Contacts of the helix formed by residues 113 - 134 (chain B) in PDB entry 3ZUU
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 SER 113 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ARG* 4.1 0.6 + - - +
112B PHE* 1.3 76.7 - - - +
114B GLU* 1.3 64.3 + - - +
115B ASP* 3.0 8.9 + - - +
116B GLU* 3.0 27.2 + - - +
117B ALA* 2.9 22.6 + - - +
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Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B PHE 3.9 0.8 + - - -
113B SER* 1.3 73.2 - - - +
115B ASP* 1.3 59.2 + - - +
117B ALA* 3.7 0.2 - - - +
118B ARG* 2.9 34.7 + - - +
211B LEU* 3.8 16.7 - - + +
245B HIS 4.4 2.6 - - - +
246B ILE* 3.3 12.4 - - + +
247B SER* 2.5 46.0 + - - -
250B CYS* 3.9 8.1 - - - -
276B TRP* 2.5 39.0 + - + +
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Residues in contact with ASP 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B SER* 3.0 7.8 + - - +
114B GLU* 1.3 78.9 - - - +
116B GLU* 1.3 59.3 + - - +
118B ARG* 2.9 34.7 + - - +
119B PHE* 2.9 26.9 + - - +
279B LYS* 4.8 5.4 + - - -
280B ASN* 3.2 18.7 + - - -
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Residues in contact with GLU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ARG* 3.3 35.8 + - - +
109B ALA* 5.7 0.7 - - - +
112B PHE* 3.7 27.9 - - + +
113B SER* 3.0 23.1 + - - +
115B ASP* 1.3 74.3 - - - +
117B ALA* 1.3 65.0 + - - +
119B PHE* 3.0 12.9 + - + +
120B PHE* 3.0 42.6 + - + -
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B PHE* 3.8 6.4 - - + +
113B SER 2.9 16.2 + - - +
114B GLU 3.7 1.6 - - - +
116B GLU* 1.3 77.2 - - - +
118B ARG* 1.3 56.5 + - - +
120B PHE 3.4 0.2 + - - -
121B PHE* 2.9 32.1 + - - +
207B LEU* 4.4 3.8 - - + -
210B MET* 3.4 31.2 - - + +
211B LEU* 3.5 31.2 - - + -
276B TRP* 4.0 2.9 - - + -
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Residues in contact with ARG 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B GLU* 2.9 25.3 + - - +
115B ASP* 2.9 42.0 + - - +
116B GLU 3.2 0.2 - - - -
117B ALA* 1.3 70.2 - - - +
119B PHE* 1.3 68.0 + - - +
121B PHE* 3.8 0.3 - - - +
122B GLN* 2.9 39.6 + - + +
276B TRP* 2.9 81.9 + - + +
277B PHE 4.8 0.2 - - - +
279B LYS* 3.4 55.1 + - - +
280B ASN* 4.0 2.2 - - - +
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Residues in contact with PHE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ASP 2.9 14.5 + - - +
116B GLU* 3.0 13.4 + - + +
118B ARG* 1.3 78.1 - - - +
120B PHE* 1.3 84.8 + + - +
122B GLN* 3.7 17.9 + - - +
123B GLN* 3.3 43.0 + - - +
153B ALA* 5.6 5.6 - - + -
154B PRO* 3.7 26.0 - - + -
155B ARG* 4.4 16.6 - - - -
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Residues in contact with PHE 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LEU* 4.2 11.7 - - + -
105B ARG* 3.8 25.8 - - - -
112B PHE* 3.6 32.3 - + - -
116B GLU* 3.0 42.6 + - + -
119B PHE* 1.3 97.1 - + - +
121B PHE* 1.3 62.9 + - - +
123B GLN* 3.1 14.9 + - - +
124B LEU* 2.9 25.8 + - - +
148B LEU* 4.0 19.1 - - + -
154B PRO* 3.9 17.9 - - + -
