Contacts of the helix formed by residues 116 - 138 (chain F) in PDB entry 2B05
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 GLN 116 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F PRO* 4.8 18.8 - - - +
111F ASN 3.8 4.7 - - - +
112F CYS* 3.5 9.1 - - + -
113F SER* 2.7 51.1 + - - +
114F GLU 4.8 0.4 - - - -
115F THR* 1.3 77.2 - - - +
117F TYR* 1.3 62.5 + - - +
118F GLU* 3.4 2.9 - - - -
119F SER* 3.4 18.6 + - - +
120F LYS* 3.1 24.5 + - - +
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Residues in contact with TYR 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F GLU* 2.9 26.3 + - - +
115F THR* 3.0 38.6 + - + +
116F GLN* 1.3 72.9 - - - +
118F GLU* 1.3 65.8 + - - +
120F LYS* 3.3 10.0 + - + +
121F VAL* 3.0 31.0 + - - +
160F ILE* 4.0 12.1 - - + -
164F HIS* 3.4 66.0 + + + +
165F MET* 5.1 6.7 - - + -
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Residues in contact with GLU 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F ASN* 4.0 12.7 + - - +
42F ARG* 3.6 19.8 + - - +
116F GLN 3.4 0.8 - - - -
117F TYR* 1.3 78.6 - - - +
119F SER* 1.3 57.9 + - - +
121F VAL* 3.6 2.1 + - - +
122F PHE* 3.1 29.7 + - - +
165F MET* 4.1 12.9 - - + +
169F HIS* 3.5 28.0 + - + +
171F ILE* 3.7 25.5 - - + +
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Residues in contact with SER 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F LEU 5.2 1.6 + - - -
42F ARG* 3.1 26.5 + - - +
112F CYS* 3.7 16.4 - - - -
116F GLN* 3.4 22.9 + - - +
117F TYR 3.2 0.2 - - - -
118F GLU* 1.3 76.9 - - - +
120F LYS* 1.3 59.3 + - - +
122F PHE* 3.3 4.4 + - - +
123F TYR* 2.9 46.7 + - - -
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Residues in contact with LYS 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109F ILE* 5.3 13.7 - - + +
112F CYS* 3.8 32.6 + - + -
113F SER 4.3 10.7 + - - +
114F GLU* 3.6 37.9 + - - +
116F GLN 3.1 8.1 + - - +
117F TYR* 3.3 11.4 + - + +
119F SER* 1.3 79.6 - - - +
121F VAL* 1.3 57.8 + - - +
123F TYR* 3.8 2.8 - - - +
124F LEU* 2.9 41.7 + - + +
156F GLU* 5.4 5.4 - - - -
160F ILE* 4.5 26.0 - - + +
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Residues in contact with VAL 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F TYR 3.0 17.9 + - - +
118F GLU 3.9 2.9 - - - +
120F LYS* 1.3 74.3 - - - +
122F PHE* 1.3 54.4 + - - +
124F LEU* 3.7 0.9 - - - +
125F LYS* 2.8 37.0 + - + +
157F ALA* 3.8 32.3 - - + +
160F ILE* 3.8 21.1 - - + -
161F SER* 3.9 9.9 - - - +
165F MET* 3.8 19.3 - - - -
171F ILE* 3.8 20.0 - - + +
175F LEU* 4.0 17.5 - - + -
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Residues in contact with PHE 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F ARG* 3.7 42.6 - - + +
43F ASN* 3.7 23.8 - - - -
46F SER* 3.9 19.1 - - - -
118F GLU 3.1 18.6 + - - +
119F SER 3.5 4.5 - - - +
121F VAL* 1.3 77.2 - - - +
123F TYR* 1.3 67.8 + + - +
125F LYS* 3.3 12.2 + - + +
126F MET* 3.0 49.1 + - + +
171F ILE* 3.9 34.2 - - + +
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Residues in contact with TYR 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F LEU* 3.5 16.7 + - + +
42F ARG* 3.3 36.5 + - + +
45F LEU* 5.0 3.1 - - + -
104F LEU* 3.7 21.9 - - + +
108F LEU* 3.4 60.9 - - + +
109F ILE* 3.6 19.9 - - + +
112F CYS* 3.8 13.9 - - - -
119F SER* 2.9 31.2 + - - +
120F LYS* 4.0 1.3 - - - +
122F PHE* 1.3 85.3 - + - +
124F LEU* 1.3 59.8 + - - +
126F MET* 3.3 6.9 + - - +
