Contacts of the helix formed by residues 112 - 133 (chain B) in PDB entry 5VXA
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 112 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B LEU* 3.5 8.3 - - - +
88B GLU* 2.6 34.2 + - - -
110B HIS 3.7 1.0 + - - -
111B SER* 1.3 75.7 - - - +
113B PRO* 1.3 75.7 - - - +
114B GLY 3.5 2.4 + - - -
115B ALA 3.2 11.4 + - - -
116B LYS* 2.9 20.8 + - - +
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Residues in contact with PRO 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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111B SER 4.4 1.1 - - - +
112B SER* 1.3 88.4 - - - +
114B GLY* 1.3 61.7 + - - +
116B LYS* 3.3 12.0 + - + +
117B LEU* 3.1 31.8 + - + +
160B THR* 4.2 5.8 - - + +
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Residues in contact with GLY 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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54B VAL* 4.0 22.1 - - - +
85B LEU* 3.7 18.2 - - - -
112B SER* 3.2 3.4 + - - -
113B PRO* 1.3 79.4 - - - +
115B ALA* 1.3 61.4 + - - +
117B LEU* 3.3 9.3 + - - +
118B VAL* 3.1 24.4 + - - +
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Residues in contact with ALA 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 3.4 7.8 - - + +
88B GLU* 3.5 46.2 - - + +
89B VAL* 4.1 13.9 - - + -
111B SER* 4.1 6.7 - - - -
112B SER* 3.2 9.5 + - - +
114B GLY* 1.3 71.7 - - - +
116B LYS* 1.3 55.7 + - - +
118B VAL* 3.2 3.8 + - - +
119B LYS* 2.7 44.1 + - - +
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Residues in contact with LYS 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ALA 3.5 10.5 - - - -
109B PRO* 3.2 25.8 + - - +
111B SER* 3.4 23.7 + - - +
112B SER 2.9 14.7 + - - +
113B PRO* 3.6 12.1 - - + +
115B ALA* 1.3 76.4 - - - +
117B LEU* 1.3 56.4 + - - +
119B LYS* 3.7 0.9 - - - +
120B LEU* 2.8 36.5 + - - +
156B GLY 4.3 8.3 + - - -
157B LEU* 3.9 26.5 - - + +
158B GLN 4.8 6.9 + - - -
160B THR* 3.3 29.5 + - + +
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Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.5 20.9 - - + +
49B ILE* 3.6 38.4 - - + -
51B ASP* 6.4 0.2 - - + -
54B VAL* 4.3 19.3 - - + -
113B PRO* 3.1 21.6 + - + +
114B GLY* 3.5 11.0 - - - +
115B ALA 3.3 0.2 - - - -
116B LYS* 1.3 76.7 - - - +
118B VAL* 1.3 62.2 + - - +
120B LEU* 3.4 3.8 + - - +
121B ALA 3.1 18.0 + - - -
160B THR* 3.7 22.4 - - + +
161B ASN* 4.0 18.4 - - + -
164B LEU* 4.1 8.4 - - + +
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Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B VAL* 4.4 4.2 - - + +
43B LEU* 4.4 5.2 - - + -
54B VAL* 4.0 28.0 - - + +
57B ALA* 4.5 9.4 - - + +
58B ALA* 4.2 17.7 - - + +
61B HIS* 3.9 36.1 - - + +
85B LEU* 5.3 1.6 - - + -
89B VAL* 4.1 15.0 - - + -
114B GLY 3.1 15.6 + - - +
115B ALA* 3.2 6.5 + - - +
117B LEU* 1.3 74.9 - - - +
119B LYS* 1.3 58.7 + - - +
121B ALA* 3.3 2.2 + - - +
122B ASP* 2.9 29.3 + - + +
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Residues in contact with LYS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLU* 3.7 23.7 + - - +
89B VAL* 3.9 17.9 - - + +
104B GLN* 5.2 8.6 + - - +
107B GLN* 4.1 17.4 + - - +
108B ALA* 4.3 7.4 - - + +
111B SER* 2.8 31.3 + - - +
115B ALA* 2.7 25.9 + - - +
116B LYS 3.7 3.6 - - - +
118B VAL* 1.3 73.0 - - - +
120B LEU* 1.3 61.4 + - - +
