Contacts of the helix formed by residues 112 - 133 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LEU* 3.6 6.1 - - - +
88A GLU* 2.5 37.7 + - - -
110A HIS 4.0 0.6 + - - -
111A SER* 1.3 75.5 - - - +
113A PRO* 1.3 74.6 - - - +
114A GLY 3.8 1.9 + - - -
115A ALA 3.2 13.2 + - - -
116A LYS* 3.0 21.6 + - - +
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Residues in contact with PRO 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A SER 4.3 2.0 - - - +
112A SER* 1.3 86.7 - - - +
114A GLY* 1.3 62.5 + - - +
116A LYS* 3.4 12.1 + - + +
117A LEU* 3.1 28.9 + - + +
160A THR* 3.8 7.9 - - + +
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Residues in contact with GLY 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A VAL* 4.2 21.6 - - - +
85A LEU* 3.6 16.4 - - - -
112A SER* 3.2 3.0 + - - -
113A PRO* 1.3 79.7 - - - +
115A ALA* 1.3 61.7 + - - +
117A LEU* 3.3 9.3 + - - +
118A VAL* 3.2 25.8 + - - +
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Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LEU* 3.2 12.7 - - + +
88A GLU* 3.5 33.7 - - + +
89A VAL* 4.0 12.5 - - + +
111A SER* 4.0 7.6 - - - -
112A SER* 3.2 17.7 + - - +
114A GLY* 1.3 72.6 - - - +
116A LYS* 1.3 59.7 + - - +
118A VAL* 3.3 3.1 + - - +
119A LYS* 2.8 38.1 + - - +
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Residues in contact with LYS 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ALA 3.5 10.5 - - - -
109A PRO* 3.2 24.3 + - - +
111A SER* 3.4 24.8 + - - +
112A SER 3.0 16.7 + - - +
113A PRO* 3.6 11.7 - - + +
115A ALA* 1.3 76.9 - - - +
117A LEU* 1.3 57.1 + - - +
119A LYS* 3.8 5.5 - - - +
120A LEU* 2.9 36.6 + - - +
156A GLY 4.2 9.8 + - - -
157A LEU* 4.1 20.9 - - + +
158A GLN 4.6 8.3 + - - -
160A THR* 3.2 28.3 - - + +
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Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 3.5 17.8 - - + +
49A ILE* 3.7 35.7 - - + -
54A VAL* 4.2 20.4 - - + -
113A PRO* 3.1 18.5 + - + +
114A GLY* 3.5 11.2 - - - +
116A LYS* 1.3 77.6 - - - +
118A VAL* 1.3 62.6 + - - +
120A LEU* 3.7 3.8 - - + +
121A ALA 3.0 18.9 + - - -
160A THR* 3.8 13.0 - - + +
161A ASN* 3.7 29.2 - - + +
164A LEU* 4.1 12.2 - - + +
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Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A VAL* 4.3 3.0 - - + +
43A LEU* 4.4 6.1 - - + -
54A VAL* 4.0 28.0 - - + +
57A ALA* 4.5 8.1 - - + +
58A ALA* 4.2 18.6 - - + +
61A HIS* 3.8 35.9 - - + +
85A LEU* 4.9 2.0 - - + -
89A VAL* 4.3 15.9 - - + -
114A GLY 3.2 14.4 + - - +
115A ALA* 3.8 6.3 - - - +
117A LEU* 1.3 75.4 - - - +
119A LYS* 1.3 58.0 + - - +
121A ALA* 3.3 2.2 + - - +
122A ASP* 2.8 32.7 + - + +
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Residues in contact with LYS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A GLU 3.8 22.3 + - - -
89A VAL* 4.0 19.5 - - + +
104A GLN* 5.3 9.9 + - - +
107A GLN* 3.9 18.6 + - - +
108A ALA* 4.4 2.9 - - + +
111A SER* 2.7 30.1 + - - +
115A ALA* 2.8 21.7 + - - +
116A LYS 3.8 3.1 - - - +
118A VAL* 1.3 77.7 - - - +
120A LEU* 1.3 62.1 + - - +
122A ASP* 3.7 6.1 - - - +
