Contacts of the helix formed by residues 131 - 154 (chain A) in PDB entry 4P9O
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 VAL 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A GLY* 1.3 66.1 + - - +
133A SER* 3.3 12.6 + - - +
134A VAL* 3.3 26.9 + - + +
135A ALA* 3.3 9.0 + - - +
213A LEU* 3.4 34.1 - - + +
216A GLY* 3.4 27.6 - - - +
217A ILE* 3.8 23.6 - - + +
220A ASP* 5.0 7.2 - - + -
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Residues in contact with GLY 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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131A VAL* 1.3 77.0 - - - +
133A SER* 1.4 56.1 + - - +
135A ALA* 3.3 9.5 + - - +
136A ALA* 3.0 26.2 + - - +
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Residues in contact with SER 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A VAL 4.2 6.8 + - - -
132A GLY* 1.4 73.6 - - - +
134A VAL* 1.3 68.1 + - - +
136A ALA* 3.5 8.9 + - - +
137A LEU* 3.0 28.1 + - - +
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Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A VAL* 3.4 25.6 - - - +
132A GLY 3.2 0.4 - - - -
133A SER* 1.3 79.9 - - - +
135A ALA* 1.4 58.7 + - - +
137A LEU* 3.3 8.0 + - + +
138A LEU* 3.0 28.1 + - - +
209A THR* 3.9 20.7 - - + +
212A ASN* 4.6 9.0 - - + +
213A LEU* 3.8 32.3 - - + +
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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
----------------------------------------------------------
131A VAL 3.3 4.8 + - - +
132A GLY* 3.5 11.9 - - - +
134A VAL* 1.4 75.4 - - - +
136A ALA* 1.3 54.5 + - - +
138A LEU* 3.5 3.7 + - - +
139A THR* 2.7 38.1 + - - -
213A LEU* 3.7 29.3 - - + +
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Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLY 3.0 16.6 + - - +
133A SER* 3.6 10.8 - - - +
134A VAL 3.3 0.2 - - - -
135A ALA* 1.3 76.5 - - - +
137A LEU* 1.4 59.5 + - - +
139A THR* 3.7 5.3 + - - -
140A VAL* 3.3 30.0 + - + +
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A SER 3.0 14.8 + - - +
134A VAL* 3.3 11.4 + - + +
136A ALA* 1.4 73.7 - - - +
138A LEU* 1.3 58.9 + - - +
140A VAL* 3.4 7.7 + - - +
141A VAL* 3.0 42.5 + - + +
205A LEU* 6.0 5.4 - - + -
209A THR* 3.8 28.0 - - + +
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Residues in contact with LEU 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 VAL 3.0 15.2 + - - +
135A ALA* 3.5 6.7 + - - +
136A ALA 3.4 0.2 - - - -
137A LEU* 1.3 76.7 - - - +
139A THR* 1.3 56.1 + - - +
141A VAL* 3.3 7.2 + - + +
142A PHE* 2.7 45.7 + - + +
175A MET* 5.2 5.2 - - + -
206A THR* 4.3 20.2 - - + -
209A THR* 3.9 25.8 - - + -
210A VAL* 3.8 33.0 - - + +
213A LEU* 4.4 17.3 - - + -
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Residues in contact with THR 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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135A ALA* 2.7 23.5 + - - +
136A ALA* 3.9 7.1 - - - -
137A LEU 3.4 0.4 - - - -
138A LEU* 1.3 74.9 - - - +
140A VAL* 1.3 53.9 + - + +
142A PHE* 3.4 5.1 + - - +
143A TYR* 2.8 62.1 + - + +
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Residues in contact with VAL 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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136A ALA* 3.3 19.1 + - + +
137A LEU* 3.7 6.1 - - - +
139A THR* 1.3 76.6 - - + +
141A VAL* 1.3 60.1 + - + +
143A TYR* 3.5 3.7 + - - +
144A ILE* 3.0 50.3 + - + +
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Residues in contact with VAL 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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137A LEU* 3.0 30.7 + - + +
138A LEU* 3.8 8.3 - - + +
140A VAL* 1.3 79.4 - - + +
142A PHE* 1.3 57.8 + - - +
144A ILE* 4.0 4.2 - - - +
145A ALA* 3.0 33.6 + - + +
202A PHE* 5.4 0.4 - - + -
205A LEU* 3.7 33.0 - - + -
206A THR* 4.2 20.2 - - + -
301A 2CV 5.3 7.9 - - + +
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Residues in contact with PHE 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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138A LEU* 2.7 30.0 + - + +
139A THR* 3.7 6.3 - - - +
141A VAL* 1.3 72.2 - - - +
143A TYR* 1.3 64.2 + + + +
145A ALA* 3.9 4.3 - - - +
146A ALA* 3.1 30.0 + - - +
168A LEU* 3.2 54.5 - - + -
171A LEU* 3.5 22.1 - - + +
172A PHE* 3.3 26.0 - + + -
175A MET* 4.6 12.8 - - - -
202A PHE* 4.1 17.0 - + - -
206A THR* 4.8 8.3 - - + -
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Residues in contact with TYR 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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139A THR* 2.8 50.4 + - + +
140A VAL* 4.1 4.0 - - - +
142A PHE* 1.3 79.1 - + + +
144A ILE* 1.4 58.1 + - + +
146A ALA* 3.4 3.6 + - - +
147A VAL* 3.0 35.6 + - + +
