Contacts of the helix formed by residues 105 - 125 (chain A) in PDB entry 2PU1
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 GLY 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A CYS* 3.8 4.3 - - - -
49A LEU* 3.9 10.7 - - - +
96A ASP* 4.1 0.2 + - - -
101A LYS* 2.9 19.2 + - - -
102A GLY 4.4 0.4 - - - -
103A LYS 3.5 1.4 - - - -
104A LEU* 1.3 79.4 - - - +
106A ALA* 1.3 66.3 + - - -
107A ASN* 3.1 15.7 - - - -
108A ALA 3.1 10.3 + - - -
109A ILE* 3.1 16.1 + - - +
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Residues in contact with ALA 106 (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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35A VAL* 5.5 0.4 - - - -
46A ALA* 3.5 30.5 - - + +
47A CYS 2.7 21.0 + - - +
48A GLU* 5.3 0.2 - - - -
101A LYS* 3.5 23.6 + - + +
105A GLY* 1.3 71.9 - - - -
107A ASN* 1.3 55.6 + - - +
109A ILE* 4.1 0.8 - - - +
110A LEU* 2.9 34.9 + - - +
345A ASN* 4.6 9.2 - - + +
348A GLY* 4.2 8.4 - - - +
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Residues in contact with ASN 107 (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 THR* 5.5 2.2 + - - +
20A VAL* 3.3 29.0 - - + +
35A VAL* 3.7 34.1 - - + +
47A CYS 3.9 0.6 + - - -
48A GLU* 3.9 15.8 - - + +
49A LEU* 2.9 54.8 + - - +
62A CYS* 3.9 13.9 - - - -
65A ALA* 3.8 10.8 - - - +
105A GLY* 3.7 4.6 - - - -
106A ALA* 1.3 76.5 - - - +
108A ALA* 1.3 61.6 + - - +
111A GLY 4.5 0.2 + - - -
345A ASN* 6.2 0.2 - - - +
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Residues in contact with ALA 108 (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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20A VAL* 4.7 0.2 - - - -
22A VAL* 4.4 0.3 - - - +
65A ALA* 3.4 26.0 - - - +
68A ASN* 4.2 1.8 - - + -
69A VAL* 3.5 25.9 - - + +
73A ILE* 4.0 13.2 - - + -
104A LEU 3.3 24.5 - - - +
105A GLY 3.1 2.7 + - - +
107A ASN* 1.3 81.8 - - - +
109A ILE* 1.3 65.6 + - - +
110A LEU 3.5 0.2 - - - -
111A GLY* 3.8 2.4 + - - -
112A CYS* 3.5 14.4 + - - -
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Residues in contact with ILE 109 (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 ILE* 4.1 20.0 - - + -
92A MET* 4.0 33.2 - - + +
93A LEU* 5.1 1.1 - - + +
96A ASP* 3.9 23.6 - - + -
101A LYS* 3.8 30.7 - - + -
104A LEU* 4.4 5.8 - - + -
105A GLY 3.1 13.3 + - - +
106A ALA* 4.1 2.5 - - - +
108A ALA* 1.3 75.0 - - - +
110A LEU* 1.3 65.6 + - - +
112A CYS* 3.1 6.8 + - - +
113A SER* 3.0 18.9 + - - -
348A GLY 3.4 16.4 - - - +
349A THR* 3.6 19.3 - - + -
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Residues in contact with LEU 110 (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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35A VAL* 4.2 13.7 - - + -
36A PRO* 4.5 2.2 - - + -
106A ALA 2.9 22.1 + - - +
109A ILE* 1.3 74.5 - - - +
111A GLY* 1.3 58.2 + - - +
113A SER* 3.1 2.9 + - - -
114A MET* 2.8 51.0 + - + +
344A ILE* 3.9 21.3 - - + +
345A ASN* 3.5 40.6 - - + +
348A GLY* 3.2 26.2 + - - +
349A THR* 4.1 4.3 - - - +
350A ILE* 4.1 17.0 - - + +
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Residues in contact with GLY 111 (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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22A VAL* 3.7 22.7 - - - +
33A SER* 3.8 9.6 - - - -
35A VAL* 3.6 20.8 - - - +
107A ASN 4.5 0.2 + - - -
108A ALA 3.8 3.0 + - - -
109A ILE 3.3 0.8 - - - -
