Contacts of the helix formed by residues 132 - 154 (chain B) 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 GLY 132 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131B VAL* 1.3 77.9 - - - +
133B SER* 1.4 55.7 + - - +
135B ALA* 3.3 9.8 + - - +
136B ALA* 3.0 26.0 + - - +
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Residues in contact with SER 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B VAL 4.2 9.5 + - - -
132B GLY* 1.4 73.0 - - - +
134B VAL* 1.3 64.3 + - - +
135B ALA 3.4 0.2 - - - -
136B ALA* 3.5 9.3 + - - +
137B LEU* 3.0 27.5 + - - +
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B VAL* 3.4 27.4 - - - +
132B GLY 3.2 0.2 - - - -
133B SER* 1.3 77.9 - - - +
135B ALA* 1.4 58.3 + - - +
137B LEU* 3.2 8.5 + - + +
138B LEU* 3.0 28.3 + - - +
209B THR* 3.9 23.8 - - + +
212B ASN* 4.3 15.3 - - - +
213B LEU* 3.8 30.3 - - + +
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B VAL 3.3 4.8 + - - +
132B GLY* 3.3 11.4 + - - +
134B VAL* 1.4 75.5 - - - +
136B ALA* 1.3 54.2 + - - +
138B LEU* 3.9 5.2 - - - +
139B THR* 2.7 38.2 + - - +
213B LEU* 3.9 29.7 - - + +
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B GLY 3.0 13.6 + - - +
133B SER* 3.6 12.8 - - - +
134B VAL 3.3 0.2 - - - -
135B ALA* 1.3 76.8 - - - +
137B LEU* 1.4 59.6 + - - +
139B THR* 3.7 6.2 + - - -
140B VAL* 3.3 30.0 + - + +
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Residues in contact with LEU 137 (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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133B SER 3.0 15.2 + - - +
134B VAL* 3.2 10.1 + - + +
136B ALA* 1.4 74.1 - - - +
138B LEU* 1.3 59.0 + - - +
140B VAL* 3.4 7.0 + - - +
141B VAL* 3.0 45.1 + - + +
205B LEU* 5.5 6.5 - - + -
209B THR* 3.8 28.9 - - + +
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A 2CV 5.9 6.3 - - + -
134B VAL 3.0 16.3 + - - +
135B ALA* 3.9 6.3 - - - +
137B LEU* 1.3 76.3 - - - +
139B THR* 1.3 54.6 + - - +
141B VAL* 3.3 7.3 + - + +
142B PHE* 2.7 44.9 + - + +
175B MET* 5.1 4.7 - - + -
206B THR* 4.3 21.8 - - + -
209B THR* 4.0 24.2 - - + -
210B VAL* 3.8 34.1 - - + +
213B LEU* 4.6 17.0 - - + -
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Residues in contact with THR 139 (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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135B ALA* 2.7 24.2 + - - +
136B ALA* 3.9 7.1 - - - -
137B LEU 3.4 0.2 - - - -
138B LEU* 1.3 75.2 - - - +
140B VAL* 1.3 55.3 + - + +
142B PHE* 3.4 5.2 + - - +
143B TYR* 2.8 60.9 + - + +
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Residues in contact with VAL 140 (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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136B ALA* 3.3 19.1 + - + +
137B LEU* 3.6 6.5 - - - +
139B THR* 1.3 77.8 - - - +
141B VAL* 1.3 59.3 + - + +
143B TYR* 3.5 4.0 + - - +
144B ILE* 3.0 51.3 + - + +
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Residues in contact with VAL 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU* 3.0 33.8 + - + +
138B LEU* 3.7 8.7 - - + +
140B VAL* 1.3 76.5 - - + +
142B PHE* 1.3 59.1 + - - +
144B ILE* 4.2 3.9 - - - +
145B ALA* 3.0 33.5 + - + +
202B PHE* 5.5 0.4 - - + -
205B LEU* 3.7 34.1 - - + -
206B THR* 4.1 20.0 - - + -
303B 2CV 4.3 12.5 - - + +
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Residues in contact with PHE 142 (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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300A 2CV 3.7 34.8 - - + -
138B LEU* 2.7 28.5 + - + +
139B THR* 3.7 6.5 - - - +
141B VAL* 1.3 72.9 - - - +
143B TYR* 1.3 61.6 + + + +
145B ALA* 4.1 3.8 - - - +
146B ALA* 3.1 30.0 + - - +
168B LEU* 3.2 54.1 - - + -
171B LEU* 3.6 22.1 - - + +
172B PHE* 3.3 22.7 - - + -
175B MET* 4.4 15.0 - - - -
202B PHE* 4.1 18.2 - + - -
206B THR* 4.9 5.2 - - + -
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Residues in contact with TYR 143 (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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300A 2CV 5.9 5.8 - - + -
139B THR* 2.8 42.6 + - + +
140B VAL* 4.0 4.3 - - - +
142B PHE* 1.3 79.0 - + + +
144B ILE* 1.4 56.9 + - + +
146B ALA* 3.3 3.5 + - - +
147B VAL* 3.0 35.5 + - + +
164B LEU* 4.2 17.8 - - + +
168B LEU* 3.8 35.1 - - + +
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Residues in contact with ILE 144 (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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140B VAL* 3.0 40.4 + - + +
141B VAL* 4.2 4.0 - - - +
143B TYR* 1.4 72.4 - - + +
145B ALA* 1.4 60.8 + - - +
147B VAL* 3.2 11.7 + - + +
148B MET* 3.0 47.1 + - + +