156B LEU* 4.2 15.7 - - + +
210B MET* 3.8 15.7 - - - -
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Residues in contact with PHE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ALA 2.9 21.2 + - - +
118B ARG 3.8 2.5 - - - +
120B PHE* 1.3 78.3 - - - +
122B GLN* 1.3 57.6 + - + +
124B LEU* 3.3 25.6 - - + +
125B ILE* 3.0 55.8 + - + +
203B CYS* 3.6 23.3 - - + -
207B LEU* 3.8 33.9 - - + -
210B MET* 4.1 7.5 - - + +
253B LEU* 4.2 13.0 - - + -
257B ILE* 4.4 15.0 - - + -
271B ILE* 4.1 15.5 - - + -
276B TRP* 3.8 18.4 - + + -
277B PHE* 4.3 8.3 - + - -
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Residues in contact with GLN 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ARG* 2.9 31.2 + - + +
119B PHE* 3.8 14.3 - - - +
120B PHE 3.2 0.2 - - - -
121B PHE* 1.3 76.1 - - + +
123B GLN* 1.3 57.3 + - + +
125B ILE* 3.2 4.3 + - - +
126B SER* 2.9 28.2 + - - -
277B PHE* 2.7 46.8 + - + +
279B LYS 2.9 23.5 + - - +
280B ASN* 4.1 2.9 - - - +
281B LEU* 3.5 30.4 - - + +
282B PRO* 3.8 14.9 - - - +
285B LEU* 4.2 9.1 - - + +
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Residues in contact with GLN 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ASN* 3.0 36.5 + - - +
119B PHE* 3.3 50.7 + - + +
120B PHE* 3.1 14.7 + - - +
122B GLN* 1.3 75.5 - - - +
124B LEU* 1.3 63.5 + - - +
126B SER* 3.3 5.5 + - - -
127B GLY* 3.0 21.3 + - - -
154B PRO 4.2 1.0 + - - -
155B ARG* 3.4 27.2 - - - +
156B LEU* 2.8 37.2 + - + +
158B ILE* 4.9 0.2 - - - +
285B LEU* 4.2 8.2 - - + +
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B PHE 2.9 13.0 + - - +
121B PHE* 3.3 34.1 - - + +
123B GLN* 1.3 76.8 - - - +
125B ILE* 1.3 57.5 + - - +
127B GLY* 3.4 0.9 + - - -
128B VAL* 3.0 35.6 + - + +
143B LEU* 4.2 26.7 - - + +
146B THR* 4.5 11.0 - - + -
156B LEU* 3.5 21.9 - - + +
158B ILE* 4.2 4.9 - - + +
203B CYS* 3.8 34.8 - - + +
206B THR* 4.3 18.4 - - + -
210B MET* 5.8 0.2 - - + -
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Residues in contact with ILE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B PHE* 3.0 50.8 + - + +
124B LEU* 1.3 72.8 - - + +
126B SER* 1.3 67.5 + - - +
128B VAL* 4.5 1.6 - - - -
129B SER* 2.9 23.7 + - - -
203B CYS* 4.1 22.2 - - + -
268B ILE* 4.1 25.4 - - + -
271B ILE* 4.2 15.3 - - + -
272B ARG* 4.1 22.4 - - + -
277B PHE* 3.5 24.0 - - + -
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Residues in contact with SER 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B HIS* 3.1 24.0 + - - -
122B GLN 2.9 17.0 + - - -
123B GLN* 3.5 5.2 - - - -
125B ILE* 1.3 77.7 - - - +
127B GLY* 1.3 57.5 + - - +
129B SER* 3.5 4.9 - - - -
130B TYR* 3.0 29.1 + - - +
272B ARG* 4.5 11.1 + - - +
277B PHE* 5.1 1.9 - - - -
285B LEU* 3.5 41.3 + - - +
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Residues in contact with GLY 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B HIS* 3.7 21.8 + - - -
76B ASN* 4.6 1.1 - - - -
77B ILE* 4.0 5.0 - - - +
123B GLN 3.0 14.3 + - - -
124B LEU 3.9 1.8 - - - -
126B SER* 1.3 76.2 - - - +