164A LEU* 4.2 18.1 - - + +
168A LEU* 3.9 38.6 - - + +
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Residues in contact with ILE 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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140A VAL* 3.0 39.9 + - + +
141A VAL* 4.3 4.3 - - - +
143A TYR* 1.4 71.9 - - + +
145A ALA* 1.4 61.4 + - - +
147A VAL* 3.2 11.7 + - + +
148A MET* 3.0 49.4 + - + +
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Residues in contact with ALA 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 VAL 3.0 20.3 + - - +
142A PHE 3.9 3.4 - - - +
144A ILE* 1.4 76.0 - - - +
146A ALA* 1.4 57.8 + - - +
148A MET* 3.3 7.5 + - - +
149A ALA* 3.0 25.8 + - - +
171A LEU* 3.7 6.5 - - + -
198A PHE* 3.4 20.6 - - + -
202A PHE* 4.0 30.1 - - + -
301A 2CV 4.6 9.4 - - + -
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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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142A PHE* 3.1 19.4 + - + +
143A TYR 3.6 3.4 - - - +
144A ILE 3.3 0.2 - - - -
145A ALA* 1.4 71.7 - - - +
147A VAL* 1.3 58.4 + - - +
149A ALA* 4.6 0.2 - - - -
150A THR* 2.7 34.0 + - - -
164A LEU* 3.6 7.8 - - + +
167A SER* 3.4 4.2 - - - -
168A LEU* 3.5 41.7 - - + +
171A LEU* 3.6 13.8 - - + +
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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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143A TYR* 3.0 23.9 + - + +
144A ILE* 3.4 14.1 - - + +
146A ALA* 1.3 73.1 - - - +
148A MET* 1.4 66.8 + - + +
150A THR* 3.3 7.6 + - - -
151A ASN* 3.1 22.2 + - + +
164A LEU* 3.8 20.2 - - + -
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Residues in contact with MET 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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144A ILE* 3.0 33.8 + - + +
145A ALA* 3.3 8.5 + - - +
147A VAL* 1.4 77.7 - - + +
149A ALA* 1.4 51.8 + - - +
151A ASN* 3.3 7.7 + - - +
152A LEU* 2.8 47.3 + - + +
198A PHE* 3.9 20.2 - - + -
301A 2CV 4.7 22.9 - - + -
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Residues in contact with ALA 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 ALA 3.0 17.2 + - - +
146A ALA 4.2 3.8 - - - +
148A MET* 1.4 72.0 - - - +
150A THR* 1.4 59.9 + - - +
152A LEU 3.2 0.2 + - - -
153A TYR* 2.8 47.1 + - + +
154A GLY 3.6 2.1 + - - -
161A PHE* 3.6 31.7 - - + +
167A SER* 4.2 2.0 - - - +
171A LEU* 4.3 6.7 - - + -
198A PHE* 4.0 13.4 - - + -
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Residues in contact with THR 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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146A ALA 2.7 18.6 + - - -
147A VAL* 3.3 11.2 + - - -
149A ALA* 1.4 75.2 - - - +
151A ASN* 1.3 58.3 + - - +
154A GLY* 3.1 25.5 + - - -
161A PHE 3.4 17.7 - - - +
162A GLY 4.8 2.0 - - - +
163A ASP* 3.3 25.0 + - - +
164A LEU* 3.7 7.1 - - + +
167A SER* 2.8 13.2 + - - -
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Residues in contact with ASN 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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147A VAL* 3.1 11.0 + - + +
148A MET* 3.4 11.1 - - - +
150A THR* 1.3 82.1 - - - +
152A LEU* 1.3 69.1 + - - +
154A GLY 4.5 1.0 + - - -
155A ALA 5.5 1.2 + - - -
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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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148A MET* 2.8 40.2 + - + +
151A ASN* 1.3 83.3 - - - +
153A TYR* 1.4 92.0 + - + +
154A GLY 4.1 0.2 + - - -
155A ALA* 5.3 0.9 + - - +
156A THR* 4.4 1.2 + - - -
192A HIS* 4.0 14.2 + - + -
198A PHE* 4.4 7.0 - - + -
301A 2CV 4.0 39.3 - - + -
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Residues in contact with TYR 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 ALA* 2.8 31.9 + - + -
152A LEU* 1.4 93.1 - - + +
154A GLY* 1.3 56.3 + - - +
155A ALA 3.3 2.9 - - - -
156A THR* 3.8 7.2 - - - -
157A PHE* 2.9 42.6 + - + +
161A PHE* 3.8 20.0 - + + -
188A VAL* 3.8 22.0 - - + -
192A HIS* 3.8 19.1 - + - -
195A ALA* 3.9 8.3 - - + -
198A PHE* 3.3 35.4 - + - +
199A PHE* 3.7 31.5 - + - -
301A 2CV 3.6 18.9 - - - -
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Residues in contact with GLY 154 (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 ALA 3.6 1.2 + - - -
150A THR* 3.1 17.6 + - - -
151A ASN 4.5 0.4 + - - -
152A LEU 3.7 1.4 - - - -
153A TYR* 1.3 77.2 - - - +
155A ALA* 1.3 57.4 + - - +
158A PRO* 3.3 28.6 - - - +
161A PHE 3.2 26.7 - - - -
162A GLY* 3.8 6.6 - - - -
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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
------------------------------------------------------------
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