Contacts of the helix formed by residues 110 - 132 (chain F) in PDB entry 2JG7
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 ILE 110 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505E GLN* 5.9 1.3 - - - +
104F SER* 4.3 0.2 - - - -
109F LYS* 1.3 75.6 - - - +
111F TYR* 1.3 66.6 + - - +
112F VAL* 3.7 22.9 - - + +
113F GLU* 2.9 38.4 + - + +
114F GLY* 3.0 9.7 + - - -
296F THR* 6.0 0.6 - - - +
333F PRO* 3.9 11.9 - - + +
335F ASP 5.9 0.4 - - - +
338F THR* 3.6 37.2 - - + +
339F LEU* 3.8 35.0 - - + +
340F TYR 4.0 3.4 - - - +
341F GLY* 4.5 8.3 - - - +
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Residues in contact with TYR 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F LYS* 3.7 39.3 - - - +
101F SER* 3.3 35.9 - - - -
104F SER* 3.7 11.4 + - - +
109F LYS 3.7 0.6 + - - -
110F ILE* 1.3 71.3 - - - +
112F VAL* 1.3 65.4 + - + +
114F GLY* 2.9 17.8 + - - -
115F VAL* 2.9 31.8 + - + +
333F PRO 3.2 17.2 + - - +
334F TRP* 4.8 16.8 - + - +
335F ASP 6.1 0.9 - - - +
336F PRO* 6.3 1.8 - - + -
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Residues in contact with VAL 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110F ILE* 3.7 24.0 - - + +
111F TYR* 1.3 88.3 - - + +
113F GLU* 1.3 62.5 + - + +
115F VAL* 3.5 9.5 + - + +
116F GLY* 2.9 22.7 + - - -
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Residues in contact with GLU 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109F LYS* 4.1 19.7 - - + +
110F ILE* 2.9 29.2 + - + +
112F VAL* 1.3 80.1 - - + +
114F GLY* 1.3 60.6 + - - +
116F GLY* 3.6 2.9 - - - +
117F GLU* 3.0 28.1 + - - +
167F PHE* 6.0 0.2 - - - -
295F GLY* 4.5 1.6 - - - -
296F THR* 3.0 37.2 + - - +
300F ARG* 3.2 26.8 + - - -
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Residues in contact with GLY 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F GLY* 3.5 22.9 - - - -
103F VAL* 4.2 18.4 - - - +
104F SER 4.8 0.7 - - - -
109F LYS* 4.1 4.0 - - - +
110F ILE 3.0 8.9 + - - -
111F TYR 2.9 7.6 + - - -
113F GLU* 1.3 75.5 - - - +
115F VAL* 1.3 63.1 + - - +
117F GLU* 3.4 5.3 + - - +
118F VAL* 3.4 24.9 + - - +
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Residues in contact with VAL 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F ILE* 3.9 34.3 - - + +
97F LYS* 4.6 2.9 - - + -
100F GLY* 4.2 4.9 - - - -
111F TYR* 2.9 49.9 + - + +
112F VAL* 3.6 12.1 - - + +
114F GLY* 1.3 74.1 - - - +
116F GLY* 1.3 65.0 + - - +
118F VAL* 3.1 7.6 + - - +
119F GLN* 3.0 21.2 + - + +
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Residues in contact with GLY 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F VAL 2.9 16.0 + - - -
113F GLU* 3.4 4.2 + - - -
114F GLY 3.3 0.4 - - - -
115F VAL* 1.3 77.5 - - - +
117F GLU* 1.3 60.1 + - - +
119F GLN* 3.3 11.1 + - - +
120F GLU* 3.1 26.1 + - - +
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Residues in contact with GLU 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F VAL* 3.8 5.0 - - + +
109F LYS* 2.8 35.2 + - - +
113F GLU 3.0 15.5 + - - +
114F GLY* 3.6 7.6 - - - +
115F VAL 3.2 0.4 - - - -
116F GLY* 1.3 74.3 - - - +
118F VAL* 1.3 66.3 + - - +
120F GLU* 3.2 24.4 + - - +
121F TYR* 3.5 4.0 + - - +
167F PHE* 2.8 31.6 - - + -
168F PRO* 3.7 5.8 - - - +
169F VAL* 2.6 36.4 + - + -
170F ALA* 2.9 24.1 + - + +
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Residues in contact with VAL 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F LEU* 4.3 14.1 - - + +