127F LYS* 2.9 26.7 + - - +
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Residues in contact with LEU 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109F ILE* 4.1 26.9 - - + -
120F LYS* 2.9 26.4 + - + +
123F TYR* 1.3 72.7 - - - +
125F LYS* 1.3 60.4 + - - +
127F LYS* 3.3 14.2 + - + +
128F GLY* 2.9 23.7 + - - -
153F ALA* 3.5 24.1 - - - +
156F GLU* 3.6 37.2 - - + +
157F ALA* 3.6 30.3 - - + +
160F ILE* 3.9 14.4 - - + -
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Residues in contact with LYS 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121F VAL* 2.8 19.8 + - + +
122F PHE* 3.4 13.4 + - + +
124F LEU* 1.3 74.0 - - - +
126F MET* 1.3 66.4 + - - +
128F GLY* 3.2 2.6 + - - +
129F ASP* 2.8 55.8 + - - +
154F TYR* 3.8 8.5 - - + -
157F ALA* 4.2 1.0 - - - +
171F ILE* 4.6 7.2 - - + +
174F GLY* 3.6 15.3 - - - -
175F LEU* 3.7 44.9 - - + +
178F ASN* 3.4 19.9 - - + +
506L LEU* 3.8 24.1 - - - +
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Residues in contact with MET 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F LEU* 4.7 17.9 - - + +
46F SER* 4.3 26.5 - - - +
49F TYR* 5.2 0.7 - - + -
100F VAL* 3.7 28.5 - - + -
104F LEU* 3.9 18.2 - - + -
122F PHE* 3.0 43.3 + - + +
123F TYR* 3.3 11.9 + - - +
125F LYS* 1.3 78.6 - - - +
127F LYS* 1.3 63.2 + - - +
129F ASP* 3.0 11.6 + - - +
130F TYR* 2.8 46.9 + - + +
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Residues in contact with LYS 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F LEU* 3.8 15.6 - - + +
104F LEU* 3.6 12.5 - - + +
105F ASP* 2.8 36.9 + - - +
109F ILE* 3.9 15.2 - - + +
123F TYR 2.9 13.8 + - - +
124F LEU* 3.4 16.7 - - + +
125F LYS 3.2 0.4 - - - -
126F MET* 1.3 75.1 - - - +
128F GLY* 1.3 61.2 + - - +
130F TYR 3.5 0.2 + - - -
131F TYR* 3.2 50.3 + - + -
149F SER 5.3 1.8 - - - -
153F ALA* 3.9 16.4 - - + -
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Residues in contact with GLY 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124F LEU 2.9 14.6 + - - -
125F LYS 3.2 3.6 + - - -
127F LYS* 1.3 76.6 - - - +
129F ASP* 1.3 56.1 + - - +
131F TYR 3.5 0.2 + - - -
132F ARG* 2.9 17.3 + - - +
150F SER* 2.8 25.2 + - - -
153F ALA* 3.6 13.1 - - - +
154F TYR* 3.4 22.7 - - - -
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Residues in contact with ASP 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125F LYS* 2.8 44.3 + - - +
126F MET* 3.0 11.3 + - - +
128F GLY* 1.3 76.6 - - - +
130F TYR* 1.3 61.5 + - + +
132F ARG* 2.9 11.5 + - - +
133F TYR* 2.9 51.8 + - + +
154F TYR* 2.5 28.8 + - - -
178F ASN* 2.8 22.7 + - - +
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Residues in contact with TYR 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F SER 4.2 2.9 + - - -
49F TYR* 3.1 12.0 - - + +
50F LYS* 3.1 33.0 + - - +
53F VAL* 3.9 23.3 - - + -
96F VAL* 5.2 0.4 - - + -
97F CYS* 3.8 18.7 - - + -
100F VAL* 3.8 31.6 - - + -
101F LEU* 4.0 23.6 - - + -
126F MET* 2.8 58.2 + - + +
129F ASP* 1.3 75.1 - - + +
131F TYR* 1.3 62.2 + - - +
133F TYR* 3.4 22.1 + + - +
134F LEU* 3.1 30.7 + - - +
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Residues in contact with TYR 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F LEU* 3.6 33.1 - - + +
105F ASP* 4.8 7.6 + - - -
127F LYS* 3.2 45.4 + - + +
130F TYR* 1.3 73.7 - - - +
132F ARG* 1.3 60.3 + - - +
134F LEU* 3.1 23.2 + - + +
135F ALA* 2.8 27.9 + - - +
146F VAL* 3.5 29.6 - - + +