122B ASP* 3.4 6.4 + - - +
123B LYS* 3.0 30.6 + - + +
153B VAL* 5.8 4.7 - - + -
157B LEU* 3.8 25.6 - - + -
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Residues in contact with LEU 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 LYS 2.8 23.9 + - - +
117B LEU* 4.7 0.2 - - - -
119B LYS* 1.3 73.5 - - - +
121B ALA* 1.3 57.9 + - - +
123B LYS* 3.4 4.3 + - - +
124B LEU* 2.9 28.8 + - - +
154B VAL* 4.1 10.8 - - + -
157B LEU* 3.7 33.2 - - + +
160B THR* 3.8 30.1 - - + -
161B ASN 4.6 1.8 - - - +
164B LEU* 3.8 25.8 - - + -
165B GLU* 3.9 20.6 - - + +
168B LEU* 3.6 27.5 - - + +
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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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39B VAL* 3.8 19.0 - - + +
42B ILE* 3.6 25.3 - - + +
43B LEU* 3.7 21.5 - - + -
117B LEU 3.1 17.5 + - - +
120B LEU* 1.3 77.1 - - - +
122B ASP* 1.3 57.2 + - - +
124B LEU* 4.2 6.3 - - - -
125B TYR* 2.9 29.8 + - - +
164B LEU* 4.4 2.7 - - + -
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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
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35B HIS* 2.9 12.5 + - - -
39B VAL* 3.9 9.8 - - + +
61B HIS* 3.0 13.8 + - + +
118B VAL* 2.9 19.6 + - + +
119B LYS* 3.6 7.1 - - - +
121B ALA* 1.3 75.4 - - - +
123B LYS* 1.3 75.5 + - - +
125B TYR* 3.5 1.2 + - - +
126B ASN* 3.1 34.0 + - - -
201B ZN 2.2 36.0 - - - -
202B NDP 4.0 5.7 + - - -
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Residues in contact with LYS 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B GLN* 3.0 28.7 + - - +
119B LYS* 3.0 22.7 + - + +
120B LEU* 3.7 4.5 - - - +
122B ASP* 1.3 87.9 + - - +
124B LEU* 1.3 56.6 + - - +
126B ASN* 3.3 5.8 + - - +
127B LEU* 2.8 38.6 + - + +
146B TYR* 4.9 8.6 + - + +
149B TRP* 3.6 25.9 - - + -
150B ALA* 3.8 24.0 - - + +
153B VAL* 4.0 23.5 - - + +
154B VAL* 4.2 21.5 - - + -
157B LEU* 5.1 0.9 - - + -
168B LEU* 4.2 4.9 - - + -
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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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42B ILE* 4.0 7.9 - - + -
46B GLU* 4.2 2.7 - - - +
120B LEU 2.9 17.2 + - - +
121B ALA* 3.7 5.2 - - - +
122B ASP 3.3 0.4 - - - -
123B LYS* 1.3 77.6 - - - +
125B TYR* 1.3 63.7 + - - +
127B LEU* 3.9 0.6 - - - +
128B ARG* 3.0 66.8 + - - +
164B LEU* 3.7 29.4 - - + +
167B ALA* 3.9 24.2 - - + -
168B LEU* 3.7 24.0 - - + +
171B LEU* 3.9 14.4 - - + -
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Residues in contact with TYR 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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13A ASP* 5.6 0.7 - - - -
24B ARG* 3.6 18.3 + - - +
30B THR* 5.6 1.9 - - - +
34B ASN* 3.6 22.4 + - - +
35B HIS* 3.2 33.5 + - + +
38B GLY* 3.7 37.0 - - - -
39B VAL* 3.9 8.7 - - + -
42B ILE* 3.7 13.8 - - + +
121B ALA 2.9 17.9 + - - +
122B ASP 3.8 3.6 - - - +
124B LEU* 1.3 76.8 - - - +
126B ASN* 1.3 59.0 + - - +
128B ARG* 3.3 7.0 + - - +
129B ASP* 2.9 39.0 + - - +
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Residues in contact with ASN 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ARG* 2.8 32.0 + - - +
35B HIS* 3.2 7.9 - - - -
122B ASP* 3.1 31.2 + - - +
123B LYS* 4.0 5.5 - - - +
125B TYR* 1.3 76.5 - - - +
127B LEU* 1.3 59.5 + - - +
