Contacts of the helix formed by residues 100 - 122 (chain A) in PDB entry 1ZTD
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 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A GLU* 4.0 26.9 - - + -
97A ASP* 3.0 19.4 + - - +
99A SER* 1.3 91.2 + - - +
101A LYS* 1.3 58.6 + - - +
102A LYS* 3.4 2.9 - - - -
103A GLU* 3.6 12.2 + - + +
104A ALA* 3.0 27.5 + - - +
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Residues in contact with LYS 101 (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 ASP* 2.8 39.5 + - - +
34A ARG 5.6 2.2 - - - -
36A PRO* 5.6 4.9 - - + -
94A GLU 3.9 6.3 - - - +
95A VAL* 3.5 21.3 - - + +
97A ASP 2.8 16.0 + - - +
98A PHE* 3.6 32.7 + - - +
100A LYS* 1.3 75.5 - - - +
102A LYS* 1.3 67.1 + - + +
104A ALA* 4.2 2.0 - - - -
105A ILE* 2.9 44.3 + - + +
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Residues in contact with LYS 102 (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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36A PRO* 3.6 29.7 - - + +
38A ALA* 4.1 19.7 - - + +
39A SER* 2.8 28.7 + - - +
42A ILE* 3.9 12.4 - - + +
98A PHE* 4.9 5.3 + - - +
99A SER 5.6 0.2 - - - -
100A LYS 3.4 1.0 - - - -
101A LYS* 1.3 76.4 - - + +
103A GLU* 1.3 63.4 + - - +
106A GLY* 3.1 10.7 + - - -
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Residues in contact with GLU 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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42A ILE* 4.2 25.0 - - + +
46A LEU* 6.0 0.5 - - - +
100A LYS* 3.6 13.8 + - + +
101A LYS 3.4 0.2 - - - -
102A LYS* 1.3 78.8 - - - +
104A ALA* 1.3 60.2 + - - +
106A GLY* 3.2 2.6 + - - -
107A ARG* 2.9 63.4 + - + +
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Residues in contact with ALA 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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90A ASN 5.0 1.9 - - - +
91A LEU* 5.7 0.7 - - - +
92A TYR* 5.5 11.1 - - + +
94A GLU* 3.8 27.4 - - + -
95A VAL* 4.4 6.5 - - + +
100A LYS 3.0 19.5 + - - +
101A LYS* 3.8 7.0 - - - +
103A GLU* 1.3 79.9 - - - +
105A ILE* 1.3 61.4 + - + +
107A ARG* 3.3 8.6 + - - +
108A ALA* 3.1 22.0 + - - +
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Residues in contact with ILE 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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19A TYR* 3.4 46.2 - - + +
33A ASP* 4.6 1.8 - - - +
34A ARG 4.9 0.7 - - - +
35A VAL* 4.1 10.1 - - + -
36A PRO* 3.7 20.2 - - + -
39A SER* 3.6 17.5 - - - +
91A LEU* 5.9 0.9 - - - -
95A VAL* 5.1 2.0 - - + -
101A LYS* 2.9 46.9 + - + +
104A ALA* 1.3 71.6 - - + +
106A GLY* 1.3 68.1 + - - +
108A ALA* 3.0 17.1 + - - +
109A LEU* 3.0 28.4 + - + +
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Residues in contact with GLY 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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39A SER* 3.2 28.5 - - - -
42A ILE* 4.4 6.1 - - - -
43A ALA* 3.4 11.4 - - - +
46A LEU* 4.3 6.0 - - - +
102A LYS 3.1 14.6 + - - -
103A GLU 3.6 3.4 - - - -
105A ILE* 1.3 76.5 - - - +
107A ARG* 1.3 59.7 + - - +
109A LEU* 3.3 2.0 + - - -
110A ALA* 3.1 21.3 + - - +
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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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42A ILE* 5.7 0.2 - - + -
