Contacts of the helix formed by residues 97 - 121 (chain A) in PDB entry 4ZIA
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 LYS 97 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ARG 4.3 17.0 + - - +
94A TYR* 3.2 11.2 + - - +
96A GLU* 1.3 92.5 - - + +
98A PRO* 1.3 65.2 - - - +
99A MET* 3.2 3.8 - - - -
100A GLU* 3.2 52.2 + - + +
101A ILE 3.6 3.8 + - - -
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Residues in contact with PRO 98 (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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50A GLU* 4.4 13.0 - - + +
53A ALA* 3.4 31.3 - - + +
54A THR* 3.5 30.3 - - + +
57A PHE* 4.0 10.5 - - + -
94A TYR 3.1 11.4 - - - +
95A LEU 4.7 3.1 - - - +
96A GLU* 3.6 8.3 - - - +
97A LYS* 1.3 88.6 - - - +
99A MET* 1.3 63.8 + - + +
100A GLU 3.2 0.2 - - - -
101A ILE* 3.0 22.8 - - + +
102A ALA* 3.1 6.4 + - - +
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Residues in contact with MET 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA* 3.2 27.0 - - - +
48A SER 3.7 15.3 - - - +
49A LYS* 3.9 0.9 - - - +
50A GLU* 3.7 46.0 - - + +
53A ALA* 3.7 12.1 - - + -
97A LYS* 3.2 1.7 - - - -
98A PRO* 1.3 76.2 - - + +
100A GLU* 1.3 61.1 + - - +
102A ALA* 3.2 4.2 + - - +
103A ARG* 2.8 55.5 + - - +
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Residues in contact with GLU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A TYR* 4.0 18.8 + - + -
97A LYS* 3.2 49.0 + - + +
99A MET* 1.3 76.9 - - - +
101A ILE* 1.3 65.2 + - - +
103A ARG* 3.2 33.8 + - + +
104A ILE* 3.2 23.7 + - + +
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Residues in contact with ILE 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A SER* 3.7 30.3 - - - +
26A PHE* 5.2 1.1 - - + -
30A LEU* 6.5 0.2 - - + -
43A TRP* 5.7 2.7 - - + -
57A PHE* 3.7 32.3 - - + -
60A LEU* 4.8 8.3 - - + -
90A LEU* 3.9 13.5 - - + -
94A TYR* 3.5 34.0 - - + -
97A LYS 3.6 1.0 + - - -
98A PRO* 3.0 24.7 - - + +
100A GLU* 1.3 78.8 - - - +
102A ALA* 1.3 63.0 + - - +
104A ILE* 3.4 7.7 + - + +
105A VAL* 3.2 34.1 + - + +
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Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TRP* 4.0 22.9 - - + +
46A ALA* 4.2 3.6 - - + +
47A ALA* 3.7 26.4 - - + +
53A ALA* 4.1 10.1 - - + -
56A VAL* 5.8 0.9 - - + -
98A PRO 3.1 18.6 + - - +
99A MET 3.4 6.1 - - - +
100A GLU 3.1 0.2 - - - -
101A ILE* 1.3 80.3 - - + +
103A ARG* 1.3 56.4 + - - +
105A VAL* 3.5 1.7 + - - +
106A ALA* 2.9 29.6 + - - +
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Residues in contact with ARG 103 (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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47A ALA* 4.0 16.7 + - + +
99A MET* 2.8 52.7 + - - +
100A GLU* 3.4 30.6 + - - +
102A ALA* 1.3 76.9 - - - +
104A ILE* 1.3 53.4 + - + +
106A ALA* 3.1 8.6 + - + +
107A ARG* 2.7 37.9 + - - +
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Residues in contact with ILE 104 (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 SER* 4.6 6.7 - - - +
25A SER* 3.8 15.5 - - - +
26A PHE* 4.1 22.9 - - + -
94A TYR* 3.3 32.1 - - + +
100A GLU* 3.2 18.4 + - + +
101A ILE* 3.5 9.9 - - + +
103A ARG* 1.3 76.4 - - + +
105A VAL* 1.3 64.0 + - - +
107A ARG* 3.1 9.3 + - - +
108A CYS* 2.8 23.4 + - + +
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Residues in contact with VAL 105 (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 PHE* 3.9 47.6 - - + -
38A ILE* 4.5 1.3 - - + -
