Contacts of the helix formed by residues 99 - 120 (chain A) in PDB entry 4AU8
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 ASP 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A ASP 4.0 1.2 + - - -
98A LEU* 1.3 71.3 - - - +
100A PRO* 1.4 72.4 - - - +
101A GLU* 3.1 25.9 + - - +
102A ILE* 2.8 48.3 + - + +
103A VAL* 3.1 9.2 + - - +
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Residues in contact with PRO 100 (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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98A LEU 3.3 6.5 - - - +
99A ASP* 1.4 89.6 - - - +
101A GLU* 1.3 63.4 + - + +
103A VAL* 3.4 13.0 - - + +
104A LYS* 3.1 26.5 + - - +
254A LYS* 4.7 19.7 - - + +
285A TYR* 4.2 2.9 + - - -
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Residues in contact with GLU 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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99A ASP* 3.0 19.9 + - - +
100A PRO* 1.3 81.2 - - + +
102A ILE* 1.3 61.6 + - + +
104A LYS* 3.3 37.3 + - - +
105A SER* 3.0 27.5 + - - -
288A ASP* 4.6 6.1 - - - +
289A PHE* 4.6 13.2 - - + -
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Residues in contact with ILE 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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90A TYR* 3.4 28.0 - - + +
98A LEU* 4.5 8.1 - - + -
99A ASP* 2.8 38.5 + - + +
101A GLU* 1.3 73.8 - - + +
103A VAL* 1.3 57.1 + - - +
105A SER* 3.3 5.5 + - - -
106A PHE* 2.8 61.8 + - + +
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Residues in contact with VAL 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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98A LEU* 3.8 17.7 - - + +
99A ASP 3.1 12.8 + - - +
100A PRO* 3.4 15.3 - - + +
102A ILE* 1.3 77.0 - - - +
104A LYS* 1.3 56.7 + - - +
106A PHE* 3.9 0.6 - - - -
107A LEU* 3.0 28.8 + - - +
192A PHE* 4.0 15.3 - - + -
195A LEU* 3.5 45.6 - - + +
196A ALA* 4.0 15.5 - - + +
255A LEU* 4.8 3.8 - - + -
285A TYR* 3.7 13.0 - - - +
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Residues in contact with LYS 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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100A PRO 3.1 15.4 + - - +
101A GLU* 3.3 29.7 + - - +
102A ILE 3.3 0.2 - - - -
103A VAL* 1.3 72.4 - - - +
105A SER* 1.3 59.4 + - - +
107A LEU* 3.4 1.3 + - - -
108A PHE* 2.9 30.7 + - - +
256A ASN* 5.8 3.4 - - - +
285A TYR* 3.4 49.5 + - + +
286A PHE* 3.5 23.5 - - + +
288A ASP* 3.3 33.3 + - - -
289A PHE* 3.6 28.9 - - + -
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Residues in contact with SER 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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101A GLU 3.0 18.1 + - - -
102A ILE* 3.3 7.4 + - - -
104A LYS* 1.3 76.2 - - - +
106A PHE* 1.4 61.3 + - - +
108A PHE* 3.3 1.7 + - - +
109A GLN* 3.0 51.7 + - - +
138A GLY 4.3 2.6 + - - -
289A PHE* 3.5 25.2 - - - -
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Residues in contact with PHE 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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87A LEU* 4.0 7.2 - - + -
90A TYR* 3.7 35.0 - + - -
98A LEU* 4.8 0.2 - - + -
102A ILE* 2.8 41.5 + - + +
105A SER* 1.4 76.8 - - - +
107A LEU* 1.3 63.2 + - - +
109A GLN* 3.9 5.3 - - - +
110A LEU* 3.0 24.4 + - - +
134A ILE* 3.6 37.2 - - + -
138A GLY* 3.5 32.5 - - - -
140A LEU* 3.6 16.7 - - + +
195A LEU* 3.8 34.1 - - + -
