Contacts of the helix formed by residues 105 - 126 (chain B) in PDB entry 4D2W
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 105 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ARG 3.8 1.6 + - - -
104B LEU* 1.3 72.8 - - - +
106B GLU* 1.4 64.4 + - - +
107B GLU* 3.5 15.2 + - - +
108B GLU* 2.9 29.8 + - - +
109B THR* 2.9 26.2 + - - -
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Residues in contact with GLU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU 3.8 0.4 + - - -
105B SER* 1.4 72.5 - - - +
107B GLU* 1.3 71.9 + - - +
109B THR* 3.5 2.4 + - - -
110B ARG* 2.9 53.4 + - - +
203B MET* 4.2 15.5 - - - +
233B SER* 2.8 32.6 + - - -
235B SER* 3.6 10.0 + - - -
236B SER* 3.6 9.3 + - - +
262B TRP* 3.5 18.5 + - + +
265B GLN* 4.9 4.0 - - - +
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Residues in contact with GLU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B SER* 3.2 12.9 - - - +
106B GLU* 1.3 94.5 + - - +
108B GLU* 1.4 61.7 + - - +
110B ARG* 3.3 23.2 + - - +
111B VAL* 3.4 18.0 + - - +
266B ASP* 4.1 19.8 - - - +
267B TYR* 5.7 0.3 - - - -
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Residues in contact with GLU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B TYR* 2.4 40.4 + - + +
101B GLN* 4.4 8.1 + - - -
104B LEU* 3.7 29.5 - - + +
105B SER* 2.9 22.2 + - - +
107B GLU* 1.4 72.1 - - - +
109B THR* 1.4 67.6 + - - +
111B VAL* 3.2 21.8 + - + +
112B VAL* 3.3 15.5 + - + +
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Residues in contact with THR 109 (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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104B LEU* 3.5 22.5 - - - +
105B SER 2.9 20.4 + - - -
106B GLU 3.6 4.7 - - - -
108B GLU* 1.4 74.9 - - - +
110B ARG* 1.4 50.6 + - - +
112B VAL* 3.3 5.4 + - - +
113B PHE* 2.7 37.5 + - + +
199B LEU* 3.8 24.7 - - + -
202B LEU* 3.7 24.5 - - + +
203B MET* 3.3 29.1 - - + +
262B TRP* 4.1 3.4 - - + -
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Residues in contact with ARG 110 (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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106B GLU* 2.9 37.9 + - - +
107B GLU* 3.5 27.5 + - - +
108B GLU 3.2 0.4 - - - -
109B THR* 1.4 72.4 - - - +
111B VAL* 1.3 66.5 + - - +
113B PHE* 4.3 0.4 - - - -
114B ARG* 3.0 41.5 + - + +
262B TRP* 2.7 60.4 + - + +
263B ILE 3.7 11.2 - - - +
265B GLN* 3.1 42.1 + - - +
266B ASP* 4.2 8.5 + - - +
267B TYR* 3.8 13.9 - - + -
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Residues in contact with VAL 111 (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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107B GLU 3.5 14.4 - - - +
108B GLU* 3.2 13.6 + - + +
110B ARG* 1.3 77.5 - - - +
112B VAL* 1.3 65.3 + - + +
114B ARG* 4.1 2.9 - - - +
115B GLN* 3.1 35.6 + - - +
267B TYR* 3.4 26.9 + - + +
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Residues in contact with VAL 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LEU* 3.9 17.0 - - + -
97B TYR* 4.8 12.1 - - + +
104B LEU* 4.9 3.8 - - + -
108B GLU* 3.3 13.2 + - + +
109B THR* 3.3 7.3 + - - +
110B ARG 3.3 0.4 - - - -
111B VAL* 1.3 83.5 - - + +
113B PHE* 1.3 62.7 + - - +
115B GLN* 3.1 24.0 + - - +
116B ILE* 3.2 16.4 + - + +
140B PHE* 4.4 23.6 - - + -
146B LEU* 3.7 19.1 - - + +
202B LEU* 4.0 22.2 - - + -