46A LEU* 3.9 39.7 - - + +
90A ASN* 4.4 7.2 - - - +
92A TYR* 6.0 7.4 - - + -
103A GLU* 2.9 47.9 + - + +
104A ALA* 3.6 10.5 - - - +
106A GLY* 1.3 76.2 - - - +
108A ALA* 1.3 61.0 + - - +
110A ALA* 3.7 2.6 + - - +
111A PRO* 3.3 18.0 - - - +
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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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19A TYR* 5.5 1.1 - - + -
87A ILE* 4.0 24.7 + - + +
90A ASN* 3.7 23.8 + - + +
91A LEU* 3.8 28.3 - - + -
104A ALA 3.1 11.9 + - - +
105A ILE* 3.0 11.3 + - - +
107A ARG* 1.3 79.8 - - - +
109A LEU* 1.3 58.9 + - + +
111A PRO* 3.4 16.2 - - - +
112A LEU* 4.7 1.0 + - - +
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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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15A ILE* 3.6 28.5 - - + -
19A TYR* 5.4 5.6 - - + -
35A VAL* 3.9 10.1 - - + -
39A SER 4.7 7.2 - - - +
40A LEU* 3.7 29.8 - - + -
43A ALA* 4.1 9.2 - - + -
69A ILE* 5.7 1.3 - - + -
87A ILE* 4.2 21.5 - - + -
105A ILE* 3.0 36.8 + - + +
106A GLY 3.3 3.6 + - - +
107A ARG 3.3 0.2 - - - -
108A ALA* 1.3 79.8 - - + +
110A ALA* 1.3 65.5 + - - +
111A PRO* 3.3 1.3 - - - -
112A LEU* 3.0 21.0 + - + +
113A LEU* 3.1 17.7 + - + +
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Residues in contact with ALA 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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43A ALA* 3.8 14.6 - - - +
46A LEU* 4.3 17.5 - - + -
47A THR* 3.3 26.7 - - + +
106A GLY 3.1 15.9 + - - +
107A ARG 3.9 4.3 - - - +
109A LEU* 1.3 76.4 - - - +
111A PRO* 1.3 68.4 - - + +
113A LEU* 3.2 3.0 + - - +
114A VAL* 3.2 19.6 + - - +
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Residues in contact with PRO 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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86A ILE* 4.1 10.5 - - + -
90A ASN* 3.3 34.5 - - - +
107A ARG 3.3 16.4 - - - +
108A ALA 3.4 8.5 - - - +
109A LEU 3.4 0.7 - - - -
110A ALA* 1.3 93.8 - - + +
112A LEU* 1.3 61.8 + - - +
114A VAL* 3.5 8.8 + - + +
115A ILE* 3.3 29.5 + - + +
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Residues in contact with LEU 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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15A ILE* 4.0 26.7 - - + -
18A LEU* 5.0 2.9 - - + -
69A ILE* 4.8 5.2 - - + -
78A ILE* 3.5 31.9 - - + -
83A ALA* 4.0 19.1 - - + +
86A ILE* 3.8 22.6 - - + +
87A ILE* 4.2 18.6 - - + -
108A ALA 5.0 0.2 - - - +
109A LEU* 3.0 17.9 + - + +
111A PRO* 1.3 82.0 - - - +
113A LEU* 1.3 58.9 + - + +
115A ILE* 3.3 3.5 + - - +
116A ILE* 2.9 47.0 + - + +
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Residues in contact with LEU 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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40A LEU* 5.8 2.2 - - + -
43A ALA* 3.7 28.7 - - + +
44A LEU* 3.9 21.8 - - + +
47A THR* 4.4 2.5 - - + -
49A LEU* 4.1 13.8 - - + +
65A ALA* 4.2 24.2 - - + +
68A LEU* 4.4 10.7 - - + +
69A ILE* 3.8 35.9 - - + -
109A LEU* 3.1 15.0 + - + +
110A ALA 3.2 5.6 + - - +
112A LEU* 1.3 74.8 - - + +
114A VAL* 1.3 60.6 + - - +
116A ILE* 3.8 5.2 - - + +
117A SER* 2.9 33.3 + - - -
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Residues in contact with VAL 114 (chain A).
