Contacts of the helix formed by residues 101 - 124 (chain B) in PDB entry 3VOD
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 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82B GLY 3.3 20.9 + - - +
83B TRP 2.9 23.4 + - - -
84B VAL* 3.5 9.9 + - - -
85B GLU* 4.0 19.0 + - + +
100B LEU* 1.3 76.3 - - - +
102B THR* 1.3 66.7 + - - +
103B GLY* 3.9 4.9 - - - +
104B GLY 4.0 0.4 - - - -
105B ALA* 2.7 33.3 + - - +
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Residues in contact with THR 102 (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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101B THR* 1.3 79.1 - - - +
103B GLY* 1.3 57.9 + - - +
105B ALA* 3.9 5.8 - - - +
106B ALA* 3.0 30.4 + - + +
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Residues in contact with GLY 103 (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 GLY 4.4 8.1 - - - -
83B TRP* 4.0 8.2 - - - -
101B THR* 3.1 5.3 - - - +
102B THR* 1.3 76.2 - - - +
104B GLY* 1.3 53.3 + - - +
106B ALA* 3.3 5.4 + - - +
107B ILE* 2.8 37.4 + - - +
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Residues in contact with GLY 104 (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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46B LEU* 4.8 1.3 - - - +
83B TRP* 3.4 42.1 - - - +
100B LEU* 3.9 9.3 - - - +
101B THR* 3.1 5.6 + - - -
103B GLY* 1.3 73.0 - - - +
105B ALA* 1.3 60.0 + - - +
107B ILE* 3.1 6.2 - - - +
108B CYS* 2.8 32.1 + - - +
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Residues in contact with ALA 105 (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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50B ARG* 4.0 10.7 + - + +
100B LEU* 3.8 21.9 - - + +
101B THR 2.7 19.7 + - - +
102B THR* 3.9 6.5 - - - +
104B GLY* 1.3 73.1 - - - +
106B ALA* 1.3 57.5 + - - +
108B CYS* 3.6 2.1 - - - +
109B GLU* 3.0 28.4 + - - +
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Residues in contact with ALA 106 (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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102B THR* 3.0 19.7 + - + +
103B GLY* 3.7 5.4 - - - +
104B GLY 3.3 0.2 - - - -
105B ALA* 1.3 74.7 - - - +
107B ILE* 1.3 59.5 + - - +
109B GLU* 3.2 7.7 + - - +
110B GLN* 3.0 43.8 + - - +
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Residues in contact with ILE 107 (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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36B LEU* 4.0 30.3 - - + +
38B ILE* 5.6 1.1 - - + -
46B LEU* 4.0 13.2 - - + -
83B TRP* 3.7 51.8 - - + +
103B GLY 2.8 19.1 + - - +
104B GLY* 3.1 14.8 - - - +
106B ALA* 1.3 71.8 - - - +
108B CYS* 1.3 60.2 + - - +
110B GLN* 3.4 16.1 + - - +
111B CYS* 3.0 38.7 + - - -
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Residues in contact with CYS 108 (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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43B PHE* 4.4 2.5 - - - -
46B LEU* 4.1 14.8 - - + -
47B CYS* 4.0 33.0 - - - -
50B ARG* 3.9 28.7 - - - +
100B LEU* 4.2 7.6 - - + -
104B GLY 2.8 18.6 + - - +
105B ALA* 3.6 5.4 - - - +
107B ILE* 1.3 79.0 - - - +
109B GLU* 1.3 56.9 + - - +
111B CYS* 3.4 9.8 - - - +
112B HIS* 3.1 29.3 + - - -
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Residues in contact with GLU 109 (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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50B ARG* 4.4 23.7 + - - +
105B ALA 3.0 17.3 + - - +
106B ALA* 3.2 7.5 + - - +
108B CYS* 1.3 73.7 - - - +
110B GLN* 1.3 60.6 + - - +
112B HIS* 3.3 9.0 + - + +
113B GLN* 3.0 42.4 + - + +
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Residues in contact with GLN 110 (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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36B LEU* 3.6 29.8 - - + +
106B ALA* 3.0 28.1 + - + +
107B ILE* 3.5 20.9 - - - +
109B GLU* 1.3 73.4 - - - +
111B CYS* 1.3 58.8 + - - +
113B GLN* 3.1 8.8 + - - +
114B LEU* 2.8 31.9 + - - +
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Residues in contact with CYS 111 (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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33B LEU* 3.6 21.1 - - + -
36B LEU* 3.7 14.6 - - - +
38B ILE* 3.8 26.0 - - - -
43B PHE* 3.2 33.0 - - + -
46B LEU* 5.1 0.2 - - - -
107B ILE* 3.0 28.4 + - - -
108B CYS* 3.4 4.5 - - - +
110B GLN* 1.3 75.6 - - - +
112B HIS* 1.3 56.4 + - - +
114B LEU* 3.8 2.2 - - - +
115B VAL* 2.9 35.6 + - - +
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Residues in contact with HIS 112 (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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16A ARG* 2.8 35.9 + - - -
43B PHE* 3.9 11.8 - + - -
47B CYS* 3.5 29.9 - - + -
50B ARG* 5.0 13.9 + - - -
108B CYS* 3.1 23.8 + - - +
109B GLU* 3.4 14.6 - - + +
111B CYS* 1.3 77.7 - - - +
113B GLN* 1.3 63.0 + - + +
115B VAL* 5.0 2.2 - - + -
116B GLY* 2.9 34.0 + - - +
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Residues in contact with GLN 113 (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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109B GLU* 3.0 32.5 + - + +
