Contacts of the helix formed by residues 48 - 71 (chain V) in PDB entry 3SDI
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 48 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47V GLY* 1.3 68.0 - - - -
49V ALA* 1.3 66.8 + - - +
50V ALA 4.2 1.3 - - - +
51V ASP* 3.2 30.7 + - - +
52V THR* 3.1 21.9 + - - +
96V GLY* 3.1 16.4 + - - +
91W ARG* 4.0 6.0 + - - +
114W ASP* 6.1 0.4 - - - +
116W ILE* 3.8 27.8 - - + -
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Residues in contact with ALA 49 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20V SER* 5.7 4.9 - - - +
47V GLY 3.0 8.2 + - - +
48V THR* 1.3 74.2 - - - +
50V ALA* 1.3 62.5 + - - +
52V THR* 2.8 24.1 + - - +
53V GLU* 3.1 13.2 + - - +
114W ASP* 5.6 1.7 + - - +
118W CYS* 3.6 23.0 - - - -
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Residues in contact with ALA 50 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48V THR* 3.3 1.2 - - - +
49V ALA* 1.3 77.8 - - - +
51V ASP* 1.3 56.9 + - - +
53V GLU* 4.0 4.2 - - - +
54V ALA* 2.9 32.1 + - - +
88W TYR* 3.6 7.3 - - + -
114W ASP* 4.8 1.1 + - - +
116W ILE* 3.6 47.1 - - + +
117W GLY 4.8 0.4 - - - -
118W CYS* 3.7 25.0 - - + +
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Residues in contact with ASP 51 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48V THR* 3.2 19.7 + - - +
50V ALA* 1.3 75.3 - - - +
52V THR* 1.3 63.7 + - - +
54V ALA* 4.0 0.3 - - - +
55V VAL* 3.0 29.6 + - - +
95V ILE* 3.3 21.9 - - + +
96V GLY 2.8 25.3 + - - +
97V ALA* 4.2 2.5 - - - +
88W TYR* 2.8 17.5 + - - -
91W ARG* 2.6 47.9 + - - -
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Residues in contact with THR 52 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35V HIS* 4.3 11.2 + - - -
45V GLY* 3.8 26.8 + - - -
46V ALA 3.5 25.4 - - - +
48V THR 3.1 13.0 + - - +
49V ALA* 2.8 24.9 + - - +
51V ASP* 1.3 74.8 - - - +
53V GLU* 1.3 62.0 + - - +
55V VAL* 3.7 2.7 - - - +
56V THR* 3.2 28.9 + - - -
97V ALA* 4.0 19.5 - - + -
98V TYR 4.3 1.1 - - - +
99V LEU* 4.2 4.9 - - + +
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Residues in contact with GLU 53 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35V HIS* 2.9 43.6 + - + +
49V ALA 3.1 13.9 + - - +
50V ALA* 4.0 4.3 - - - +
52V THR* 1.3 81.5 + - - +
54V ALA* 1.3 59.2 + - - +
56V THR* 3.2 5.3 + - - +
57V GLN* 3.0 66.6 + - - +
118W CYS* 6.1 2.5 - - - -
119W ILE* 6.5 1.1 - - + -
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Residues in contact with ALA 54 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50V ALA 2.9 20.6 + - - +
51V ASP 4.0 0.4 - - - +
53V GLU* 1.3 78.5 - - - +
55V VAL* 1.3 57.2 + - - +
57V GLN* 3.3 8.3 + - - +
58V LEU* 2.9 30.8 + - - +
88W TYR* 3.4 41.3 - - + +
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Residues in contact with VAL 55 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51V ASP 3.0 18.4 + - - +
52V THR 3.7 5.8 - - - +
54V ALA* 1.3 74.8 - - - +
56V THR* 1.3 67.3 + - - +
58V LEU* 4.5 4.7 - - - +
59V ILE* 3.3 29.9 + - + +
83V LEU* 3.6 22.2 - - + +
86V HIS* 3.3 36.6 - - + +
87V LEU* 4.1 15.5 - - + -
95V ILE* 4.6 6.1 - - + -
97V ALA* 4.1 11.0 - - + -
99V LEU* 4.0 16.4 - - + -
88W TYR* 5.9 0.4 - - - +
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Residues in contact with THR 56 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35V HIS* 3.5 34.2 - - + -
