Contacts of the helix formed by residues 115 - 136 (chain C) in PDB entry 5AQM
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 TYR 115 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C ASP* 4.0 20.7 + - + -
100C ARG* 3.5 47.7 + - + -
101C PRO 3.9 7.4 - - - -
102C LYS* 3.7 37.1 + - + -
114C PHE* 1.3 74.6 - - - +
116C PRO* 1.4 71.4 - - - +
117C GLU* 3.5 21.3 - - - +
118C GLU* 2.9 44.3 + - + +
119C VAL* 3.2 10.3 + - - +
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Residues in contact with PRO 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ALA* 3.9 12.5 - - + +
73C LEU* 3.7 34.3 - - + +
74C ILE* 3.7 26.5 - - - +
75C GLY 5.2 0.7 - - - +
100C ARG* 4.8 2.2 - - - +
101C PRO* 3.3 26.7 - - + +
102C LYS* 4.9 0.7 - - - -
103C VAL* 5.9 2.9 - - + -
114C PHE 3.8 1.1 - - - +
115C TYR* 1.4 86.9 - - + +
117C GLU* 1.4 62.3 + - - +
119C VAL* 3.1 11.9 + - + +
120C SER* 2.9 31.7 + - - -
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Residues in contact with GLU 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ILE* 4.0 12.4 - - + +
75C GLY 5.2 1.7 + - - -
100C ARG* 2.7 36.4 + - - -
115C TYR* 3.5 16.1 - - + +
116C PRO* 1.4 77.0 - - - +
118C GLU* 1.4 62.2 + - + +
120C SER* 4.4 0.2 - - - -
121C SER* 2.8 29.5 + - - -
157C ALA* 3.3 38.5 - - - +
160C ASP* 4.5 11.0 - - + +
161C ALA* 3.4 10.9 - - - +
164C ILE* 4.2 16.4 - - + -
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Residues in contact with GLU 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C LYS* 4.6 1.4 + - - -
113C SER 4.4 1.9 - - - +
114C PHE* 3.5 25.8 - - + -
115C TYR* 2.9 51.2 + - + +
117C GLU* 1.4 75.2 - - + +
119C VAL* 1.3 65.4 + - - +
121C SER* 2.6 25.4 + - - +
122C MET* 3.2 18.4 + - + +
164C ILE* 4.5 16.8 - - + -
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Residues in contact with VAL 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C SER 5.8 2.2 - - - +
42C VAL* 4.0 18.8 - - + -
44C PHE* 5.7 3.1 - - + -
67C VAL* 4.0 21.3 - - + +
68C PHE* 6.0 0.2 - - - -
70C ALA* 3.8 19.7 - - + -
103C VAL* 3.8 30.5 - - + -
114C PHE* 4.0 9.9 - - + -
115C TYR 3.8 9.9 - - - +
116C PRO* 3.1 10.4 + - + +
118C GLU* 1.3 75.4 - - - +
120C SER* 1.3 61.7 + - - +
122C MET* 3.0 25.2 + - - +
123C VAL* 3.2 14.7 + - + +
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Residues in contact with SER 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 4.2 17.7 - - - +
70C ALA* 3.8 16.7 - - - +
71C LYS* 4.6 3.3 + - - +
74C ILE* 3.9 16.4 - - - +
116C PRO 2.9 17.1 + - - -
119C VAL* 1.3 75.5 - - - +
121C SER* 1.4 58.0 + - - +
123C VAL* 3.2 10.8 + - - +
124C LEU* 2.8 31.7 + - - +
161C ALA* 3.8 19.1 - - - -
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Residues in contact with SER 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C GLU 2.8 17.5 + - - -
118C GLU* 2.6 19.2 + - - -
120C SER* 1.4 75.7 - - - +
122C MET* 1.3 59.0 + - - +
124C LEU* 3.4 2.0 + - - -
125C THR* 2.8 33.4 + - - -
161C ALA* 3.2 27.3 - - - +
164C ILE* 3.4 29.2 - - - +
165C ALA* 3.5 5.4 - - - +
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Residues in contact with MET 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C VAL* 3.7 33.2 - - + -
