Contacts of the helix formed by residues 111 - 132 (chain B) in PDB entry 1UKW
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 CYS 111 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ILE* 3.7 18.2 - - + +
59B ALA* 4.0 9.0 - - + -
107B LEU 3.3 3.7 + - - +
108B ALA* 3.2 6.9 + - - -
110B ALA* 1.3 83.6 - - - +
112B MET* 1.3 60.4 + - - +
113B GLY* 3.5 6.7 - - - -
114B ILE* 3.3 33.9 - - + +
115B TYR* 3.0 26.9 + - - +
236B ALA* 5.0 4.0 - - - -
381B LYS* 3.1 31.4 - - - +
382B LEU* 6.5 0.4 - - - -
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Residues in contact with MET 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ALA* 3.4 27.3 + - - +
111B CYS* 1.3 70.2 - - - +
113B GLY* 1.3 61.6 + - - +
115B TYR* 3.2 21.2 + - + +
116B THR* 2.9 41.5 + - - +
119B MET* 4.1 10.3 - - - -
234B GLN* 3.1 15.9 - - + +
276B VAL* 5.3 2.2 - - - +
279B GLY* 3.9 11.4 - - - -
283B VAL* 3.7 19.3 - - + +
385B ASP* 4.1 20.4 + - + +
389B ASN* 3.4 25.4 - - - +
392B TYR* 3.2 25.6 - - + +
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Residues in contact with GLY 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B CYS* 3.3 7.8 - - - -
112B MET* 1.3 79.4 - - - +
114B ILE* 1.3 60.9 + - - +
116B THR* 3.3 6.9 + - - -
117B ILE 3.9 0.7 + - - -
234B GLN* 3.5 38.1 - - - +
236B ALA* 4.4 2.0 - - - -
237B SER* 3.2 30.4 + - - -
385B ASP* 4.2 3.4 + - - -
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Residues in contact with ILE 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ILE* 3.9 39.7 - - + -
58B VAL* 4.5 14.1 - - + -
59B ALA* 4.5 13.9 - - - -
62B TYR* 4.9 3.1 - - + -
69B PRO* 4.0 21.3 - - + -
72B VAL* 4.2 14.6 - - + -
76B LEU* 5.8 3.1 - - + -
111B CYS* 3.3 20.6 - - + -
113B GLY* 1.3 73.1 - - - +
115B TYR* 1.3 66.3 + - - +
117B ILE* 3.2 14.2 + - + +
118B PRO* 3.1 17.5 - - + +
236B ALA* 3.6 22.0 - - + -
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Residues in contact with TYR 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ILE* 5.6 0.6 - - - +
100B GLU* 4.4 4.5 + - - +
103B VAL* 5.6 0.9 - - + -
104B GLY* 3.5 31.2 - - - -
107B LEU* 3.6 31.4 - - + -
108B ALA* 3.5 30.5 - - + +
111B CYS 3.0 19.2 + - - +
112B MET* 3.2 15.7 + - + +
114B ILE* 1.3 77.3 - - - +
116B THR* 1.3 63.0 + - - +
118B PRO* 3.0 18.1 - - + +
119B MET* 3.1 36.7 + - + +
122B ASP* 5.5 2.3 + - - -
275B PRO* 3.6 32.8 + - - +
279B GLY* 4.2 4.5 - - - -
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Residues in contact with THR 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B MET* 2.9 13.9 + - - +
113B GLY 3.4 9.0 - - - -
114B ILE 3.1 0.6 - - - -
115B TYR* 1.3 77.4 - - - +
117B ILE* 1.3 56.6 + - - +
119B MET* 3.9 10.3 - - + -
120B ALA* 2.8 30.3 + - + +
188B SER* 4.2 13.2 - - - +
234B GLN* 2.5 32.0 + - - +
237B SER* 3.2 18.6 - - - +
392B TYR* 2.9 26.2 + - + +
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Residues in contact with ILE 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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68B VAL* 4.2 10.8 - - + -
69B PRO* 3.9 33.7 - - + -
73B ILE* 4.0 16.6 - - + -
82B LEU* 6.4 0.2 - - + -
113B GLY 4.0 1.3 - - - +
114B ILE* 3.5 14.6 - - + +
115B TYR 3.1 0.8 - - - -
116B THR* 1.3 77.7 - - - +
118B PRO* 1.3 72.5 - - + +
121B SER* 3.1 8.5 + - - -
150B LEU* 3.5 34.5 - - + -
189B ASN* 2.8 33.9 - - - +
236B ALA 3.9 10.5 - - - +
237B SER* 4.0 17.5 - - - -
238B GLY 4.9 0.4 - - - +