96F ILE* 3.7 30.5 - - + +
99F LEU* 3.8 38.4 - - + +
100F GLY* 3.9 12.1 - - - +
103F VAL* 4.9 0.4 - - + -
114F GLY 3.4 14.8 + - - +
115F VAL 3.1 8.1 + - - +
117F GLU* 1.3 75.2 - - - +
119F GLN* 1.3 62.6 + - - +
121F TYR* 3.0 15.1 + - - +
122F VAL* 3.0 16.9 + - + +
169F VAL* 4.4 14.6 - - + -
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Residues in contact with GLN 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F ARG* 4.5 8.7 - - - +
96F ILE* 3.5 20.8 - - + +
115F VAL* 3.0 13.2 + - + +
116F GLY* 3.3 14.1 - - - +
117F GLU 3.2 0.2 - - - -
118F VAL* 1.3 77.7 - - - +
120F GLU* 1.3 51.1 + - - +
122F VAL* 3.2 20.6 + - - +
123F ASP* 2.7 71.9 + - - +
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Residues in contact with GLU 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F GLY 3.1 16.4 + - - +
117F GLU* 3.2 15.5 + - - +
119F GLN* 1.3 74.1 - - - +
121F TYR* 1.3 58.6 + - - +
123F ASP* 4.6 0.8 - - - +
124F VAL* 3.0 31.8 + - - +
167F PHE* 5.6 5.6 - - + -
170F ALA* 4.0 15.0 - - + +
174F TRP* 3.8 31.2 + - - +
461F ALA 5.2 7.2 - - - +
462F GLU* 5.8 0.7 - - - -
463F ILE* 3.7 26.1 + - - +
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Residues in contact with TYR 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F ILE* 3.9 3.6 - - + +
92F LEU* 3.5 26.0 - - + -
117F GLU 3.5 5.0 + - - +
118F VAL 3.0 11.7 + - - +
120F GLU* 1.3 77.3 - - - +
122F VAL* 1.3 65.7 + - - +
124F VAL* 3.3 5.9 - - + +
125F CYS* 3.0 40.2 + - - -
169F VAL* 3.8 24.0 - - + +
170F ALA* 5.1 2.4 - - - +
172F TYR* 3.8 8.8 - + - -
173F GLY* 3.5 40.6 - - - -
174F TRP 5.5 0.2 - - - +
176F ASN* 2.6 35.0 + - + +
177F ALA* 4.8 0.7 - - + -
201F VAL* 4.1 21.5 - - + -
205F VAL* 3.9 9.1 - - + +
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Residues in contact with VAL 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F GLY* 3.8 22.2 - - - +
92F LEU* 3.9 15.7 - - + +
93F ARG* 3.4 51.4 - - + +
96F ILE* 5.1 2.7 - - + -
118F VAL* 3.0 21.4 + - + +
119F GLN* 3.2 21.1 + - - +
121F TYR* 1.3 74.8 - - - +
123F ASP* 1.3 62.7 + - - +
125F CYS* 3.2 20.7 + - - +
126F ASP* 3.3 10.8 + - - +
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Residues in contact with ASP 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F ARG* 5.3 1.2 + - - -
119F GLN* 2.7 53.7 + - - +
120F GLU* 4.7 0.3 - - - +
122F VAL* 1.3 74.8 - - - +
124F VAL* 1.3 58.6 + - - +
126F ASP* 3.4 12.5 + - - +
127F TYR* 3.1 24.8 + - - +
463F ILE* 3.3 26.2 - - + +
83G GLU* 5.6 2.4 - - - +
133G ARG* 4.3 20.4 + - - +
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Residues in contact with VAL 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120F GLU 3.0 16.5 + - - +
121F TYR* 3.3 21.3 + - + +
123F ASP* 1.3 73.4 - - - +
125F CYS* 1.3 60.0 + - - +
127F TYR* 3.5 10.4 - - + +
128F ALA* 2.9 28.2 + - - +
173F GLY 3.8 16.2 - - - +
174F TRP* 3.7 22.4 - - + +
177F ALA* 3.8 18.7 - - + +
178F ILE* 4.8 4.3 - - + -
463F ILE* 4.0 9.4 - - + +
479F SER* 3.6 29.6 - - - +
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Residues in contact with CYS 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F VAL* 3.6 38.9 - - - +
86F ARG* 5.1 0.4 - - - +
88F ILE* 4.3 4.0 - - - -
89F GLY* 3.9 20.2 - - - -
121F TYR* 3.0 45.6 + - - -
122F VAL 3.2 10.3 + - - +
124F VAL* 1.3 76.9 - - - +
126F ASP* 1.3 60.1 + - - +
128F ALA* 3.1 5.5 + - - +
129F VAL* 3.0 31.4 + - - +