123A LYS* 3.0 30.6 + - + +
153A VAL* 5.7 5.4 - - + -
157A LEU* 4.0 30.1 - - + -
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LYS 2.9 24.0 + - - +
117A LEU* 3.7 4.0 - - - +
118A VAL 3.3 0.2 - - - -
119A LYS* 1.3 77.2 - - - +
121A ALA* 1.3 57.7 + - - +
123A LYS* 3.4 4.6 + - - +
124A LEU* 2.9 28.7 + - - +
154A VAL* 4.0 9.6 - - + -
157A LEU* 3.7 31.2 - - + +
160A THR* 3.8 28.9 - - + -
161A ASN 4.5 3.1 - - - +
164A LEU* 3.9 24.2 - - + -
165A GLU* 3.8 23.6 - - + +
168A LEU* 3.7 26.0 - - + +
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Residues in contact with ALA 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A VAL* 3.7 28.6 - - + +
42A ILE* 3.7 20.0 - - + +
43A LEU* 3.7 20.4 - - + -
117A LEU 3.0 18.1 + - - +
118A VAL 3.9 0.2 - - - +
120A LEU* 1.3 76.7 - - - +
122A ASP* 1.3 58.4 + - - +
124A LEU* 3.3 3.9 + - - +
125A TYR* 2.9 30.0 + - - +
164A LEU* 4.2 2.9 - - + +
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Residues in contact with ASP 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A HIS* 2.7 20.3 + - - -
39A VAL* 3.8 10.5 - - + +
61A HIS* 3.1 13.2 + - + +
62A ASP* 5.3 0.2 - - - +
118A VAL* 2.8 19.7 + - + +
119A LYS* 3.7 7.1 - - - +
121A ALA* 1.3 72.4 - - - +
123A LYS* 1.3 74.3 + - - +
125A TYR* 3.3 2.8 + - - +
126A ASN* 3.0 27.0 + - - -
201A ZN 2.2 36.1 - - - -
202A NDP 3.5 7.7 + - - -
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Residues in contact with LYS 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A GLN* 3.0 25.6 + - - +
119A LYS* 3.0 22.7 + - + +
120A LEU 3.7 4.7 - - - +
122A ASP* 1.3 84.3 + - - +
124A LEU* 1.3 62.6 + - - +
126A ASN* 3.2 6.2 + - - +
127A LEU* 3.0 30.6 + - + +
146A TYR* 4.6 11.9 + - + +
149A TRP* 3.6 29.1 - - - -
150A ALA* 3.7 23.1 - - + +
153A VAL* 4.1 22.9 - - + +
154A VAL* 4.2 22.2 - - + -
157A LEU* 5.2 0.4 - - + -
168A LEU* 4.2 7.0 - - + -
202A NDP 5.8 0.2 + - - -
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Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ILE* 3.9 20.6 - - + -
46A GLU* 4.0 4.0 - - - +
120A LEU 2.9 17.8 + - - +
121A ALA* 3.6 6.1 - - - +
122A ASP 3.2 0.4 - - - -
123A LYS* 1.3 74.9 - - - +
125A TYR* 1.3 62.7 + - - +
127A LEU* 4.0 1.0 - - - +
128A ARG* 3.1 70.7 + - - +
164A LEU* 3.9 16.6 - - + +
167A ALA* 4.1 21.5 - - + -
168A LEU* 3.8 19.7 - - + +
171A LEU* 3.8 20.0 - - + -
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Residues in contact with TYR 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ARG* 3.7 18.9 + - - +
30A THR* 5.7 1.4 - - - +
34A ASN* 3.6 20.8 + - - +
35A HIS* 3.2 35.1 + - + +
38A GLY* 3.8 35.0 - - - -
39A VAL* 3.9 8.7 - - + -
42A ILE* 3.8 15.6 - - + +
121A ALA 2.9 16.8 + - - +
122A ASP 3.7 4.3 - - - +
124A LEU* 1.3 77.7 - - - +
126A ASN* 1.3 56.8 + - - +
128A ARG* 3.7 6.7 - - + +
129A ASP* 2.9 36.8 + - - +
13B ASP* 5.7 0.4 - - - -
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Residues in contact with ASN 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ARG* 2.8 34.6 + - - -
35A HIS* 3.3 8.5 + - - -
122A ASP* 3.0 26.7 + - - +
123A LYS* 3.2 6.5 + - - +