149F SER* 3.6 38.3 + - - -
150F SER* 3.6 13.5 - - - -
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Residues in contact with ARG 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F ARG* 4.1 2.2 - - - +
128F GLY 2.9 19.0 + - - +
129F ASP* 2.9 28.9 + - - +
131F TYR* 1.3 75.9 - - - +
133F TYR* 1.3 66.1 + - - +
135F ALA* 3.0 9.8 + - - +
136F GLU* 3.0 34.2 + - - +
150F SER* 3.7 10.4 + - - +
154F TYR* 2.9 16.4 + - - -
178F ASN* 3.5 18.5 + - - +
181F VAL* 4.1 13.9 - - - +
182F PHE* 3.9 30.7 - - + +
185F GLU* 6.2 0.2 - - - -
186F ILE* 3.8 19.5 - - + +
505L SEP 2.7 45.8 + - - -
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Residues in contact with TYR 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F LYS* 5.3 8.3 - - + +
53F VAL* 4.1 21.5 - - + -
57F ARG* 3.2 49.0 + - - -
93F LEU* 4.0 15.4 - - + +
97F CYS* 4.0 10.1 - - - -
129F ASP* 2.9 39.4 + - + +
130F TYR* 3.7 35.9 - + - +
131F TYR 3.2 0.2 - - - -
132F ARG* 1.3 83.2 + - - +
134F LEU* 1.3 66.2 + - - +
136F GLU* 3.3 25.2 + - - +
137F VAL* 3.8 3.6 + - - +
505L SEP 2.5 28.1 + - - -
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Residues in contact with LEU 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F LEU* 4.9 0.9 - - + -
94F GLU* 3.8 37.4 - - + +
97F CYS* 3.6 23.3 - - + -
98F GLN* 5.4 7.0 - - + +
101F LEU* 4.0 14.8 - - + -
130F TYR 3.1 15.9 + - - +
131F TYR* 3.1 34.4 + - + +
133F TYR* 1.3 75.9 - - - +
135F ALA* 1.3 61.2 + - - +
137F VAL* 3.4 8.8 + - - +
138F ALA* 3.2 23.9 + - - +
142F LYS* 6.2 2.2 - - - -
146F VAL* 4.0 20.4 - - + -
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Residues in contact with ALA 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131F TYR 2.8 12.9 + - - +
132F ARG* 3.0 13.9 + - - +
134F LEU* 1.3 75.7 - - - +
136F GLU* 1.3 63.6 + - - +
137F VAL 3.3 0.7 + - - -
138F ALA* 3.4 17.1 + - - +
143F ARG* 3.8 13.6 + - - +
146F VAL* 3.7 11.9 - - + -
147F VAL* 3.8 31.2 - - + +
182F PHE* 5.8 0.2 - - + -
186F ILE* 4.3 14.6 - - + -
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Residues in contact with GLU 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F ARG* 2.8 53.0 + - - +
60F TRP* 3.6 22.3 - - + -
61F ARG* 4.7 5.3 + - - -
132F ARG* 3.0 22.5 + - - +
133F TYR* 3.3 20.2 + - - +
135F ALA* 1.3 78.3 - - - +
137F VAL* 1.3 63.5 + - + +
138F ALA 4.9 1.2 - - - +
186F ILE* 4.4 16.1 - - + +
505L SEP 4.4 0.2 + - - -
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Residues in contact with VAL 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F TRP* 3.5 50.4 - - + +
90F GLU* 3.9 25.8 - - + +
93F LEU* 4.6 19.3 - - + -
94F GLU* 3.7 30.0 - - + +
133F TYR 4.3 9.6 - - - +
134F LEU 3.4 11.1 + - - +
135F ALA 3.2 0.2 - - - -
136F GLU* 1.3 81.0 - - + +
138F ALA* 1.3 64.2 + - - +
139F THR* 4.1 5.8 + - - +
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Residues in contact with ALA 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F GLU* 5.5 1.1 - - - +
134F LEU 3.2 18.8 + - - +
135F ALA* 3.4 7.4 + - - +
136F GLU 4.9 1.2 - - - +
137F VAL* 1.3 81.3 - - + +
139F THR* 1.3 67.1 + - - +
142F LYS* 4.2 21.8 - - + +
143F ARG* 3.5 43.6 + - + +
146F VAL* 4.3 2.7 - - + -
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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
------------------------------------------------------------
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