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Residues in contact with LEU 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 VAL 3.0 18.3 + - - +
104A LYS* 3.9 3.6 - - - +
106A PHE* 1.3 77.2 - - - +
108A PHE* 1.3 63.1 + - - +
110A LEU* 3.3 16.3 + - + +
111A LEU* 2.9 41.9 + - + +
188A ALA* 4.2 12.3 - - + +
192A PHE* 3.7 58.8 - - + -
195A LEU* 4.0 9.5 - - + +
262A LEU* 3.8 9.6 - - + -
266A LEU* 4.9 3.8 - - + -
285A TYR* 4.1 0.9 - - + -
286A PHE* 3.7 19.5 - - + -
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Residues in contact with PHE 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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104A LYS 2.9 21.6 + - - +
105A SER 3.3 5.1 + - - +
107A LEU* 1.3 72.2 - - - +
109A GLN* 1.3 66.2 + - + +
111A LEU 3.4 0.2 + - - -
112A LYS* 2.9 64.2 + - + +
281A LEU* 3.7 25.3 - - + +
286A PHE* 3.7 30.2 - + + -
289A PHE* 3.5 43.7 - + + -
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Residues in contact with GLN 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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62A ASN* 3.2 36.4 + - - +
105A SER* 3.0 40.8 + - - +
106A PHE* 3.9 8.7 - - - +
108A PHE* 1.3 81.8 - - + +
110A LEU* 1.4 65.1 + - - +
112A LYS* 3.3 2.6 + - - -
113A GLY* 3.0 18.9 + - - -
138A GLY 3.0 18.8 + - - -
139A GLU* 3.2 11.1 - - - +
140A LEU* 2.8 34.4 + - + +
289A PHE* 6.3 0.2 - - + -
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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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106A PHE 3.0 17.9 + - - +
107A LEU* 3.6 15.7 - - + +
109A GLN* 1.4 76.5 - - - +
111A LEU* 1.3 57.0 + - - +
113A GLY* 3.3 2.4 + - - -
114A LEU* 2.8 36.6 + - + +
127A LEU* 4.1 19.3 - - + -
132A LEU* 3.8 22.9 - - + -
140A LEU* 3.8 14.2 - - + +
142A LEU* 3.7 19.2 - - + +
188A ALA* 4.1 28.0 - - + -
191A ILE* 4.2 21.5 - - + -
195A LEU* 5.9 0.9 - - + -
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Residues in contact with LEU 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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107A LEU* 2.9 37.7 + - + +
108A PHE 3.7 3.8 - - - +
110A LEU* 1.3 75.7 - - + +
112A LYS* 1.3 54.6 + - - +
114A LEU* 4.3 5.6 - - + -
115A GLY* 2.7 30.8 + - - -
185A MET* 3.7 28.9 - - + -
188A ALA* 4.5 15.3 - - + -
262A LEU* 4.9 0.7 - - + -
266A LEU* 4.8 4.3 - - + -
277A ALA* 3.7 10.1 - - + +
280A ALA* 3.8 22.2 - - + -
281A LEU* 3.9 17.2 - - + +
286A PHE* 3.7 29.4 - - + -
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Residues in contact with LYS 112 (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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60A HIS* 3.8 15.6 + - + +
61A LYS* 6.1 4.5 - - - +
62A ASN* 3.6 15.3 - - - +
108A PHE* 2.9 55.5 + - + +
109A GLN* 3.6 6.1 - - - +
110A LEU 3.3 0.2 - - - -
111A LEU* 1.3 72.8 - - - +
113A GLY* 1.3 60.9 + - - +
115A GLY* 3.5 1.1 + - - -
116A PHE* 3.1 28.1 + - - +
281A LEU* 3.9 22.7 - - + +
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Residues in contact with GLY 113 (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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60A HIS* 4.1 7.2 - - - -
62A ASN* 3.9 26.4 - - - +
63A ILE* 4.3 3.7 - - - +
109A GLN 3.0 11.1 + - - -
110A LEU 3.7 2.2 - - - -
112A LYS* 1.3 74.7 - - - +
114A LEU* 1.3 63.5 + - - +
116A PHE* 3.4 4.5 + - - +
117A CYS* 3.1 26.7 + - - -
142A LEU* 4.1 9.4 - - - -