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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47A THR* 3.5 23.8 - - + +
49A LEU* 5.3 1.8 - - - -
110A ALA 3.2 16.1 + - - +
111A PRO* 3.7 10.1 - - + +
112A LEU 3.3 0.2 - - - -
113A LEU* 1.3 76.7 - - - +
115A ILE* 1.3 65.7 + - + +
117A SER* 2.8 21.7 + - - +
118A GLU* 3.0 37.2 + - + +
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Residues in contact with ILE 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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78A ILE* 4.8 5.8 - - + -
86A ILE* 3.3 38.6 - - + -
111A PRO* 3.3 15.5 + - + +
112A LEU 3.7 6.3 - - - +
114A VAL* 1.3 79.9 - - + +
116A ILE* 1.3 62.8 + - - +
118A GLU* 3.4 11.6 + - - +
119A ARG* 3.1 62.8 + - + +
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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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68A LEU* 3.8 26.2 - - + +
69A ILE* 3.8 32.3 - - + -
72A ALA* 3.4 29.2 - - + +
78A ILE* 4.1 23.1 - - + -
112A LEU* 2.9 41.9 + - + +
113A LEU* 3.8 6.1 - - + +
115A ILE* 1.3 75.8 - - - +
117A SER* 1.3 63.8 - - - +
119A ARG* 3.2 7.5 + - - +
120A LEU* 3.1 24.7 + - + +
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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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49A LEU* 4.1 28.8 - - - +
68A LEU* 4.5 9.0 - - - -
113A LEU 2.9 19.1 + - - -
114A VAL* 2.8 24.3 + - - +
116A ILE* 1.3 75.7 - - - +
118A GLU* 1.3 63.5 + - - +
120A LEU* 3.6 9.4 + - - +
121A TYR* 3.0 40.9 + - - -
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Residues in contact with GLU 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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114A VAL* 3.0 39.9 + - + +
115A ILE* 3.7 11.9 - - - +
116A ILE 3.2 0.2 - - - -
117A SER* 1.3 80.2 + - - +
119A ARG* 1.3 58.5 + - + +
121A TYR* 3.6 6.4 + - - +
122A SER* 2.9 34.3 + - - +
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Residues in contact with ARG 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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77A LEU* 2.9 42.8 + - + +
78A ILE* 4.1 4.9 - - - +
82A GLU* 2.6 44.3 + - - -
115A ILE* 3.1 36.5 + - + +
116A ILE* 3.2 6.9 + - - +
118A GLU* 1.3 78.1 - - + +
120A LEU* 1.3 57.2 + - - +
122A SER* 3.3 7.0 + - - -
123A SER* 2.6 34.9 + - - -
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Residues in contact with LEU 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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68A LEU* 3.5 38.4 - - + +
71A LYS* 4.0 32.5 - - + +
72A ALA* 4.1 8.5 - - + -
75A MET* 5.4 3.1 - - + -
77A LEU* 3.4 24.7 - - + -
116A ILE* 3.1 29.3 + - + +
117A SER* 3.9 4.7 - - - +
119A ARG* 1.3 75.4 - - - +
121A TYR* 1.3 65.3 + - + +
123A SER* 3.2 15.9 + - - -
124A GLN* 3.9 9.8 + - - +
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Residues in contact with TYR 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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49A LEU* 5.5 7.0 - - + +
52A ASN* 5.1 9.4 + - - +
64A TYR* 5.8 0.3 + - - -
117A SER* 3.0 35.0 + - - +
118A GLU* 3.9 6.1 - - - +
120A LEU* 1.3 82.2 - - + +
122A SER* 1.3 61.0 + - - +
123A SER 3.1 1.4 + - - -
124A GLN* 3.4 39.5 + - - +
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Residues in contact with SER 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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118A GLU* 2.9 20.8 + - - +
119A ARG* 3.3 8.0 + - - -
120A LEU 3.3 0.2 - - - -
121A TYR* 1.3 76.4 - - - +
123A SER* 1.3 58.9 + - - +
124A GLN 3.3 5.7 - - - +
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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