43A TRP* 3.2 59.2 - - + +
60A LEU* 5.8 3.1 - - + -
101A ILE* 3.2 21.7 + - + +
102A ALA 3.9 0.9 - - - +
104A ILE* 1.3 75.0 - - - +
106A ALA* 1.3 64.5 + - - +
108A CYS* 3.0 2.9 + - - +
109A LEU* 2.9 28.4 + - + +
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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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43A TRP* 3.8 32.5 - - + +
44A ALA* 4.1 9.4 - - + +
47A ALA* 5.0 1.8 - - + -
102A ALA 2.9 15.1 + - - +
103A ARG* 3.1 12.3 + - + +
105A VAL* 1.3 77.6 - - - +
107A ARG* 1.3 61.3 + - - +
109A LEU* 3.4 4.8 + - - +
110A TRP* 3.1 23.4 + - - +
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Residues in contact with ARG 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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103A ARG 2.7 19.3 + - - +
104A ILE* 3.4 8.1 - - - +
106A ALA* 1.3 71.8 - - - +
108A CYS* 1.3 60.2 + - - +
110A TRP* 3.2 39.3 + - - +
111A GLU* 2.9 52.5 + - + +
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Residues in contact with CYS 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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21A LEU* 3.7 29.8 - - - +
22A TYR* 3.5 33.9 - - - -
26A PHE* 3.9 17.7 - - + -
104A ILE* 2.8 14.6 + - + +
105A VAL 3.6 6.3 - - - +
107A ARG* 1.3 79.1 - - - +
109A LEU* 1.3 57.4 + - - +
111A GLU* 3.1 8.2 + - - +
112A GLU* 2.9 40.7 + - - +
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Residues in contact with LEU 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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3A GLN* 3.4 11.0 + - - +
26A PHE* 5.0 3.4 - - + -
31A ARG* 3.6 23.3 - - - +
38A ILE* 4.2 16.8 - - + +
39A GLU* 5.2 6.7 - - + -
41A GLN 5.4 0.7 - - - +
43A TRP* 3.5 37.9 - - + +
105A VAL* 2.9 20.0 + - + +
106A ALA* 3.9 4.7 - - - +
108A CYS* 1.3 75.7 - - - +
110A TRP* 1.3 62.0 + - - +
112A GLU* 3.2 23.1 + - - +
113A SER* 3.2 24.8 + - - -
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Residues in contact with TRP 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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106A ALA 3.1 14.3 + - - +
107A ARG* 3.3 39.3 - - - +
108A CYS 3.2 0.2 - - - -
109A LEU* 1.3 76.9 - - - +
111A GLU* 1.3 73.2 + - + +
113A SER* 3.2 9.0 + - - -
114A ARG* 2.9 76.2 + - + +
117A GLN* 6.2 0.2 - - - +
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Residues in contact with GLU 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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21A LEU* 3.4 32.3 - - + +
107A ARG* 2.9 38.4 + - + +
108A CYS* 3.1 8.9 + - - +
110A TRP* 1.3 85.0 - - + +
112A GLU* 1.3 59.0 + - - +
114A ARG* 3.7 23.5 - - - +
115A LEU* 2.9 30.7 + - - +
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Residues in contact with GLU 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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3A GLN* 2.9 18.2 + - - +
7A LEU* 3.4 27.8 - - + +
21A LEU* 4.0 14.6 - - + -
22A TYR* 2.8 23.8 + - - +
31A ARG* 2.5 48.4 + - - -
108A CYS* 2.9 27.2 + - - +
109A LEU* 3.2 11.5 - - - +
110A TRP 3.3 0.2 - - - -
111A GLU* 1.3 75.9 - - - +
113A SER* 1.3 59.2 + - - +
115A LEU* 3.5 3.8 + - - +
116A LEU* 3.0 33.1 + - - +
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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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3A GLN* 3.3 20.8 + - - -
109A LEU 3.2 11.6 + - - -
