Contacts of the helix formed by residues 96 - 117 (chain A) in PDB entry 2LP8
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 ASN 96 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A GLY* 2.9 25.6 + - - +
95A VAL* 1.3 83.9 + - - +
97A TRP* 1.3 83.4 + - + +
98A GLY 3.6 1.6 - - - +
99A ARG* 3.4 12.5 - - + +
100A ILE* 3.4 24.7 + - - +
145A ASN* 5.1 6.9 + - - -
1013B ASP* 4.8 9.0 - - - +
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Residues in contact with TRP 97 (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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96A ASN* 1.3 92.0 - - + +
98A GLY* 1.3 63.4 + - - +
100A ILE* 3.2 16.7 + - - +
101A VAL* 3.6 1.7 - - - +
145A ASN* 2.9 58.1 + - + +
147A GLY 4.7 4.9 - - - -
150A THR* 3.9 3.9 - - + +
151A PHE* 3.4 46.9 - + + -
154A LEU* 3.6 33.6 - - + +
155A TYR* 6.1 0.7 - - + -
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Residues in contact with GLY 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ALA* 5.3 0.4 - - - -
96A ASN* 4.6 1.8 - - - +
97A TRP* 1.3 77.5 - - - +
99A ARG* 1.3 64.1 + - - +
101A VAL* 3.0 36.3 - - - +
151A PHE* 3.7 5.8 - - - -
155A TYR* 6.0 3.6 - - - -
1015B ILE* 3.1 31.2 - - - +
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Residues in contact with ARG 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A VAL* 6.1 0.6 - - - +
90A LEU* 2.7 58.6 + - + +
91A PHE* 4.4 1.4 - - - +
93A ASP 5.9 0.7 - - - +
94A GLY 3.0 17.3 - - - +
95A VAL* 3.3 37.2 - - - +
96A ASN* 3.4 26.2 + - + +
97A TRP 3.2 0.2 - - - -
98A GLY* 1.3 78.2 - - - +
100A ILE* 1.3 63.8 + - - +
102A ALA* 3.0 20.1 + - - +
103A PHE* 3.3 18.8 - - - +
133A TYR* 5.6 1.0 - - - -
138A LEU* 3.4 19.2 - - - +
1012B GLY 4.7 13.0 - - - +
1013B ASP* 6.0 1.3 - - - -
1015B ILE* 4.4 6.2 - - - +
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Residues in contact with ILE 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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50A LEU* 5.4 9.6 - - + -
95A VAL* 3.6 16.8 - - + -
96A ASN 3.4 13.7 - - - +
97A TRP* 3.2 10.4 + - - +
98A GLY 3.2 0.8 - - - -
99A ARG* 1.3 98.0 - - - +
101A VAL* 1.3 65.6 + - - +
103A PHE* 3.0 18.9 + - + +
104A PHE* 3.2 7.5 + - + +
134A LEU* 4.7 14.6 - - + -
138A LEU* 3.7 22.4 - - + -
142A ILE* 3.2 36.1 - - + -
148A TRP* 6.0 2.2 - - + +
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Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 4.5 7.0 - - + -
53A ALA* 3.3 38.6 - - + +
54A GLY* 3.6 1.1 - - - +
57A PHE* 4.5 0.9 - - + -
97A TRP 3.6 1.3 - - - +
98A GLY* 3.0 25.5 + - - +
100A ILE* 1.3 75.5 - - + +
102A ALA* 1.3 57.4 + - - +
104A PHE* 2.8 37.3 - - + -
105A SER* 2.9 16.8 + - - -
151A PHE* 3.4 36.8 - - + -
1015B ILE* 3.6 11.2 - - + -
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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
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57A PHE* 3.3 40.4 - - + -
90A LEU* 3.9 17.3 - - + +
99A ARG* 3.0 16.9 + - - +
101A VAL* 1.3 83.0 - - - +
103A PHE* 1.3 54.8 + - - +
106A PHE* 2.9 30.0 + - - +
1012B GLY* 4.7 1.6 - - - -
1015B ILE* 3.5 15.9 - - + -
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Residues in contact with PHE 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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9A VAL* 5.1 1.3 - - + -
80A TYR* 5.5 0.7 - - - -
83A PHE* 3.3 37.9 - + - -
87A VAL* 3.4 34.3 - - + -
90A LEU* 3.5 9.8 - - + +
99A ARG* 3.3 19.9 + - - +
100A ILE* 3.0 13.1 + - + +