177F ALA* 4.2 4.5 - - - -
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Residues in contact with ASP 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F ARG* 4.6 17.7 - - - +
89F GLY* 5.5 0.9 - - - -
93F ARG* 3.2 28.4 + - - -
122F VAL* 3.3 11.8 + - - +
123F ASP* 3.8 12.9 - - - +
124F VAL 3.4 0.2 - - - -
125F CYS* 1.3 78.7 - - - +
127F TYR* 1.3 61.9 + - - +
129F VAL* 3.2 17.1 + - - +
130F GLY 3.4 8.7 + - - -
86G ARG* 3.4 21.6 - - - +
126G ASP 4.5 1.2 - - - +
129G VAL* 3.8 21.9 - - + +
130G GLY 4.3 7.8 + - - -
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Residues in contact with TYR 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F ASP 3.1 15.0 + - - +
124F VAL* 3.5 11.9 - - + +
126F ASP* 1.3 76.1 - - - +
128F ALA* 1.3 61.8 + - - +
130F GLY* 3.1 12.1 + - - -
131F LEU* 3.1 40.0 + - + +
178F ILE* 4.6 5.2 - - + -
463F ILE* 3.8 18.4 - - + -
464F GLY* 3.8 6.3 + - - -
479F SER* 3.8 18.2 - - - -
480F GLY* 3.7 8.0 - - - -
481F SER* 3.5 27.7 + - - -
129G VAL* 5.0 1.9 - - - +
130G GLY* 4.2 12.7 - - - -
133G ARG* 3.8 39.7 - - + +
134G MET* 3.9 27.6 - - + +
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Residues in contact with ALA 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F GLY* 5.4 0.4 - - - -
85F VAL* 3.9 8.5 - - + -
124F VAL 2.9 14.5 + - - +
125F CYS 3.4 9.0 - - - +
127F TYR* 1.3 74.1 - - - +
129F VAL* 1.3 59.9 + - - +
131F LEU* 3.1 12.7 + - - +
132F SER* 2.9 25.8 + - - -
177F ALA* 3.7 15.7 - - + +
178F ILE* 4.4 6.1 - - + -
181F THR* 3.2 29.7 - - - +
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Residues in contact with VAL 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F GLY 3.6 25.8 - - - +
83F GLU* 6.0 0.4 - - - -
85F VAL* 4.6 0.7 - - + -
86F ARG* 3.7 27.4 - - + +
125F CYS 3.0 20.1 + - - +
126F ASP* 3.4 13.7 - - - +
127F TYR 3.2 0.4 - - - -
128F ALA* 1.3 76.1 - - - +
130F GLY* 1.3 61.8 + - - +
132F SER* 2.6 26.9 + - - +
133F ARG* 4.1 7.1 + - - +
126G ASP* 3.8 33.9 - - + +
127G TYR* 5.3 1.2 - - - -
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Residues in contact with GLY 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F ASP 3.4 4.8 + - - -
127F TYR 3.1 8.2 + - - -
129F VAL* 1.3 80.3 - - - +
131F LEU* 1.3 60.1 + - - +
133F ARG* 3.3 13.9 + - - +
134F MET* 3.3 23.0 - - - +
126G ASP 4.3 2.4 + - - -
127G TYR* 4.2 14.7 - - - -
130G GLY* 3.7 21.3 - - - -
134G MET* 5.5 0.4 - - - -
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Residues in contact with LEU 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127F TYR* 3.1 43.2 + - + +
128F ALA* 3.1 10.8 + - - +
130F GLY* 1.3 70.5 - - - +
132F SER* 1.3 54.8 + - - +
133F ARG 3.0 5.2 - - - -
134F MET* 2.8 27.4 + - + -
135F ILE* 2.9 27.1 + - + +
178F ILE* 3.7 24.2 - - + -
181F THR* 4.2 6.3 - - + -
479F SER 5.0 1.6 - - - +
481F SER 5.1 2.0 - - - +
484F TRP* 4.4 32.5 - - + +
134G MET* 3.9 28.5 - - + -
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Residues in contact with SER 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F ALA* 3.3 34.6 - - - +
79F PRO* 3.2 30.7 + - - +
82F GLY* 3.8 13.2 - - - -
128F ALA 2.9 14.3 + - - -
129F VAL* 2.6 22.0 + - - +
131F LEU* 1.3 76.9 - - - +
133F ARG* 1.3 59.6 + - - +
134F MET 3.4 0.2 - - - -
135F ILE* 4.8 0.9 - - - -
181F THR* 3.6 16.1 - - - +
141H PRO* 3.4 5.3 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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