110A TRP* 3.2 13.1 + - - -
111A GLU 3.2 0.2 - - - -
112A GLU* 1.3 77.1 - - - +
114A ARG* 1.3 60.9 + - - +
116A LEU* 3.1 8.1 + - - +
117A GLN* 2.8 45.9 + - - +
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Residues in contact with ARG 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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110A TRP* 2.9 64.4 + - + +
111A GLU* 3.7 16.2 - - - +
113A SER* 1.3 75.8 - - - +
115A LEU* 1.3 60.5 + - - +
117A GLN* 3.4 16.3 + - + +
118A THR* 3.3 24.4 + - - +
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Residues in contact with LEU 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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7A LEU* 4.8 1.6 - - + -
10A LEU* 3.6 33.4 - - + -
14A TYR* 3.9 25.5 - - + +
17A GLN* 3.9 36.8 - - + +
18A LEU* 4.0 23.3 - - + +
21A LEU* 4.5 5.8 - - + -
111A GLU 2.9 18.6 + - - +
112A GLU 3.6 4.0 - - - +
114A ARG* 1.3 74.3 - - - +
116A LEU* 1.3 60.8 + - - +
118A THR* 3.0 24.0 + - - +
119A ALA* 3.2 12.5 + - - +
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Residues in contact with LEU 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 GLN* 4.4 16.4 - - + +
6A GLN* 3.9 45.3 - - + +
7A LEU* 3.6 27.6 - - + -
10A LEU* 3.9 20.2 - - + -
112A GLU 3.0 20.8 + - - +
113A SER* 3.1 6.3 + - - +
115A LEU* 1.3 76.9 - - - +
117A GLN* 1.3 58.1 + - + +
119A ALA* 3.9 4.3 - - + +
120A ALA* 2.8 33.6 + - - +
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Residues in contact with GLN 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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110A TRP* 6.2 0.2 - - - +
113A SER* 2.8 35.4 + - - +
114A ARG* 3.6 13.5 - - - +
115A LEU 3.2 0.2 - - - -
116A LEU* 1.3 78.2 - - + +
118A THR* 1.3 59.4 + - - +
120A ALA* 3.9 5.2 - - - -
121A THR* 2.9 33.9 + - + +
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Residues in contact with THR 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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14A TYR* 3.7 26.2 - - + +
17A GLN* 6.3 0.9 - - - +
114A ARG* 3.3 12.7 + - - +
115A LEU* 3.0 15.2 + - + +
117A GLN* 1.3 77.8 - - - +
119A ALA* 1.3 62.6 + - - +
121A THR* 3.4 6.6 + - - -
122A ALA* 3.0 26.6 + - + +
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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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10A LEU* 4.0 18.6 - - + -
11A ASP* 5.2 4.5 - - + +
14A TYR* 3.5 36.3 - - + -
115A LEU 3.2 4.8 + - - +
116A LEU* 4.0 6.3 - - + +
118A THR* 1.3 79.9 - - - +
120A ALA* 1.3 65.2 + - - +
122A ALA* 3.1 18.9 + - - +
123A ALA* 5.0 1.0 - - - +
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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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116A LEU 2.8 21.5 + - - +
117A GLN* 4.0 6.3 - - - +
119A ALA* 1.3 79.3 - - - +
121A THR* 1.3 61.2 + - + +
122A ALA 3.2 3.5 + - - -
123A ALA* 3.8 15.9 + - - +
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Residues in contact with THR 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 GLN* 2.9 24.7 + - + +
118A THR* 3.4 8.0 + - - -
120A ALA* 1.3 76.8 - - + +
122A ALA* 1.3 55.6 + - - +
123A ALA 3.2 8.1 + - - -
124A GLN* 3.9 23.1 + - - +
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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
------------------------------------------------------------
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