102A ALA* 1.3 80.5 - - - +
104A PHE* 1.3 65.3 + - + +
107A GLY* 3.0 21.7 + - - -
130A MET* 3.1 48.5 - - + +
133A TYR* 3.6 17.5 - + + -
134A LEU* 4.4 8.5 - - + -
138A LEU* 3.6 23.6 - - + -
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Residues in contact with PHE 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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8A LEU* 3.0 25.4 - - + -
9A VAL* 4.3 9.0 - - + -
12A PHE* 3.2 53.7 - + + +
50A LEU* 2.9 62.4 - - + -
51A ARG* 4.7 1.1 - - + -
54A GLY* 3.8 8.1 - - - -
100A ILE* 3.2 7.1 + - + +
101A VAL* 2.8 39.7 - - - -
103A PHE* 1.3 83.8 - - + +
105A SER* 1.3 60.7 + - - +
108A GLY* 3.0 18.9 + - - -
130A MET* 3.4 19.3 - - + +
134A LEU* 6.2 2.5 - - + -
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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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12A PHE* 3.2 18.0 - - - -
54A GLY* 3.0 27.9 + - - -
57A PHE* 3.5 17.1 - - - -
58A GLU* 3.2 17.3 - - - +
61A TYR* 3.5 8.3 + - - -
101A VAL 2.9 20.1 + - - -
104A PHE* 1.3 76.1 - - - +
106A PHE* 1.3 61.5 + - - +
107A GLY 3.1 0.9 - - - -
108A GLY 3.0 2.4 + - - -
109A ALA 2.9 22.3 + - - -
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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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57A PHE* 4.1 7.1 - - + -
61A TYR* 3.8 27.4 - + - -
65A PHE* 4.0 19.3 - + - -
68A LEU* 4.3 11.4 - - + -
72A LEU* 3.7 38.6 - - + -
83A PHE* 3.7 22.4 - + + -
86A VAL* 4.6 4.5 - - + -
102A ALA 2.9 17.8 + - - +
105A SER* 1.3 75.4 + - - +
107A GLY* 1.3 51.9 + - - +
109A ALA* 3.5 4.2 - - + -
110A LEU* 2.7 40.4 + - + +
113A GLU* 3.9 9.9 - - - -
1004B VAL* 4.3 0.2 - - + -
1008B LEU* 4.0 37.5 - - + -
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Residues in contact with GLY 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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83A PHE* 3.7 9.3 - - - -
103A PHE 3.0 13.9 + - - -
106A PHE* 1.3 76.2 - - - +
108A GLY* 1.3 63.5 + - - +
110A LEU* 3.1 10.3 + - - +
111A CYS* 3.1 19.4 + - - +
126A ILE* 3.6 3.0 - - - +
130A MET* 3.4 35.3 - - - +
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Residues in contact with GLY 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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12A PHE* 3.8 1.3 - - - -
13A LEU* 3.5 22.2 - - - -
16A LYS* 3.2 30.5 - - - +
104A PHE 3.0 15.2 + - - -
105A SER 3.0 4.0 + - - -
107A GLY* 1.3 76.1 - - - +
109A ALA* 1.3 57.0 + - - +
111A CYS* 3.0 20.6 - - - +
112A VAL* 3.5 1.9 + - - +
130A MET* 3.8 0.6 - - - +
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Residues in contact with ALA 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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16A LYS* 4.1 5.5 - - + +
58A GLU* 5.6 0.4 - - - +
61A TYR* 3.5 24.2 - - + +
65A PHE* 3.3 29.9 - - + -
105A SER 2.9 5.4 + - - +
106A PHE* 3.5 10.3 - - + +
108A GLY* 1.3 75.3 - - - +
110A LEU* 1.3 53.7 + - - +
111A CYS 3.1 1.3 - - - -
112A VAL* 3.0 8.6 + - - +
113A GLU* 2.7 39.1 + - - +
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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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72A LEU* 4.0 3.6 - - + -
74A ILE* 3.9 22.7 - - + -
79A ALA* 3.9 24.2 - - + +
80A TYR* 5.6 0.7 - - - -
83A PHE* 3.7 37.5 - - + -
106A PHE* 2.7 23.8 + - + +
107A GLY* 3.1 14.8 + - - +
109A ALA* 1.3 70.0 - - - +
111A CYS* 1.3 70.3 + - - +
113A GLU* 3.1 19.9 + - - +
114A SER* 3.0 23.2 + - - +