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Residues in contact with PRO 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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76B LEU* 4.2 28.0 - - + -
81B LEU 5.1 7.4 - - - +
82B LEU* 4.4 15.3 - - + -
83B ASN 5.5 1.7 + - - +
107B LEU* 4.3 9.2 - - + -
114B ILE 3.1 14.8 - - - +
115B TYR* 3.0 35.2 - - + +
117B ILE* 1.3 86.7 - - + +
119B MET* 1.3 54.2 + - - +
121B SER* 3.2 8.8 + - - -
122B ASP* 2.9 37.9 + - - +
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Residues in contact with MET 119 (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 MET* 4.1 8.1 - - - -
115B TYR* 3.1 56.8 + - + +
116B THR* 3.8 10.1 - - + +
118B PRO* 1.3 77.7 - - - +
120B ALA* 1.3 64.5 + - - +
122B ASP* 3.2 12.8 + - - +
123B LEU* 3.1 18.9 + - - +
272B THR* 5.4 1.6 - - - +
275B PRO* 4.0 11.2 - - + -
276B VAL* 3.7 28.9 - - + -
392B TYR* 3.3 32.1 - - + +
393B GLU* 3.6 23.5 - - - +
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B THR* 2.8 25.5 + - + +
119B MET* 1.3 77.3 - - + +
121B SER* 1.3 61.7 + - - +
123B LEU* 3.0 31.4 + - + +
124B GLY 3.0 6.4 + - - -
151B ALA 3.8 4.1 - - - +
152B ALA* 4.6 2.6 - - - -
153B PHE 4.8 0.5 + - - -
188B SER* 3.5 32.5 - - - +
189B ASN* 3.7 11.0 - - - +
393B GLU* 5.6 0.4 - - - -
421B FAD 5.1 0.7 - - - +
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Residues in contact with SER 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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82B LEU* 5.1 0.2 - - - -
83B ASN* 2.5 28.6 + - - -
117B ILE 3.1 14.3 + - - -
118B PRO* 3.2 13.4 + - - -
120B ALA* 1.3 78.3 - - - +
122B ASP* 1.3 61.1 + - - +
124B GLY 3.3 1.4 + - - -
125B ILE* 3.1 25.2 + - - +
150B LEU* 3.6 8.6 - - - -
151B ALA* 3.0 37.1 + - - +
189B ASN* 3.5 3.7 + - - -
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Residues in contact with ASP 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ASN* 3.7 20.6 + - - -
84B ALA 4.5 0.9 + - - -
85B ILE* 3.4 42.5 - - + +
100B GLU* 4.3 15.3 - - - +
115B TYR* 5.5 2.6 + - - -
118B PRO* 2.9 24.8 + - - +
119B MET* 3.2 11.7 + - - +
121B SER* 1.3 75.9 - - - +
123B LEU* 1.3 57.7 + - - +
125B ILE* 3.4 2.1 + - - +
126B THR* 2.8 32.7 + - - +
272B THR* 5.0 2.0 - - + -
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Residues in contact with LEU 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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119B MET 3.1 9.3 + - - +
120B ALA* 3.0 22.6 + - + +
122B ASP* 1.3 74.1 - - - +
124B GLY* 1.3 57.2 + - - +
126B THR* 3.3 4.3 + - - -
127B PRO* 2.9 25.5 - - - +
153B PHE* 3.3 38.3 - - + +
268B THR* 3.6 15.7 - - + -
269B LEU* 4.3 5.6 - - + -
272B THR* 3.4 41.7 - - + +
393B GLU* 4.0 24.5 - - + +
421B FAD 4.6 15.7 - - + +
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Residues in contact with GLY 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 ALA 3.0 11.1 + - - -
121B SER 3.3 3.3 + - - -
123B LEU* 1.3 77.3 - - - +
125B ILE* 1.3 57.9 + - - +
127B PRO* 3.0 15.3 - - - +
128B VAL* 4.3 1.0 - - - +
151B ALA* 4.3 0.2 - - - -
152B ALA 3.3 33.4 - - - -
153B PHE* 3.9 4.0 - - - +
195B TRP* 3.6 10.3 - - - -
197B VAL* 3.1 17.9 - - - +
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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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83B ASN* 3.6 39.7 - - + +
85B ILE* 3.8 10.1 - - + -
86B ILE* 3.9 22.4 - - + -
121B SER* 3.1 22.5 + - - +
122B ASP* 3.6 8.5 - - - +