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Residues in contact with PHE 113 (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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109B THR* 2.7 25.7 + - + +
110B ARG* 4.0 5.4 - - - +
112B VAL* 1.3 73.2 - - - +
114B ARG* 1.3 55.8 + - - +
116B ILE* 3.1 21.5 + - + +
117B VAL* 2.9 44.0 + - + +
195B MET* 3.1 38.8 - - + -
198B LEU* 4.7 2.9 - - + -
199B LEU* 3.8 32.3 - - + -
202B LEU* 4.4 5.2 - - + -
239B LEU* 4.6 2.9 - - + -
243B MET* 3.8 25.8 - - + -
257B LEU* 4.7 1.6 - - + -
262B TRP* 3.9 10.3 - + + -
263B ILE* 3.7 22.7 - - + -
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Residues in contact with ARG 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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110B ARG* 3.0 23.9 + - + +
111B VAL 4.1 4.3 - - - +
113B PHE* 1.3 75.3 - - - +
115B GLN* 1.3 56.7 + - + +
117B VAL* 3.6 3.3 + - - -
118B SER* 3.1 26.2 + - - -
263B ILE* 2.9 45.7 + - + +
267B TYR* 3.6 44.7 - - + +
269B TYR* 3.1 53.3 + - - -
270B PRO 3.4 10.5 + - - -
271B VAL* 3.7 30.0 - - + +
272B GLU 4.8 1.2 - - - +
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Residues in contact with GLN 115 (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 HIS* 3.3 37.1 - - + +
111B VAL* 3.1 34.2 + - - +
112B VAL* 3.1 15.9 + - - +
114B ARG* 1.3 75.7 - - + +
116B ILE* 1.3 63.9 + - - +
118B SER* 3.4 3.7 + - - -
119B ALA* 3.2 22.5 + - - +
140B PHE* 5.6 1.0 - - - -
144B HIS 4.6 7.7 + - - -
145B LYS* 3.5 14.3 - - + +
146B LEU* 2.8 44.2 + - + +
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Residues in contact with ILE 116 (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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94B LEU* 4.0 16.8 - - + -
112B VAL* 3.6 21.1 - - + +
113B PHE* 3.1 23.8 + - + +
115B GLN* 1.3 74.3 - - - +
117B VAL* 1.3 62.2 + - - +
119B ALA* 3.4 6.5 + - - +
120B VAL* 3.1 29.4 + - + +
133B LEU* 5.6 2.5 - - + -
138B LEU* 3.8 35.7 - - + -
146B LEU* 3.9 8.7 - - + -
148B LEU* 6.5 0.2 - - + -
195B MET* 4.1 25.1 - - + -
198B LEU* 4.3 18.2 - - + -
202B LEU* 4.5 4.7 - - + -
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Residues in contact with VAL 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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113B PHE* 2.9 49.0 + - + +
114B ARG 3.9 4.7 - - - +
115B GLN 3.3 0.2 - - - -
116B ILE* 1.3 73.6 - - - +
118B SER* 1.3 54.8 + - - +
120B VAL* 3.4 0.5 + - - +
121B ALA* 2.8 37.2 + - - +
195B MET* 4.3 9.6 - - - -
254B MET* 4.4 4.5 - - - +
257B LEU* 3.9 30.1 - - + +
258B LEU* 3.8 26.0 - - + -
263B ILE* 4.2 7.4 - - + -
271B VAL* 4.1 13.5 - - + -
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Residues in contact with SER 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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66B HIS* 3.3 18.8 + - - -
67B GLN* 4.2 0.9 + - - -
68B HIS* 3.7 13.3 - - - -
114B ARG 3.1 19.0 + - - -
115B GLN* 3.5 6.5 - - - -
116B ILE 3.3 0.2 - - - -
117B VAL* 1.3 75.2 - - - +
119B ALA* 1.3 63.5 + - - +
122B TYR* 3.2 21.3 + - - +
271B VAL* 3.7 16.2 - - - +
272B GLU 3.1 19.6 + - - -
273B TRP* 3.5 10.9 - - - +
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Residues in contact with ALA 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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66B HIS* 3.8 12.9 - - - -
68B HIS* 3.6 32.8 - - + +
69B ILE* 4.5 2.9 - - + +
115B GLN 3.2 5.9 + - - +