36V ARG 3.9 14.1 - - - +
37V ILE* 4.4 13.7 - - + +
43V CYS* 3.2 23.7 - - - -
52V THR 3.2 22.5 + - - -
53V GLU* 3.5 6.3 - - - +
55V VAL* 1.3 79.2 - - - +
57V GLN* 1.3 63.9 + - + +
59V ILE* 5.1 0.4 - - - -
60V GLY* 2.9 26.2 + - - -
83V LEU* 5.1 2.2 - - - +
99V LEU* 4.2 6.4 - - - +
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Residues in contact with GLN 57 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102O ARG* 5.8 1.1 - - - +
104O GLY* 5.5 7.3 - - - -
53V GLU* 3.0 46.2 + - - +
54V ALA* 3.3 6.4 + - - +
56V THR* 1.3 80.3 - - + +
58V LEU* 1.3 59.9 + - - +
60V GLY* 3.7 0.8 - - - -
61V SER* 2.9 31.1 + - - -
81W GLN* 4.8 16.1 + - - +
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Residues in contact with LEU 58 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102O ARG* 3.8 34.5 - - - +
54V ALA 2.9 17.9 + - - +
55V VAL* 4.4 3.8 - - - +
57V GLN* 1.3 76.4 - - - +
59V ILE* 1.3 65.8 + - + +
61V SER* 3.5 4.4 + - - -
62V ASN* 3.1 40.7 + - - +
86V HIS* 3.9 33.2 - - + +
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Residues in contact with ILE 59 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37V ILE* 4.5 9.0 - - + -
55V VAL* 3.3 30.2 + - + +
56V THR 4.4 0.9 - - - +
58V LEU* 1.3 87.4 - - + +
60V GLY* 1.3 61.0 - - - +
62V ASN* 3.3 7.7 + - - +
63V ILE* 2.9 36.4 + - + +
79V ALA* 4.2 20.2 - - + +
82V MET* 3.9 24.5 - - + +
83V LEU* 3.6 32.1 - - + +
86V HIS* 4.5 18.2 - - + -
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Residues in contact with GLY 60 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36V ARG 5.3 0.4 - - - -
37V ILE* 3.3 31.3 - - - +
56V THR 2.9 20.0 + - - -
57V GLN* 3.4 1.5 + - - -
59V ILE* 1.3 76.5 - - - +
61V SER* 1.3 61.0 + - - +
63V ILE* 3.4 3.2 + - - +
64V GLU* 3.1 22.2 + - - +
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Residues in contact with SER 61 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97O HIS* 2.8 29.0 - - - -
101O LYS* 5.9 4.5 - - - +
102O ARG* 2.8 37.9 + - - -
57V GLN 2.9 19.0 + - - -
58V LEU* 3.5 5.6 - - - -
60V GLY* 1.3 74.8 - - - +
62V ASN* 1.3 62.5 + - - +
64V GLU* 3.1 16.1 + - - +
65V LEU* 3.2 14.4 + - - +
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Residues in contact with ASN 62 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94O LYS* 5.8 2.6 - - - -
102O ARG* 3.0 20.4 + - - +
58V LEU* 3.1 34.8 + - - +
59V ILE* 3.3 5.2 + - - +
61V SER* 1.3 78.3 - - - +
63V ILE* 1.3 56.8 + - - +
64V GLU 3.3 0.2 - - - -
65V LEU* 3.5 12.0 + - - +
66V HIS* 3.0 27.5 + - - +
82V MET* 3.3 27.6 - - + +
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Residues in contact with ILE 63 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37V ILE* 4.5 9.6 - - + -
38V SER* 4.0 19.5 - - - -
41V ILE* 5.2 0.9 - - + -
59V ILE* 2.9 27.7 + - + +
60V GLY* 3.7 6.7 - - - +
62V ASN* 1.3 73.8 - - - +
64V GLU* 1.3 62.5 + - - +
66V HIS* 3.5 12.1 + - + +
67V SER* 2.9 26.9 + - - -
74V PRO* 3.6 27.9 - - + +
75V ARG 4.4 5.4 - - - +
78V SER* 3.8 28.5 - - - -
79V ALA* 3.9 10.3 - - + +
82V MET* 3.9 15.7 - - - -
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Residues in contact with GLU 64 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72O PRO* 5.1 5.5 - - - +