125A TYR* 1.3 75.1 - - - +
127A LEU* 1.3 58.3 + - - +
129A ASP* 3.2 7.2 + - - +
130A LEU* 2.9 33.2 + - - +
146A TYR* 3.5 27.1 + - + +
202A NDP 2.7 40.5 + - + -
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LYS* 3.0 16.4 + - + +
124A LEU 4.0 3.1 - - - +
126A ASN* 1.3 74.1 - - - +
128A ARG* 1.3 64.0 + - - +
130A LEU* 3.3 2.6 + - - +
131A ASN* 3.0 28.6 + - - -
146A TYR* 3.6 33.0 - - + -
147A PHE* 3.6 39.4 - - + -
150A ALA* 4.1 11.2 - - + -
168A LEU* 3.8 18.8 - - + -
171A LEU* 4.1 11.2 - - + -
172A PHE* 3.6 34.5 - - + -
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Residues in contact with ARG 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ILE* 3.9 12.1 - - - +
46A GLU* 2.6 44.8 + - - -
124A LEU* 3.1 47.3 + - - +
125A TYR* 3.7 6.5 - - - +
127A LEU* 1.3 74.6 - - - +
129A ASP* 1.3 57.3 + - - +
131A ASN* 3.2 10.0 + - - +
132A ARG* 2.9 30.1 + - - +
167A ALA* 4.3 8.1 - - - +
171A LEU* 4.0 16.8 - - + +
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Residues in contact with ASP 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ARG* 2.7 31.5 + - - +
26A ASP* 5.7 0.3 - - - -
125A TYR* 2.9 26.6 + - + +
126A ASN 3.2 9.2 + - - +
128A ARG* 1.3 76.4 - - - +
130A LEU* 1.3 56.0 + - - +
132A ARG* 3.0 39.3 + - - +
133A CYS* 2.9 31.0 + - - +
202A NDP 3.3 22.0 + - - +
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Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ASN 2.9 18.4 + - - +
127A LEU* 3.7 5.4 - - + +
129A ASP* 1.3 76.9 - - - +
131A ASN* 1.3 64.5 + - - +
133A CYS 3.5 15.8 + - - +
134A THR* 3.8 7.4 + - - -
135A PRO* 3.4 35.9 - - + -
138A TRP* 3.9 12.8 - - + -
143A VAL* 4.1 19.8 - - + +
146A TYR* 3.3 49.4 - - + -
147A PHE* 4.2 12.3 - - + -
175A ARG* 4.8 0.9 + - - -
202A NDP 3.5 17.0 - - + +
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Residues in contact with ASN 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LEU 3.0 18.2 + - - -
128A ARG* 3.6 9.0 - - - +
130A LEU* 1.3 76.7 - - - +
132A ARG* 1.3 64.5 + - - +
147A PHE* 3.4 12.5 - - - -
171A LEU* 3.8 26.7 + - - +
174A GLN* 4.8 8.0 - - - +
175A ARG* 2.7 41.6 + - - +
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Residues in contact with ARG 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ASP* 3.1 37.8 + - - +
28A GLU* 5.1 6.7 + - - -
30A THR* 4.5 2.2 + - - -
128A ARG 2.9 14.9 + - - +
129A ASP* 3.0 30.7 + - - +
131A ASN* 1.3 79.8 - - - +
133A CYS* 1.3 75.4 + - - +
205A BME 3.3 23.7 - - - -
20B ARG* 5.9 2.8 - - - +
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Residues in contact with CYS 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ASP* 4.6 2.4 - - + +
27A PRO* 3.4 31.0 - - + -
129A ASP 2.9 15.7 + - - +
130A LEU* 3.5 5.9 - - - +
131A ASN 3.4 1.0 - - - -
132A ARG* 1.3 100.9 - - - +
134A THR* 1.3 66.2 + - - +
135A PRO* 3.3 9.2 - - - +
202A NDP 5.0 3.5 + - - -
205A BME 2.0 54.7 - - - -
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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
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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