129B ASP* 3.3 7.0 + - - +
130B LEU* 3.0 33.2 + - - +
146B TYR* 3.8 25.3 + - + +
202B NDP 2.7 38.2 + - + -
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Residues in contact with LEU 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 LYS* 2.8 23.5 + - + +
124B LEU 4.0 2.7 - - - +
126B ASN* 1.3 73.9 - - - +
128B ARG* 1.3 64.8 + - - +
130B LEU* 3.4 2.4 + - - +
131B ASN* 3.1 20.1 + - - -
146B TYR* 3.6 35.4 - - + -
147B PHE* 3.5 43.8 - - + -
150B ALA* 4.0 11.7 - - + -
168B LEU* 3.8 15.0 - - + -
171B LEU* 4.0 12.6 - - + -
172B PHE* 3.6 34.5 - - + -
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Residues in contact with ARG 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 4.1 10.7 - - - +
46B GLU* 2.7 43.6 + - - -
124B LEU* 3.0 47.5 + - - +
125B TYR* 3.6 6.7 - - - +
127B LEU* 1.3 75.0 - - - +
129B ASP* 1.3 57.5 + - - +
131B ASN* 3.3 8.2 + - - +
132B ARG* 2.8 30.2 + - - +
167B ALA* 4.0 11.9 - - - +
171B LEU* 4.2 14.8 - - + +
205B TRS 4.5 30.1 + - - +
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Residues in contact with ASP 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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24B ARG* 2.6 35.8 + - - +
26B ASP* 5.5 0.3 - - - +
125B TYR* 2.9 31.3 + - + +
126B ASN 3.4 6.3 - - - +
127B LEU 3.2 0.2 - - - -
128B ARG* 1.3 75.8 - - - +
130B LEU* 1.3 56.8 + - - +
132B ARG* 3.0 39.3 + - - +
133B CYS* 2.9 31.3 + - - +
202B NDP 3.3 21.1 + - - +
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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 ASN 3.0 17.7 + - - +
127B LEU* 3.7 6.7 - - + +
128B ARG 3.3 0.2 - - - -
129B ASP* 1.3 77.7 - - - +
131B ASN* 1.3 63.5 + - - +
132B ARG 3.4 0.2 + - - -
133B CYS 3.5 18.1 + - - -
134B THR* 3.7 8.0 + - - -
135B PRO* 3.5 33.9 - - + -
138B TRP* 3.9 13.2 - - + -
143B VAL* 4.2 13.9 - - + +
146B TYR* 3.3 44.6 - - + -
147B PHE* 3.9 21.5 - - + -
175B ARG* 5.5 0.2 + - - -
202B NDP 3.5 16.2 - - + -
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Residues in contact with ASN 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 LEU 3.1 13.7 + - - +
128B ARG* 3.6 9.1 - - - +
130B LEU* 1.3 77.2 - - - +
132B ARG* 1.3 61.8 + - - +
134B THR 5.4 0.2 + - - -
147B PHE* 3.4 17.6 - - - -
171B LEU* 3.7 29.7 + - - +
174B GLN* 5.5 3.4 + - - +
175B ARG* 2.8 35.2 + - - +
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Residues in contact with ARG 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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20A ARG* 5.6 2.4 - - - +
26B ASP* 2.9 35.0 + - - +
28B GLU* 3.0 22.0 + - - -
30B THR* 4.4 2.6 + - - -
128B ARG 2.8 16.6 + - - +
129B ASP* 3.0 33.3 + - - +
131B ASN* 1.3 80.0 - - - +
133B CYS* 1.3 70.3 + - + +
204B BME 3.4 17.2 - - - +
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Residues in contact with CYS 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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26B ASP* 4.6 3.2 - - + +
27B PRO* 3.5 26.5 - - + -
28B GLU* 5.6 0.2 - - - -
129B ASP 2.9 15.2 + - - +
130B LEU* 3.5 3.6 - - - +
131B ASN 3.4 0.8 - - - -
132B ARG* 1.3 94.0 - - - +
134B THR* 1.3 69.1 + - - +
135B PRO* 3.2 8.1 - - - +
202B NDP 4.9 4.9 + - - -
204B BME 2.1 58.6 - - + -
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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