128B VAL* 1.3 56.7 + - - +
130B TYR* 3.5 1.7 + - - +
131B CYS* 3.0 34.6 + - - +
158B ILE* 4.2 15.7 - - - -
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Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B LEU* 3.0 24.3 + - + +
125B ILE* 3.9 4.9 - - - +
127B GLY* 1.3 73.9 - - - +
129B SER* 1.3 61.6 + - - +
131B CYS* 3.2 5.6 + - - +
132B HIS* 2.8 59.2 + - + +
141B LEU* 4.8 4.0 - - + -
143B LEU* 3.9 35.0 - - + -
158B ILE* 4.5 2.0 - - + -
199B ASP* 4.6 8.7 - - + +
203B CYS* 4.0 14.1 - - - -
268B ILE* 3.9 15.3 - - + -
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Residues in contact with SER 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ILE 2.9 19.8 + - - -
126B SER 3.5 3.8 - - - -
128B VAL* 1.3 76.2 - - - +
130B TYR* 1.3 63.0 + - - -
132B HIS* 3.2 7.8 + - - +
133B ALA* 2.9 24.5 + - - +
268B ILE* 3.9 22.9 - - - +
272B ARG* 3.7 29.3 + - - -
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Residues in contact with TYR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B SER 3.1 14.7 + - - -
72B LEU* 3.4 26.2 - - + -
73B ARG* 2.9 35.2 + - + +
74B HIS* 3.6 39.3 - + + -
77B ILE* 4.8 0.9 - - + -
126B SER 3.0 18.4 + - - +
127B GLY 3.7 3.1 - - - +
129B SER* 1.3 74.7 + - - +
131B CYS* 1.3 71.8 + - - +
133B ALA* 3.1 10.4 + - + +
134B MET* 3.0 41.4 + - + +
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Residues in contact with CYS 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B LEU* 4.5 15.9 - - - -
77B ILE* 3.3 34.8 - - - -
127B GLY 3.0 15.2 + - - +
128B VAL 3.6 4.0 - - - +
130B TYR* 1.3 81.1 - - - +
132B HIS* 1.3 64.1 + - - +
134B MET* 3.2 9.4 + - - +
135B GLN 3.2 0.2 + - - -
136B VAL* 2.9 41.7 + - + +
141B LEU* 3.8 27.8 - - + -
158B ILE* 6.0 0.4 - - - -
160B ALA* 5.3 0.2 - - - -
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Residues in contact with HIS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B VAL* 2.8 38.9 + - + +
129B SER* 3.5 6.5 - - - +
131B CYS* 1.3 75.8 - - - +
133B ALA* 1.3 56.3 + - - +
134B MET 3.0 0.9 - - - -
135B GLN* 2.6 23.6 + - - +
136B VAL 3.5 20.2 - - - +
137B CYS* 4.4 0.2 - - - -
141B LEU* 4.6 1.6 - - + -
196B LYS* 3.0 77.4 + - + +
199B ASP* 3.0 23.0 + - + -
268B ILE* 4.0 18.6 - - + +
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Residues in contact with ALA 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B SER 2.9 13.6 + - - +
130B TYR* 3.1 13.9 + - + +
132B HIS* 1.3 74.3 - - - +
134B MET* 1.3 63.9 + - + +
135B GLN* 3.4 12.1 + - - +
196B LYS* 5.2 0.2 - - - +
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Residues in contact with MET 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ASN* 5.4 2.4 - - - +
71B SER* 3.0 51.6 - - - +
72B LEU* 4.2 10.5 - - + +
130B TYR* 3.0 42.6 + - + +
131B CYS 3.2 3.8 + - - +
132B HIS 3.0 1.2 - - - -
133B ALA* 1.3 82.2 - - + +
135B GLN* 1.3 68.0 + - - +
136B VAL* 3.3 12.4 + - + +
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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