126A ILE* 3.4 23.1 - - + -
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Residues in contact with CYS 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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13A LEU* 3.3 25.6 - - + -
17A LEU* 3.3 31.6 - - - -
107A GLY 3.1 2.6 + - - -
108A GLY 3.0 15.3 - - - +
110A LEU* 1.3 76.3 - - - +
112A VAL* 1.3 56.0 + - - +
114A SER* 2.9 20.4 + - - -
115A VAL* 2.8 14.6 - - - +
123A VAL* 3.2 37.0 - - - +
126A ILE* 3.4 12.0 - - - +
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Residues in contact with VAL 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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16A LYS* 3.5 34.3 - - + +
17A LEU* 3.5 20.0 - - + -
19A GLN* 5.9 0.4 - - - +
20A LYS* 3.4 36.1 - - + -
65A PHE* 5.0 9.4 - - + -
108A GLY 3.8 2.5 - - - +
109A ALA* 3.0 9.6 + - - +
111A CYS* 1.3 69.3 - - - +
113A GLU* 1.3 52.1 + - - +
114A SER 2.9 5.4 - - - -
115A VAL* 2.9 15.9 + - + -
116A ASP* 2.6 38.9 + - + +
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Residues in contact with GLU 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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65A PHE* 3.4 27.7 - - + +
69A THR* 3.2 28.3 + - + +
72A LEU* 3.2 24.9 - - - +
74A ILE* 3.1 36.6 - - + +
106A PHE* 3.9 6.9 - - - -
109A ALA 2.7 16.4 + - - +
110A LEU* 3.1 38.6 + - - +
111A CYS 3.2 0.2 - - - -
112A VAL* 1.3 72.8 - - - +
114A SER* 1.3 59.7 + - - +
116A ASP* 3.3 17.7 - - - +
117A LYS* 3.3 11.8 - - - +
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Residues in contact with SER 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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74A ILE* 3.8 8.7 - - - +
75A THR 4.6 0.7 + - - -
79A ALA* 5.0 0.5 - - - +
110A LEU* 3.0 14.1 + - - +
111A CYS 2.9 12.2 + - - -
113A GLU* 1.3 73.8 - - - +
115A VAL* 1.3 58.3 + - - +
116A ASP 3.1 1.6 - - - -
117A LYS 3.2 7.4 + - - -
119A MET* 2.7 49.7 + - - +
122A LEU* 3.2 40.6 - - - +
123A VAL 4.8 0.7 - - - -
126A ILE* 3.6 2.9 - - - +
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Residues in contact with VAL 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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17A LEU* 3.6 9.6 - - + -
20A LYS* 5.2 0.2 - - + -
22A TYR* 3.8 41.2 + - + -
111A CYS 2.8 20.4 - - - +
112A VAL* 3.2 25.4 - - + +
114A SER* 1.3 72.4 - - - +
116A ASP* 1.3 61.5 + - - +
118A GLU* 2.8 22.7 + - - +
120A GLN* 3.3 29.1 + - + +
123A VAL* 3.4 21.8 - - + -
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Residues in contact with ASP 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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22A TYR* 5.4 1.4 + - - -
69A THR* 4.8 7.3 + - - +
112A VAL* 2.6 21.1 + - + +
113A GLU* 3.3 14.8 - - - +
115A VAL* 1.3 80.3 - - - +
117A LYS* 1.3 79.2 + - - +
118A GLU* 3.2 9.5 + - - +
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Residues in contact with LYS 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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69A THR* 3.8 30.0 + - - -
73A HIS* 4.9 0.6 - - - +
74A ILE* 3.0 29.5 + - - +
113A GLU 3.3 12.1 - - - +
114A SER 3.2 1.2 + - - -
116A ASP* 1.3 93.3 - - - +
118A GLU* 1.3 72.0 + - - +
119A MET* 3.3 37.6 - - + +
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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
------------------------------------------------------------
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