Contacts of the helix formed by residues 130 - 153 (chain A) in PDB entry 1BV1
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 ALA 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A VAL 3.8 2.6 + - - -
129A LYS* 1.3 71.5 - - - +
131A GLU* 1.3 60.5 + - + +
133A VAL* 3.4 11.2 + - - +
134A LYS* 2.9 30.9 + - - +
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Residues in contact with GLU 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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129A LYS* 3.0 7.2 + - + +
130A ALA* 1.3 77.5 - - + +
132A GLN* 1.3 60.6 + - - +
134A LYS* 3.7 34.2 + - - +
135A ALA* 2.9 31.4 + - - +
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Residues in contact with GLN 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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64A PHE* 4.4 13.5 - - - -
90A PRO* 3.7 36.9 - - + +
95A LEU* 5.5 2.5 - - + -
98A ILE* 4.6 3.4 - - - +
120A TYR* 3.9 25.7 + - + -
128A VAL* 4.9 6.3 - - + -
129A LYS* 2.8 25.3 + - + +
131A GLU* 1.3 78.2 - - - +
133A VAL* 1.3 63.4 + - - +
135A ALA* 3.3 8.1 + - - +
136A SER* 3.3 30.4 + - - -
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Residues in contact with VAL 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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5A TYR* 4.1 34.3 - - + -
118A ASN* 5.1 1.7 + - - +
120A TYR* 3.8 16.8 - - - +
128A VAL* 3.6 29.8 - - + -
129A LYS 3.4 2.9 + - - +
130A ALA* 3.4 11.6 + - - +
131A GLU 3.3 0.2 - - - -
132A GLN* 1.3 76.0 - - - +
134A LYS* 1.3 62.3 + - - +
136A SER* 3.2 14.2 + - - -
137A LYS* 3.3 43.1 + - - +
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Residues in contact with LYS 134 (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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130A ALA 2.9 18.6 + - - +
131A GLU* 3.7 32.3 + - - +
133A VAL* 1.3 79.2 - - - +
135A ALA* 1.3 56.4 + - - +
137A LYS* 3.2 13.2 + - + +
138A GLU* 3.0 49.2 + - - +
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Residues in contact with ALA 135 (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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64A PHE* 6.6 0.2 - - + -
131A GLU 2.9 17.7 + - - +
132A GLN* 3.7 10.1 - - - +
133A VAL 3.3 0.4 - - - -
134A LYS* 1.3 75.4 - - - +
136A SER* 1.3 57.7 + - - +
138A GLU* 3.5 8.9 + - - +
139A MET* 3.0 30.3 + - - +
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Residues in contact with SER 136 (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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98A ILE* 5.7 1.9 - - - +
118A ASN* 3.9 22.2 - - - -
120A TYR* 3.8 6.5 + - - -
132A GLN* 3.3 22.5 + - - -
133A VAL 3.2 10.1 + - - -
135A ALA* 1.3 76.0 - - - +
137A LYS* 1.3 64.4 + - - +
139A MET* 3.5 6.7 + - - +
140A GLY* 3.1 19.6 + - - -
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Residues in contact with LYS 137 (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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5A TYR* 4.2 12.9 + - - +
6A GLU 3.8 10.0 + - - -
7A THR* 2.8 43.0 + - + +
118A ASN* 4.9 9.3 - - - +
133A VAL* 3.4 37.3 - - - +
134A LYS* 3.2 11.6 + - - +
136A SER* 1.3 79.1 - - - +
138A GLU* 1.3 55.2 + - - +
140A GLY* 3.3 2.4 + - - -
141A GLU* 3.0 36.3 + - - +
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Residues in contact with GLU 138 (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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134A LYS* 3.0 44.2 + - - +
135A ALA* 3.5 9.8 - - - +