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Residues in contact with LEU 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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110A LEU* 2.8 30.7 + - + +
111A LEU* 3.9 7.2 - - + +
113A GLY* 1.3 71.5 - - - +
115A GLY* 1.3 57.7 + - - +
117A CYS* 3.1 5.5 + - + +
118A HIS* 2.8 52.4 + - + +
124A HIS* 4.6 2.9 - - + -
127A LEU* 3.9 27.4 - - + -
142A LEU* 3.8 17.8 - - + +
184A ASP* 3.8 35.2 - - + +
185A MET* 4.4 8.3 - - - -
188A ALA* 4.0 18.8 - - + -
277A ALA* 4.3 4.0 - - + -
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Residues in contact with GLY 115 (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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111A LEU 2.7 22.8 + - - -
112A LYS* 3.8 2.2 - - - -
113A GLY 3.3 0.2 - - - -
114A LEU* 1.3 72.6 - - - +
116A PHE* 1.3 56.9 + - - +
118A HIS* 3.5 3.9 + - - +
119A SER* 3.0 31.5 + - - -
277A ALA* 3.7 16.8 - - - +
278A GLU* 5.1 2.9 - - - -
281A LEU* 5.6 3.1 - - - -
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Residues in contact with PHE 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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57A GLU 4.8 0.2 - - - -
58A LEU* 3.8 27.1 - - + -
59A LYS 3.4 26.7 - - - -
60A HIS* 3.5 27.1 - + + -
63A ILE* 3.4 19.5 - - + -
112A LYS 3.1 13.6 + - - +
113A GLY 3.5 8.5 - - - +
114A LEU 3.2 0.2 - - - -
115A GLY* 1.3 75.7 - - - +
117A CYS* 1.4 60.6 + - - +
119A SER* 2.8 19.7 + - - -
120A ARG* 3.1 63.9 + - - +
1292A SO4 3.9 11.0 - - - -
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Residues in contact with CYS 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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58A LEU* 4.3 10.1 - - - -
63A ILE* 3.7 21.8 - - - -
113A GLY 3.1 18.4 + - - +
114A LEU* 3.1 10.8 + - + +
116A PHE* 1.4 74.7 - - - +
118A HIS* 1.3 62.2 + - + +
120A ARG* 2.9 16.8 + - - +
121A ASN 3.1 0.2 + - - -
122A VAL* 2.9 41.9 + - + +
123A LEU* 5.7 0.2 - - - -
124A HIS* 5.7 2.9 - - + +
142A LEU* 4.5 6.3 - - - -
145A PHE* 3.8 28.5 - - - -
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Residues in contact with HIS 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 LEU* 2.8 35.5 + - + +
115A GLY* 4.0 5.2 - - - +
117A CYS* 1.3 74.1 - - + +
119A SER* 1.4 58.4 + - - +
121A ASN* 3.0 20.8 + - - +
122A VAL 3.2 18.6 - - - -
181A THR* 3.5 50.1 + - + +
184A ASP* 2.8 33.0 + - + +
185A MET* 3.7 20.3 - - - +
277A ALA* 4.2 8.0 + - + +
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Residues in contact with SER 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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115A GLY 3.0 15.6 + - - -
116A PHE* 2.8 8.5 + - - -
118A HIS* 1.4 76.3 - - - +
120A ARG* 1.3 91.6 + - - +
121A ASN* 3.3 9.4 + - - +
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Residues in contact with ARG 120 (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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57A GLU 5.0 2.5 - - - -
58A LEU* 4.0 17.5 - - + -
116A PHE* 3.1 60.2 + - - +
117A CYS 2.9 10.5 + - - +
119A SER* 1.3 107.1 + - - +
121A ASN* 1.3 73.4 + - - +
122A VAL 3.3 0.7 + - - -
151A PHE* 4.9 0.7 - - - -
1292A SO4 3.1 39.7 + - - +
120B ARG 5.1 1.6 - - - +
121B ASN* 5.1 8.9 + - - +
151B PHE* 3.5 22.6 - - + -
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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