303B 2CV 4.8 8.3 - - + -
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Residues in contact with ALA 145 (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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141B VAL 3.0 20.0 + - - +
142B PHE 4.1 3.4 - - - +
144B ILE* 1.4 74.9 - - - +
146B ALA* 1.4 57.2 + - - +
148B MET* 3.3 3.1 + - - +
149B ALA* 3.0 25.5 + - - +
171B LEU* 3.7 6.5 - - + -
198B PHE* 3.4 21.6 - - + -
202B PHE* 4.0 25.6 - - + -
303B 2CV 3.8 20.6 - - + +
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Residues in contact with ALA 146 (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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142B PHE 3.1 20.2 + - - +
143B TYR 3.6 3.4 - - - +
145B ALA* 1.4 72.5 - - - +
147B VAL* 1.3 58.0 + - - +
149B ALA* 4.6 0.2 - - - -
150B THR* 2.7 33.6 + - - -
164B LEU* 3.6 7.3 - - + +
167B SER* 3.4 4.7 - - - -
168B LEU* 3.4 40.6 - - + +
171B LEU* 3.6 13.9 - - + +
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Residues in contact with VAL 147 (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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143B TYR* 3.0 22.0 + - + +
144B ILE* 3.4 12.8 - - + +
146B ALA* 1.3 74.5 - - - +
148B MET* 1.4 66.8 + - + +
150B THR* 3.3 8.7 + - - -
151B ASN* 3.2 22.2 + - + +
164B LEU* 3.8 19.3 - - + -
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Residues in contact with MET 148 (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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144B ILE* 3.0 31.0 + - + +
145B ALA* 3.3 6.7 + - - +
147B VAL* 1.4 78.0 - - + +
149B ALA* 1.4 50.2 - - - +
151B ASN* 3.3 7.3 + - - +
152B LEU* 2.8 50.0 + - + +
198B PHE* 4.0 19.3 - - + -
303B 2CV 4.6 40.4 - - + +
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Residues in contact with ALA 149 (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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145B ALA 3.0 17.4 + - - +
146B ALA 4.2 3.8 - - - +
147B VAL 3.4 0.2 - - - -
148B MET* 1.4 70.6 - - - +
150B THR* 1.4 58.7 - - - +
152B LEU* 4.7 0.2 - - - -
153B TYR* 2.8 46.7 + - + -
154B GLY 3.6 2.8 + - - -
161B PHE* 3.5 33.8 - - + +
167B SER* 4.3 0.7 - - - +
171B LEU* 4.4 5.4 - - + -
198B PHE* 4.0 14.8 - - + -
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Residues in contact with THR 150 (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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146B ALA 2.7 18.9 + - - -
147B VAL* 3.3 11.2 + - - -
149B ALA* 1.4 74.6 - - - +
151B ASN* 1.3 59.2 + - - +
154B GLY* 3.1 24.9 + - - -
161B PHE 3.4 17.5 - - - +
162B GLY 4.7 1.8 - - - +
163B ASP* 3.3 26.1 + - - +
164B LEU* 3.7 7.2 - - + +
167B SER* 2.8 13.5 + - - -
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Residues in contact with ASN 151 (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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147B VAL* 3.2 10.9 + - + +
148B MET* 3.4 10.9 - - - +
150B THR* 1.3 81.8 - - - +
152B LEU* 1.3 69.4 + - - +
154B GLY 4.5 1.0 + - - -
155B ALA* 5.5 1.4 + - - +
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Residues in contact with LEU 152 (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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148B MET* 2.8 43.6 + - + +
149B ALA 3.9 1.6 - - - +
151B ASN* 1.3 83.0 - - - +
153B TYR* 1.4 93.3 + - + +
154B GLY 3.7 0.2 - - - -
155B ALA* 5.3 1.2 + - - +
156B THR* 4.4 1.0 + - - +
192B HIS* 3.9 14.0 + - - +
198B PHE* 4.6 8.7 - - + -
303B 2CV 4.1 37.9 - - + +
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Residues in contact with TYR 153 (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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149B ALA* 2.8 33.2 + - + -
152B LEU* 1.4 97.2 - - + +
154B GLY* 1.3 55.9 + - - +
155B ALA 3.3 2.9 - - - -
156B THR* 3.7 7.0 - - - -
157B PHE* 2.9 45.0 + - + +
161B PHE* 3.8 19.7 - + + -
188B VAL* 3.8 13.0 - - + -
192B HIS* 3.6 24.2 - + - -
195B ALA* 3.9 3.8 - - + -
198B PHE* 3.3 32.4 - + - +
199B PHE* 3.7 31.6 - + - -
303B 2CV 3.4 25.1 + - - -
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Residues in contact with GLY 154 (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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149B ALA 3.6 1.4 + - - -
150B THR* 3.1 17.2 + - - -
151B ASN 4.5 0.4 + - - -
152B LEU 3.7 1.0 - - - -
153B TYR* 1.3 78.5 - - - +
155B ALA* 1.3 56.4 + - - +
158B PRO* 3.3 28.9 - - - +
161B PHE 3.2 26.5 - - - -
162B GLY* 3.8 6.5 - - - -
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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