44C PHE* 4.2 4.9 - - + -
49C ARG* 3.6 41.1 - - - +
51C ILE* 3.8 15.5 - - + +
114C PHE* 3.9 34.8 - - + -
118C GLU* 3.2 20.6 + - + +
119C VAL* 3.0 13.1 + - - +
121C SER* 1.3 80.5 + - - +
123C VAL* 1.4 64.6 + - - +
125C THR* 3.4 8.5 + - - +
126C LYS* 3.1 21.5 + - - +
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Residues in contact with VAL 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 3.8 13.0 - - + -
16C SER* 3.6 30.1 - - - +
38C THR* 5.8 0.9 - - + -
39C PRO 4.9 3.1 - - - +
40C SER* 4.0 32.1 - - - +
41C TYR 4.3 2.5 - - - +
42C VAL* 4.0 17.5 - - + -
51C ILE* 4.2 8.3 - - + -
119C VAL* 3.2 15.6 + - + +
120C SER* 3.2 10.5 + - - +
122C MET* 1.4 76.2 - - - +
124C LEU* 1.3 56.2 + - - +
126C LYS* 3.1 6.0 + - + +
127C MET* 3.0 29.2 + - + +
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Residues in contact with LEU 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ILE* 3.8 37.0 - - + -
11C LEU* 4.0 27.6 - - + -
120C SER 2.8 14.7 + - - +
121C SER 3.7 4.7 - - - +
123C VAL* 1.3 76.4 - - - +
125C THR* 1.3 56.3 + - - +
127C MET* 3.2 4.4 + - + +
128C LYS* 2.9 29.6 + - - +
144C VAL* 4.6 11.2 - - + -
158C THR 4.5 2.5 - - - +
161C ALA* 3.7 16.2 - - + -
162C GLY* 3.5 34.5 - - - +
165C ALA* 3.8 10.8 - - + -
167C LEU* 4.2 11.3 - - + +
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Residues in contact with THR 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ARG* 5.6 7.6 - - - +
121C SER 2.8 23.8 + - - -
122C MET* 3.6 9.3 - - - +
123C VAL 3.3 0.2 - - - -
124C LEU* 1.3 74.8 - - - +
126C LYS* 1.3 58.9 + - - +
128C LYS* 3.3 10.4 + - + +
129C GLU* 2.9 56.3 + - + +
165C ALA* 3.5 23.5 + - - +
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Residues in contact with LYS 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ASN* 5.1 1.3 - - - +
32C ASP* 2.8 33.4 + - - +
38C THR* 4.2 15.3 - - + -
51C ILE* 3.7 44.8 + - + -
52C GLY* 5.4 0.4 - - - -
53C ASP 5.9 0.9 - - - +
122C MET 3.1 4.8 + - - +
123C VAL* 3.1 10.6 + - + +
125C THR* 1.3 77.2 - - - +
127C MET* 1.4 57.0 + - - +
129C GLU* 3.2 20.7 + - + +
130C ILE* 2.8 56.8 + - + +
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Residues in contact with MET 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ILE* 4.1 28.0 - - + -
16C SER* 3.7 24.7 - - - +
17C CYS* 3.7 24.5 - - - +
18C VAL* 3.7 36.1 - - + +
29C ILE 6.0 0.4 - - - +
36C ARG 5.9 0.2 - - - +
37C THR* 5.7 0.4 - - - -
38C THR* 3.8 26.5 - - - +
123C VAL* 3.0 23.2 + - + +
124C LEU* 3.2 7.4 + - + +
126C LYS* 1.4 76.0 - - - +
128C LYS* 1.3 62.0 + - - +
130C ILE* 3.3 17.2 + - + +
131C ALA* 3.0 23.0 + - - +
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Residues in contact with LYS 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C VAL* 6.0 0.4 - - - -
9C ILE* 4.9 3.5 - - - +
124C LEU 2.9 13.9 + - - +
125C THR* 3.4 13.2 - - + +
127C MET* 1.3 75.5 - - - +
129C GLU* 1.4 58.1 + - + +
131C ALA* 3.2 8.8 + - - +
132C GLU* 2.9 54.9 + - - +
138C THR* 4.7 5.3 - - - +
139C VAL* 2.8 36.9 + - + +
140C THR* 4.7 2.5 + - - +
165C ALA 3.7 19.5 - - - +
166C GLY* 3.9 21.8 - - - -