97O HIS* 2.7 36.5 + - - +
101O LYS* 4.9 2.9 + - - -
106O TYR* 2.7 27.4 + - - -
60V GLY 3.1 11.3 + - - +
61V SER* 3.1 10.6 + - - +
63V ILE* 1.3 76.4 - - - +
65V LEU* 1.3 65.4 + - - +
67V SER* 2.9 17.3 + - - -
68V LEU* 3.0 30.6 + - + +
74V PRO* 6.1 0.2 - - - -
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Residues in contact with LEU 65 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93O ARG* 3.6 40.8 - - + +
94O LYS* 3.9 32.5 - - + +
97O HIS* 4.0 18.2 - - + +
102O ARG* 4.2 21.5 - - - +
61V SER 3.2 9.1 + - - +
62V ASN* 3.8 13.7 - - - +
63V ILE 3.4 0.2 - - - -
64V GLU* 1.3 77.4 - - - +
66V HIS* 1.3 56.4 + - - +
68V LEU* 3.4 8.4 + - + +
69V TYR* 2.9 31.8 + - - +
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Residues in contact with HIS 66 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99U PHE* 3.5 21.3 - + - -
103U TYR* 3.5 43.4 - + + -
105U TYR* 3.0 39.0 - + - -
62V ASN 3.0 18.2 + - - +
63V ILE* 3.6 15.9 + - + +
65V LEU* 1.3 76.9 - - - +
67V SER* 1.3 59.4 + - - +
69V TYR* 3.7 5.5 - + + -
70V THR* 2.9 48.6 + - + +
74V PRO* 5.9 4.8 - - - +
78V SER* 4.7 3.4 + - - -
82V MET* 5.5 0.7 - - + -
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Residues in contact with SER 67 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63V ILE 2.9 18.2 + - - -
64V GLU* 2.9 9.6 + - - -
66V HIS* 1.3 79.5 - - - +
68V LEU* 1.3 63.3 + - - +
70V THR* 3.9 2.5 - - - -
71V SER* 2.9 24.3 + - - -
72V ARG 2.5 32.5 + - - +
73V GLU* 4.3 1.9 + - - -
74V PRO* 4.0 21.0 - - - +
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Residues in contact with LEU 68 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69O LEU* 4.5 27.8 - - + +
70O LEU 4.8 2.9 - - - +
93O ARG* 3.7 57.4 + - + +
97O HIS* 5.9 1.6 - - + -
114U LYS* 4.6 1.7 + - - -
64V GLU* 3.0 37.3 + - + +
65V LEU* 3.7 10.8 - - + +
67V SER* 1.3 78.6 - - - +
69V TYR* 1.3 64.5 + - - +
70V THR 3.3 0.7 + - - -
71V SER* 3.3 15.1 + - - +
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Residues in contact with TYR 69 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90O ASP* 3.6 29.6 - - + +
93O ARG* 4.4 0.6 - - - +
111U VAL* 4.1 26.4 - - + +
114U LYS* 3.4 48.1 + - + +
115U ARG* 3.5 32.6 + - + -
118U ASN* 3.2 17.0 + - - +
65V LEU 2.9 17.8 + - - +
66V HIS* 3.8 7.9 - + + +
68V LEU* 1.3 78.0 - - - +
70V THR* 1.3 59.6 + - + +
71V SER* 3.5 1.1 + - - -
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Residues in contact with THR 70 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99U PHE* 4.5 2.5 - - + -
105U TYR* 4.2 8.2 + - - +
110U ASP* 4.2 2.3 - - - +
111U VAL* 3.7 34.2 - - + +
66V HIS* 2.9 52.2 + - + +
67V SER* 3.7 4.0 + - - -
69V TYR* 1.3 82.9 - - + +
71V SER* 1.3 69.9 + - - +
72V ARG* 3.0 43.8 + - - +
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Residues in contact with SER 71 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110U ASP* 5.6 2.2 - - - -
67V SER 2.9 12.1 + - - -
68V LEU 3.3 10.8 + - - -
69V TYR 5.0 0.7 + - - -
70V THR* 1.3 80.1 - - - +
72V ARG* 1.3 61.4 + - - +
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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
------------------------------------------------------------
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