110B GLN* 3.1 7.4 + - - +
112B HIS* 1.3 80.5 - - - +
114B LEU* 1.3 61.0 + - - +
116B GLY* 4.6 1.6 + - - -
117B GLN* 5.4 3.3 + - - +
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Residues in contact with LEU 114 (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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32B TYR* 3.4 26.8 - - - +
33B LEU* 4.6 4.3 - - + -
35B PRO* 4.2 23.6 - - + -
36B LEU* 3.8 32.1 - - + -
110B GLN 2.8 15.0 + - - +
111B CYS* 3.8 4.0 - - - +
113B GLN* 1.3 80.3 - - - +
115B VAL* 1.3 62.0 + - - +
117B GLN 5.1 0.5 + - - -
118B ASP* 3.6 20.7 + - - +
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Residues in contact with VAL 115 (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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29B LEU* 3.5 25.8 - - + -
32B TYR* 3.6 29.2 - - + +
33B LEU* 3.6 35.0 - - + +
43B PHE* 5.3 5.4 - - + -
111B CYS 2.9 14.3 + - - +
112B HIS* 4.5 2.5 - - + +
114B LEU* 1.3 79.2 - - + +
116B GLY* 1.3 69.8 + - - +
117B GLN 3.3 1.1 + - - -
118B ASP* 3.4 3.8 + - - +
119B LEU* 3.1 36.7 + - + +
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Residues in contact with GLY 116 (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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112B HIS* 2.9 22.6 + - - -
113B GLN 4.6 0.8 - - - -
114B LEU 3.6 1.2 - - - -
115B VAL* 1.3 82.4 - - - +
117B GLN* 1.3 62.4 + - - +
119B LEU* 4.0 3.2 - - - +
120B HIS* 3.4 21.0 + - - +
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Residues in contact with GLN 117 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B GLN 5.4 3.1 + - - +
114B LEU 5.1 0.6 + - - -
115B VAL 3.6 0.6 - - - -
116B GLY* 1.3 73.4 - - - +
118B ASP* 1.3 61.3 + - - +
120B HIS* 3.5 6.9 + - - +
121B GLN* 3.0 40.7 + - + +
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Residues in contact with ASP 118 (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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32B TYR* 3.5 31.1 + - + -
114B LEU* 3.6 16.4 + - - +
115B VAL 3.4 5.6 + - - +
117B GLN* 1.3 76.8 - - - +
119B LEU* 1.3 56.4 + - - +
121B GLN* 3.1 7.9 + - - +
122B GLU* 2.8 35.7 + - - +
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Residues in contact with LEU 119 (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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15A GLY* 5.1 8.3 - - - -
25B LYS* 3.8 20.2 - - + +
28B LEU* 3.5 34.5 - - + -
29B LEU* 4.0 21.1 - - + +
32B TYR* 3.9 14.2 - - + -
115B VAL* 3.1 36.1 + - + +
116B GLY* 4.0 3.6 - - - +
118B ASP* 1.3 75.7 - - - +
120B HIS* 1.3 60.3 + - - +
122B GLU* 3.3 1.3 + - - +
123B LEU* 2.8 46.3 + - + +
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Residues in contact with HIS 120 (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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13A PRO* 4.7 11.4 - - + +
14A LEU* 3.8 22.6 + - + +
15A GLY 5.0 2.6 + - - +
116B GLY 3.4 11.3 + - - +
117B GLN* 3.7 9.0 - - - +
118B ASP 3.3 0.4 - - - -
119B LEU* 1.3 80.5 - - - +
121B GLN* 1.3 65.4 + - - +
123B LEU* 3.4 6.0 + - - +
124B THR* 2.7 62.6 + - + +
132B VAL* 4.1 10.8 - - + +
136B GLU* 3.3 25.8 - - - -
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Residues in contact with GLN 121 (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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117B GLN* 3.0 27.5 + - + +
118B ASP* 3.1 10.3 + - - +
120B HIS* 1.3 86.7 - - - +
122B GLU* 1.3 59.4 + - - +
124B THR* 3.8 11.2 + - - -
125B LYS* 3.4 22.7 + - - +
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Residues in contact with GLU 122 (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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24B LYS* 4.5 7.5 + - - +
28B LEU* 3.4 31.0 - - + +
32B TYR* 3.1 27.7 + - + +
118B ASP 2.8 11.9 + - - +
119B LEU 3.8 2.9 - - - +
121B GLN* 1.3 72.5 - - - +
123B LEU* 1.3 65.0 + - - +
124B THR 3.2 0.7 + - - -
125B LYS* 2.7 57.6 + - - +
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Residues in contact with LEU 123 (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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14A LEU* 4.1 23.3 - - + -
15A GLY* 4.4 16.2 - - - +
18A ILE* 4.8 5.6 - - + -
142A VAL* 3.4 47.4 - - + +
21B VAL* 4.6 3.8 - - + +
24B LYS* 4.0 23.6 + - + +
25B LYS* 4.2 27.4 - - + +
28B LEU* 4.0 9.6 - - + -
119B LEU* 2.8 41.4 + - + +
120B HIS* 3.8 4.7 - - - +
122B GLU* 1.3 74.1 - - - +
124B THR* 1.3 58.2 + - - +
125B LYS 3.7 0.7 + - - -
126B ASN* 4.9 3.1 + - - +
127B LEU* 4.7 0.7 - - - +
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Residues in contact with THR 124 (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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14A LEU* 3.5 28.5 - - + -
120B HIS* 2.7 44.4 + - + +
121B GLN* 3.8 13.5 + - - -
123B LEU* 1.3 75.9 - - - +
125B LYS* 1.3 61.8 + - - +
126B ASN 3.3 2.9 - - - -
127B LEU* 3.1 29.2 + - + +
132B VAL* 3.7 29.0 - - + +
135B LEU* 5.9 0.4 - - + -
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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