137A LYS* 1.3 74.0 - - - +
139A MET* 1.3 66.4 + - - +
141A GLU* 3.3 15.4 + - - +
142A THR* 3.0 38.0 + - + +
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Residues in contact with MET 139 (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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37A ALA* 4.0 27.4 - - - +
38A ILE* 4.8 8.1 - - + -
58A PHE* 4.1 14.6 - - + -
62A LEU* 3.6 36.3 - - + -
135A ALA 3.0 19.8 + - - +
136A SER* 3.7 8.1 - - - +
138A GLU* 1.3 74.4 - - - +
140A GLY* 1.3 62.9 + - - +
142A THR* 2.9 21.3 + - - -
143A LEU* 3.1 27.4 + - + +
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Residues in contact with GLY 140 (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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9A THR* 6.4 1.6 - - - -
22A PHE* 4.3 7.7 - - - -
136A SER 3.1 15.4 + - - -
137A LYS* 3.7 3.4 - - - -
139A MET* 1.3 76.4 - - - +
141A GLU* 1.3 60.6 + - - +
143A LEU* 3.3 9.9 + - - +
144A LEU* 3.0 25.1 + - - +
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Residues in contact with GLU 141 (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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7A THR* 5.8 3.8 - - - +
9A THR* 4.2 26.7 + - + +
137A LYS* 3.0 21.0 + - - +
138A GLU* 3.7 16.3 - - - +
140A GLY* 1.3 75.1 - - - +
142A THR* 1.3 59.0 + - - +
144A LEU* 3.2 7.6 + - + +
145A ARG* 2.9 56.1 + - - +
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Residues in contact with THR 142 (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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34A ALA* 4.9 2.3 - - - +
36A GLN* 5.4 10.0 + - - -
37A ALA* 4.5 12.6 - - - +
138A GLU* 3.0 22.4 + - + +
139A MET* 2.9 23.9 + - - -
141A GLU* 1.3 74.8 - - - +
143A LEU* 1.3 59.7 + - - +
145A ARG* 3.8 22.7 - - - +
146A ALA* 3.0 28.6 + - - +
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Residues in contact with LEU 143 (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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22A PHE* 3.8 13.9 - - + -
30A PHE* 4.0 34.5 - - + -
34A ALA* 3.9 23.1 - - + -
37A ALA* 4.3 8.5 - - + -
38A ILE* 3.9 26.2 - - + -
139A MET* 3.1 31.9 + - + +
140A GLY* 3.7 7.2 - - - +
142A THR* 1.3 78.6 + - - +
144A LEU* 1.3 61.1 + - - +
146A ALA* 3.3 4.5 + - - +
147A VAL* 2.9 34.3 + - - +
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Residues in contact with LEU 144 (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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9A THR* 3.8 35.9 - - + +
10A THR 4.2 11.7 - - - +
11A SER* 4.4 7.0 - - - +
18A LEU* 4.0 29.8 - - + -
22A PHE* 3.6 19.5 - - + -
114A LEU* 4.0 28.0 - - + -
140A GLY 3.0 17.7 + - - +
141A GLU* 3.6 6.7 - - - +
143A LEU* 1.3 77.8 - - - +
145A ARG* 1.3 59.0 + - + +
147A VAL* 3.3 1.4 + - - +
148A GLU* 2.8 34.6 + - + +
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Residues in contact with ARG 145 (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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141A GLU* 2.9 39.7 + - - +
142A THR* 3.8 33.5 - - - +
144A LEU* 1.3 80.0 - - + +
146A ALA* 1.3 57.7 + - - +
148A GLU* 3.2 18.9 + - - +
149A SER* 2.9 34.2 + - - +
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Residues in contact with ALA 146 (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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33A VAL* 3.6 37.5 - - + +
34A ALA* 3.9 10.8 - - + -
36A GLN* 5.6 2.2 - - - +
142A THR 3.0 20.7 + - - +
143A LEU 3.5 4.9 - - - +