110A LEU* 1.3 77.3 - - - +
112A CYS* 1.3 56.8 + - - +
114A MET* 3.5 8.5 + - - +
115A ALA* 3.0 30.8 + - - +
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Residues in contact with CYS 112 (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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6A VAL* 4.3 7.2 - - - -
22A VAL* 3.9 22.9 - - - +
24A VAL* 4.5 1.5 - - - +
69A VAL* 4.1 16.4 - - - -
73A ILE* 3.7 22.2 - - - -
77A LEU* 4.2 7.2 - - + -
92A MET* 3.5 17.3 - - - -
108A ALA 3.5 14.6 - - - -
109A ILE 3.1 8.9 + - - +
111A GLY* 1.3 74.7 - - - +
113A SER* 1.3 59.1 + - - +
115A ALA* 3.3 1.1 + - - +
116A ILE* 2.9 38.5 + - - +
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Residues in contact with SER 113 (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 GLN* 3.2 20.4 + - - +
89A ASP* 2.6 31.2 + - - -
92A MET* 3.8 6.9 - - - +
109A ILE 3.0 11.3 + - - -
110A LEU* 3.1 9.2 + - - -
112A CYS* 1.3 75.8 - - - +
114A MET* 1.3 63.7 + - - +
116A ILE* 3.6 2.3 + - - +
117A SER* 3.3 13.0 + - - -
349A THR* 4.1 8.5 - - - -
350A ILE* 2.8 31.1 + - - +
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Residues in contact with MET 114 (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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33A SER* 3.3 21.5 - - - +
34A ALA 3.5 21.5 - - - +
35A VAL* 4.9 0.2 - - - -
36A PRO* 5.6 0.4 - - + -
110A LEU* 2.8 48.0 + - + +
111A GLY* 4.4 2.5 - - - -
113A SER* 1.3 77.4 - - - +
115A ALA* 1.3 62.1 + - - +
117A SER* 2.7 22.2 + - - -
118A LYS* 3.1 11.1 + - - +
344A ILE* 3.8 14.4 - - + -
350A ILE* 3.9 13.2 - - + -
378A ASP* 3.5 18.2 - - - +
380A TYR* 3.5 44.4 - - + -
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Residues in contact with ALA 115 (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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22A VAL* 3.9 10.8 - - + +
24A VAL* 3.5 20.6 - - + +
31A PHE* 3.5 26.4 - - - +
33A SER* 3.4 11.0 - - - +
111A GLY 3.0 18.2 + - - +
112A CYS 4.0 0.4 - - - +
114A MET* 1.3 73.5 - - - +
116A ILE* 1.3 66.2 + - - +
118A LYS* 3.2 6.2 + - - +
119A ALA* 2.9 24.4 + - - +
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Residues in contact with ILE 116 (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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3A ILE* 4.3 15.3 - - + -
24A VAL* 4.1 10.5 - - + +
77A LEU* 3.9 22.4 - - + -
82A GLU* 3.3 27.3 - - - +
85A GLN* 3.5 19.1 - - - +
88A LEU* 4.1 29.8 - - + -
89A ASP* 5.3 0.7 - - - +
92A MET* 4.0 16.4 - - + -
112A CYS 2.9 25.7 + - - +
113A SER* 3.7 5.2 - - - +
115A ALA* 1.3 74.0 - - - +
117A SER* 1.3 57.2 + - - +
119A ALA* 3.2 8.5 + - - +
120A ALA* 2.9 26.9 + - - +
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Residues in contact with SER 117 (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 GLN* 3.3 24.0 - - - -
113A SER 3.3 5.5 + - - -
114A MET 2.7 19.3 + - - -
116A ILE* 1.3 78.8 - - - +
118A LYS* 1.3 56.5 + - - +
120A ALA* 3.4 0.6 + - - -
121A ALA* 2.9 24.8 + - - +
128A LEU* 3.9 3.6 - - - +
131A TYR* 3.5 17.7 - - - -
132A LEU* 4.1 13.9 - - - -
350A ILE* 5.0 0.4 - - - -
380A TYR* 2.7 30.6 + - - -
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Residues in contact with LYS 118 (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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31A PHE* 3.7 19.6 - - + +