116B ILE* 3.4 9.4 + - - +
118B SER* 1.3 76.8 - - - +
120B VAL* 1.3 58.7 + - + +
122B TYR* 3.2 6.8 + - - +
123B VAL* 2.9 31.7 + - - +
138B LEU* 5.8 2.5 - - + -
148B LEU* 4.3 17.5 - - + -
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Residues in contact with VAL 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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116B ILE* 3.1 21.9 + - + +
117B VAL 4.2 0.2 - - - +
119B ALA* 1.3 72.8 - - + +
121B ALA* 1.3 65.5 + - - +
123B VAL* 3.3 7.9 + - + +
124B HIS* 3.0 52.2 + - + +
130B HIS* 5.8 1.6 - - + -
133B LEU* 3.8 30.5 - - + -
148B LEU* 4.6 8.5 - - + -
191B ASP* 4.1 11.0 - - + +
195B MET* 3.8 20.9 - - + -
254B MET* 3.8 9.2 - - + -
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Residues in contact with ALA 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 VAL 2.8 19.8 + - - +
120B VAL* 1.3 78.4 - - - +
122B TYR* 1.3 56.1 + - - +
124B HIS* 3.5 2.7 + - - +
125B SER* 3.0 27.7 + - - -
254B MET* 3.7 32.6 - - + +
258B LEU* 3.9 8.3 - - + -
273B TRP* 3.6 29.4 - - + -
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Residues in contact with TYR 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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63B ASN 4.0 3.3 + - - -
64B LEU* 3.7 21.3 - - + -
65B ARG 2.9 41.0 + - - -
66B HIS* 3.5 37.5 - + + -
69B ILE* 3.8 11.4 - - + -
118B SER 3.2 5.5 + - - +
119B ALA 3.2 7.7 + - - +
121B ALA* 1.3 74.5 - - - +
123B VAL* 1.3 69.7 + - - +
125B SER* 2.7 28.2 + - - -
126B GLN* 3.2 31.7 + - + +
273B TRP* 3.6 16.5 - + - +
275B SER* 3.7 23.5 - - - -
279B PHE* 4.2 7.6 - - - -
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Residues in contact with VAL 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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64B LEU* 4.3 7.2 - - + -
69B ILE* 3.7 23.6 - - + -
119B ALA 2.9 21.1 + - - +
120B VAL* 3.6 9.9 - - + +
122B TYR* 1.3 76.0 - - - +
124B HIS* 1.4 65.1 + - + +
126B GLN* 3.2 14.0 + - - +
127B GLY 3.6 0.2 + - - -
128B TYR* 3.2 44.4 + - + +
129B ALA 4.4 0.2 - - - -
130B HIS* 4.1 17.9 - - + +
148B LEU* 4.2 7.9 - - + -
151B PHE* 3.9 23.6 - - + -
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Residues in contact with HIS 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 VAL* 3.0 29.9 + - + +
121B ALA* 3.8 5.4 - - - +
123B VAL* 1.4 76.0 - - + +
125B SER* 1.3 64.9 + - - +
127B GLY* 3.1 14.9 + - - -
128B TYR 3.2 20.4 - - - -
188B SER* 3.2 41.6 + - - +
191B ASP* 2.7 35.2 + - + +
192B VAL* 4.8 3.1 - - + +
254B MET* 3.6 24.9 - - + +
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Residues in contact with SER 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 ALA 3.0 10.4 + - - -
122B TYR* 2.7 25.0 + - - -
124B HIS* 1.3 76.3 - - - +
126B GLN* 1.3 65.8 + - - +
127B GLY 3.3 1.4 + - - -
273B TRP* 3.4 37.4 - - - -
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Residues in contact with GLN 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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63B ASN* 4.2 13.1 + - - +
64B LEU* 3.7 18.2 - - + -
122B TYR* 3.7 42.8 + - + +
123B VAL 3.2 9.5 + - - +
124B HIS 3.1 1.2 - - - -
125B SER* 1.3 84.2 + - - +
127B GLY* 1.3 58.0 + - - +
128B TYR* 3.3 20.3 - - + -
156B LYS* 5.6 0.5 - - - +
279B PHE* 5.7 2.4 - - - -
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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