144A LEU 3.2 0.2 - - - -
145A ARG* 1.3 76.4 - - - +
147A VAL* 1.3 62.0 + - - +
149A SER* 3.4 7.6 + - - -
150A TYR* 3.1 21.7 + - - +
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Residues in contact with VAL 147 (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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18A LEU* 4.6 4.7 - - + -
21A ALA* 4.1 17.0 - - + -
22A PHE* 3.9 21.8 - - + +
29A LEU* 4.1 28.7 - - + -
30A PHE* 3.8 24.0 - - + -
33A VAL* 4.1 11.4 - - + -
143A LEU 2.9 19.9 + - - +
144A LEU 3.8 3.4 - - - +
146A ALA* 1.3 75.3 - - - +
148A GLU* 1.3 62.6 + - - +
150A TYR* 3.3 8.1 + - - +
151A LEU* 3.0 30.7 + - + +
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Residues in contact with GLU 148 (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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10A THR 4.5 3.1 - - - +
11A SER* 2.9 16.5 + - - +
12A VAL* 2.9 43.5 + - + +
13A ILE* 3.9 21.9 - - + +
18A LEU* 5.7 1.8 - - + +
144A LEU* 2.8 21.2 + - + +
145A ARG* 3.3 22.6 - - - +
147A VAL* 1.3 78.4 - - - +
149A SER* 1.3 61.8 + - - +
151A LEU* 3.4 4.5 + - - +
152A LEU* 3.1 34.2 + - + +
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Residues in contact with SER 149 (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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145A ARG* 2.9 20.5 + - - +
146A ALA* 3.8 6.4 - - - -
148A GLU* 1.3 75.1 - - - +
150A TYR* 1.3 64.2 + - - +
152A LEU* 3.3 11.2 + - - +
153A ALA* 3.0 24.9 + - - +
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Residues in contact with TYR 150 (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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29A LEU* 4.7 19.0 - - + +
32A LYS* 6.5 0.2 - - + -
33A VAL* 3.6 25.8 - - + -
146A ALA 3.1 14.1 + - - +
147A VAL* 3.4 10.5 - - - +
149A SER* 1.3 76.9 - - - +
151A LEU* 1.3 68.3 + - + +
153A ALA* 3.2 2.2 + - - -
154A HIS* 2.8 71.6 + + - +
157A ALA* 4.1 21.8 - - + +
158A TYR* 4.4 12.1 - + - -
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Residues in contact with LEU 151 (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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13A ILE* 4.1 34.5 - - + -
17A ARG* 3.0 53.0 + - + +
18A LEU* 4.6 3.8 - - + -
21A ALA* 4.0 19.3 - - + -
147A VAL* 3.0 27.3 + - + +
148A GLU 3.8 3.6 - - - +
149A SER 3.4 0.4 - - - -
150A TYR* 1.3 82.1 - - + +
152A LEU* 1.3 61.4 + - - +
154A HIS 3.1 12.6 - - - +
155A SER* 3.6 2.1 + - - -
157A ALA* 4.0 5.6 - - + +
158A TYR* 3.5 32.3 - - + -
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Residues in contact with LEU 152 (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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12A VAL* 4.1 21.8 - - + -
13A ILE* 4.1 19.7 - - + -
17A ARG* 5.4 2.5 - - - +
148A GLU* 3.1 27.8 + - + +
149A SER* 3.7 7.6 - - - +
150A TYR 3.2 0.2 - - - -
151A LEU* 1.3 76.4 - - - +
153A ALA* 1.3 60.3 + - - +
154A HIS 3.7 0.2 + - - -
155A SER* 4.4 7.3 + - - -
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Residues in contact with ALA 153 (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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149A SER 3.0 16.4 + - - +
150A TYR* 3.8 3.8 - - - +
152A LEU* 1.3 75.9 - - - +
154A HIS* 1.3 76.3 + - + +
155A SER 3.8 1.7 + - - -
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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
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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