123B LEU 3.2 0.2 - - - -
124B GLY* 1.3 77.5 - - - +
126B THR* 1.3 65.2 + - - +
128B VAL* 3.1 8.1 + - - +
129B LEU* 3.1 40.1 + - + -
141B LEU* 4.7 8.1 - - + -
144B LEU* 3.9 10.8 - - + -
151B ALA* 3.8 11.4 - - + -
195B TRP* 4.3 7.6 - - + -
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Residues in contact with THR 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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85B ILE* 4.5 5.9 - - - +
122B ASP* 2.8 19.2 + - - +
123B LEU 3.5 6.7 - - - -
125B ILE* 1.3 76.1 - - - +
127B PRO* 1.3 67.4 - - - +
129B LEU* 3.1 11.0 + - - +
130B LEU* 2.9 35.8 + - + +
268B THR* 3.3 35.7 - - + +
271B LYS* 5.2 10.6 - - + +
272B THR* 3.7 11.2 - - + +
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Residues in contact with PRO 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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123B LEU 2.9 27.4 - - - +
124B GLY 3.0 12.6 - - - +
126B THR* 1.3 80.5 - - - +
128B VAL* 1.3 52.7 + - - +
130B LEU* 3.2 2.0 + - + +
131B ALA* 2.7 39.0 + - - +
153B PHE* 3.9 21.1 - - + -
197B VAL* 3.8 13.7 - - + -
199B PHE* 4.3 2.0 - - + -
255B LEU* 3.7 19.0 - - + +
264B ILE* 3.9 15.7 - - + -
268B THR* 3.5 17.3 - - - +
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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
----------------------------------------------------------
124B GLY 4.3 2.2 - - - +
125B ILE 3.1 7.7 + - - +
127B PRO* 1.3 76.5 - - - +
129B LEU* 1.3 60.7 + - - +
132B GLY* 2.9 32.6 + - - +
136B GLN* 4.3 6.5 - - + +
137B LYS* 3.8 26.2 - - + +
140B PHE* 4.3 8.3 - - + -
141B LEU* 3.8 23.6 - - + -
195B TRP* 3.9 29.8 - - + -
215B VAL* 4.3 6.5 - - + -
255B LEU* 3.8 23.3 - - + -
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Residues in contact with LEU 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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85B ILE* 4.1 27.8 - - + +
87B PRO* 3.5 31.9 - - + -
125B ILE* 3.1 32.9 + - + +
126B THR* 3.1 11.9 + - - +
128B VAL* 1.3 78.0 - - - +
130B LEU* 1.3 64.1 + - + +
137B LYS* 3.6 27.4 + - + +
141B LEU* 3.8 17.7 - - + -
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Residues in contact with LEU 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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126B THR* 2.9 26.3 + - + +
127B PRO* 3.8 3.6 - - + +
129B LEU* 1.3 82.0 - - + +
131B ALA* 1.3 60.9 + - + +
132B GLY 5.1 0.4 - - - +
264B ILE* 4.4 6.7 - - + +
267B GLN* 4.0 28.0 - - + +
268B THR* 3.5 37.0 - - - +
271B LYS* 3.8 26.2 - - + +
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Residues in contact with ALA 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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127B PRO 2.7 16.9 + - - +
130B LEU* 1.3 73.4 - - - +
132B GLY* 1.3 65.8 + - - +
133B THR* 3.8 3.8 + - - +
136B GLN* 4.4 0.7 - - - +
255B LEU* 3.9 10.8 - - + -
256B GLY* 4.0 19.4 + - - +
263B LYS* 6.2 0.7 - - - +
264B ILE* 3.5 35.4 - - + -
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Residues in contact with GLY 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B PRO 3.8 0.6 + - - -
128B VAL* 2.9 36.5 + - - +
129B LEU 5.0 0.2 - - - +
130B LEU 5.1 0.7 - - - +
131B ALA* 1.3 77.3 - - - +
133B THR* 1.3 66.1 + - - -
136B GLN* 3.1 14.6 - - - -
137B LYS* 3.4 16.5 + - - -
255B LEU* 4.3 4.8 - - - +
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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