3.1 17.7 - - + +
88A ASN* 2.6 34.9 + - + +
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Residues in contact with ILE 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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23A TYR* 5.1 2.0 - - - +
81A MET* 2.7 38.3 + - + +
82A ASN* 3.3 16.6 - - - +
84A VAL* 1.3 79.8 - - + +
86A VAL* 1.3 53.4 + - - +
88A ASN* 3.4 8.4 - - + +
89A VAL* 2.5 57.7 + - + +
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Residues in contact with VAL 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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19A VAL* 5.8 0.2 - - + -
22A ALA* 5.2 8.1 - - + +
23A TYR* 3.3 52.0 - - + +
26A PRO* 5.5 6.7 - - + -
37A SER* 6.3 3.6 - - - -
41A LEU* 4.2 11.9 - - + -
82A ASN 2.6 10.3 + - - -
83A CYS* 2.7 35.9 - - - +
85A ILE* 1.3 71.9 - - - +
87A LEU* 1.3 54.3 + - - +
89A VAL* 3.5 11.2 - - + +
90A SER* 2.6 40.2 + - - -
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Residues in contact with LEU 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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38A ILE* 2.9 39.5 - - + -
41A LEU* 3.2 25.1 - - + -
83A CYS 2.7 6.5 + - - +
84A VAL* 3.1 18.8 - - + +
86A VAL* 1.3 76.0 - - - +
88A ASN* 1.3 55.6 + - - +
90A SER* 2.6 7.8 + - - +
91A GLN* 2.6 49.0 + - + +
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Residues in contact with ASN 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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84A VAL 2.6 19.9 + - - +
85A ILE* 3.0 11.4 + - + +
87A LEU* 1.3 74.3 - - - +
89A VAL* 1.3 54.1 + - + +
91A GLN* 3.2 8.5 + - - +
92A ARG* 2.6 38.1 + - - +
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Residues in contact with VAL 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 ILE* 2.5 46.3 + - + +
86A VAL* 3.5 12.1 - - + +
88A ASN* 1.3 72.3 - - + +
90A SER* 1.3 54.6 + - - +
92A ARG* 3.2 32.4 + - - +
93A THR* 2.6 39.7 + - + -
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Residues in contact with SER 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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26A PRO* 6.2 4.5 - - - -
34A CYS* 4.7 24.2 - - - +
37A SER* 4.8 7.4 + - - -
38A ILE* 4.5 6.1 - - - +
86A VAL* 2.6 22.4 + - - -
87A LEU* 2.6 32.1 + - - +
89A VAL* 1.3 71.8 - - - +
91A GLN* 1.3 59.7 + - - +
93A THR* 2.7 34.8 - - - +
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Residues in contact with GLN 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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38A ILE* 5.2 3.6 - - - +
87A LEU* 2.6 37.5 + - + +
88A ASN* 3.3 12.3 - - - +
90A SER* 1.3 71.1 + - - +
92A ARG* 1.3 66.4 + - - +
93A THR* 3.1 7.3 - - - +
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Residues in contact with ARG 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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88A ASN* 2.6 25.2 + - - +
89A VAL* 3.2 40.6 + - - +
91A GLN* 1.3 74.3 - - - +
93A THR* 1.3 68.1 + - - +
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Residues in contact with THR 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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34A CYS* 4.8 11.7 - - - -
89A VAL* 2.6 21.2 + - + +
90A SER* 2.7 53.2 - - - +
91A GLN 3.1 6.4 - - - +
92A ARG* 1.3 86.7 - - - +
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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
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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