32A ARG 3.4 30.7 + - - +
33A SER* 3.2 23.8 - - - +
114A MET 3.1 8.0 + - - +
115A ALA* 3.2 7.6 + - - +
117A SER* 1.3 75.2 - - - +
119A ALA* 1.3 63.6 + - - +
121A ALA* 3.4 4.3 + - - +
122A ALA* 3.1 22.7 + - - +
128A LEU* 3.9 32.1 - - + +
378A ASP* 5.9 0.7 - - - +
380A TYR* 4.4 9.2 - - + -
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Residues in contact with ALA 119 (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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24A VAL* 4.0 11.7 - - + -
26A THR* 3.9 22.3 + - + -
28A LYS* 5.5 0.5 - - - +
31A PHE* 3.6 28.3 - - + -
82A GLU* 3.9 11.3 - - + +
115A ALA 2.9 13.3 + - - +
116A ILE 3.5 7.9 - - - +
118A LYS* 1.3 77.9 - - - +
120A ALA* 1.3 56.5 + - - +
122A ALA* 3.3 4.3 + - - +
123A ALA* 2.9 26.3 + - - +
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Residues in contact with ALA 120 (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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82A GLU* 3.4 30.0 - - - +
83A LEU* 3.7 15.0 - - + +
116A ILE 2.9 11.2 + - - +
117A SER* 3.7 0.9 - - - +
118A LYS 3.2 0.2 - - - -
119A ALA* 1.3 74.3 - - - +
121A ALA* 1.3 65.0 + - - +
123A ALA* 3.1 4.5 + - - +
124A LYS* 2.9 21.5 + - - +
131A TYR* 3.3 35.2 - - + +
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Residues in contact with ALA 121 (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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117A SER 2.9 16.0 + - - +
118A LYS* 3.6 8.1 - - - +
120A ALA* 1.3 74.3 - - - +
122A ALA* 1.3 57.3 + - - +
124A LYS* 3.2 3.3 + - - +
125A GLY 2.9 22.3 + - - -
126A VAL* 3.1 26.1 + - - +
128A LEU* 3.9 16.6 - - + +
131A TYR* 3.5 34.0 - - + -
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Residues in contact with ALA 122 (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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28A LYS* 4.1 21.7 - - + +
31A PHE* 3.3 42.0 - - + -
118A LYS 3.1 5.4 + - - +
119A ALA 3.5 4.3 - - - +
120A ALA 3.1 0.2 - - - -
121A ALA* 1.3 74.0 - - - +
123A ALA* 1.3 66.7 + - - +
125A GLY* 3.0 15.6 + - - +
126A VAL 4.8 1.3 - - - -
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Residues in contact with ALA 123 (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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1A MET* 4.9 21.3 - - + +
28A LYS* 4.5 19.4 - - + +
82A GLU* 3.7 17.7 - - - +
83A LEU* 4.3 14.6 - - + -
119A ALA 2.9 14.4 + - - +
120A ALA* 3.4 11.0 - - - +
122A ALA* 1.3 78.2 - - - +
124A LYS* 1.3 59.6 + - - +
125A GLY 3.5 0.3 + - - -
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Residues in contact with LYS 124 (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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83A LEU* 3.6 41.4 - - + +
120A ALA 2.9 9.4 + - - +
121A ALA 3.2 7.8 + - - +
123A ALA* 1.3 75.7 - - - +
125A GLY* 1.3 62.5 + - - +
126A VAL* 3.6 22.1 + - + +
131A TYR* 4.0 15.9 - - + -
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Residues in contact with GLY 125 (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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121A ALA 2.9 4.6 + - - -
122A ALA* 3.0 16.1 + - - -
123A ALA 3.2 1.2 + - - -
124A LYS* 1.3 78.1 - - - +
126A VAL* 1.3 62.5 + - - +
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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