167C LEU* 3.8 22.0 - - + -
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Residues in contact with GLU 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C THR* 2.9 39.2 + - + +
126C LYS* 3.5 23.0 + - + +
128C LYS* 1.4 73.8 - - + +
130C ILE* 1.3 59.4 + - - +
132C GLU* 3.3 16.0 + - - +
133C ALA* 2.9 31.8 + - - +
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Residues in contact with ILE 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C VAL* 3.7 13.2 - - + -
29C ILE* 3.7 23.7 - - + +
30C ALA 3.8 13.4 - - - +
31C ASN* 3.6 20.6 - - + +
32C ASP* 4.8 2.0 - - - +
38C THR* 3.3 26.2 - - - +
126C LYS* 2.8 49.1 + - + +
127C MET* 3.5 18.8 - - + +
128C LYS 3.3 0.2 - - - -
129C GLU* 1.3 71.6 - - - +
131C ALA* 1.4 64.5 + - - +
133C ALA* 3.4 6.5 + - - +
134C TYR* 3.2 22.0 + - - +
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Residues in contact with ALA 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C VAL* 4.0 15.5 - - + -
18C VAL* 4.2 5.8 - - + +
29C ILE* 3.7 25.4 - - + -
127C MET 3.0 13.3 + - - +
128C LYS* 3.2 8.5 + - - +
130C ILE* 1.4 77.0 - - - +
132C GLU* 1.4 57.9 + - - +
134C TYR* 3.3 2.8 + - - +
135C LEU* 2.9 33.9 + - + +
139C VAL* 3.9 20.2 - - + -
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Residues in contact with GLU 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET* 4.4 17.4 - - + +
128C LYS* 2.9 48.2 + - - +
129C GLU* 3.7 16.9 - - - +
131C ALA* 1.4 75.4 - - - +
133C ALA* 1.4 57.1 + - - +
136C GLY* 2.8 30.8 + - - -
137C LYS 3.4 22.5 + - - +
138C THR* 3.5 11.5 - - - +
139C VAL* 2.9 29.0 + - + +
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Residues in contact with ALA 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ASP* 6.6 0.2 - - + -
129C GLU 2.9 17.9 + - - +
130C ILE* 3.8 7.0 - - - +
132C GLU* 1.4 75.4 - - - +
134C TYR* 1.3 63.0 + - - +
136C GLY* 4.1 4.2 + - - -
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Residues in contact with TYR 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C VAL* 4.3 3.8 - - + -
22C GLN* 4.0 13.6 + - - -
27C GLU* 3.3 41.6 - - + +
29C ILE* 3.3 39.9 - - + -
30C ALA 5.2 2.7 - - - +
130C ILE 3.2 7.0 + - - +
131C ALA 3.7 1.6 - - - +
132C GLU 3.3 0.2 - - - -
133C ALA* 1.3 79.3 - - - +
135C LEU* 1.3 86.9 + - + +
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Residues in contact with LEU 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C PRO* 3.8 25.6 - - + -
7C VAL* 4.6 2.2 - - + -
20C VAL* 4.1 14.4 - - + -
22C GLN* 3.6 35.7 - - - +
29C ILE* 5.0 0.4 - - + -
131C ALA* 2.9 24.7 + - + +
132C GLU 4.4 0.2 - - - +
134C TYR* 1.3 92.3 - - + +
136C GLY* 1.3 61.4 + - - +
137C LYS* 3.4 28.2 + - + +
139C VAL* 3.7 23.6 - - + -
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Residues in contact with GLY 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET* 3.4 26.2 - - - +
2C SER* 4.7 1.0 + - - -
132C GLU 2.8 13.0 + - - -
133C ALA* 4.1 4.2 + - - -
134C TYR 3.4 2.6 - - - -
135C LEU* 1.3 77.2 - - - +
137C LYS* 1.3 62.4 + - - +
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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