Contacts of the helix formed by residues 144 - 161 (chain B) in PDB entry 3P3B
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 ASP 144 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B LEU* 3.4 2.7 - - - +
143B ALA* 1.3 79.5 - - + +
145B GLU* 1.3 68.5 + - - +
146B ARG* 3.3 24.3 + - - +
147B ALA* 3.1 29.1 + - + +
148B ALA* 3.1 19.9 + - - +
186B ARG* 4.2 1.3 - - - -
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Residues in contact with GLU 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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143B ALA 3.7 4.4 + - - -
144B ASP* 1.3 72.2 + - - +
146B ARG* 1.3 73.6 + - - +
148B ALA* 2.8 7.1 + - - +
149B VAL* 2.6 39.7 + - + +
185B LYS* 2.9 34.4 + - - +
186B ARG* 4.0 26.5 + - + +
189B ALA* 3.6 30.8 - - + +
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Residues in contact with ARG 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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144B ASP* 3.3 19.9 + - - +
145B GLU* 1.3 94.9 + - - +
147B ALA* 1.3 57.8 + - - +
149B VAL* 3.8 11.1 - - - +
150B ALA* 2.8 32.2 + - - +
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Residues in contact with ALA 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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142B LEU* 3.7 22.7 - - + +
144B ASP* 3.1 26.8 + - + +
145B GLU 3.2 0.4 - - - -
146B ARG* 1.3 78.6 - - - +
148B ALA* 1.3 57.2 + - - +
150B ALA* 3.8 5.0 - - - +
151B LEU* 2.9 30.3 + - - +
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Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ASP* 3.7 13.9 - - + +
142B LEU* 3.6 13.6 - - + +
144B ASP 3.1 9.2 + - - +
145B GLU 2.8 8.9 + - - +
147B ALA* 1.3 75.5 - - - +
149B VAL* 1.3 63.7 + - - +
151B LEU* 3.4 2.3 + - - +
152B MET* 3.0 28.8 + - - +
186B ARG* 3.4 40.4 - - - +
190B ILE* 3.8 2.5 - - + -
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Residues in contact with VAL 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 GLU* 2.6 26.1 + - + +
146B ARG* 3.8 11.4 - - - +
148B ALA* 1.3 73.2 - - - +
150B ALA* 1.3 52.7 + - - +
152B MET* 3.1 1.4 + - - +
153B GLN* 2.7 68.9 + - + +
186B ARG* 6.1 0.2 - - - -
189B ALA* 3.8 35.7 - - + +
190B ILE* 3.9 11.0 - - + +
193B GLY* 4.0 10.3 - - - -
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Residues in contact with ALA 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ARG 2.8 23.0 + - - +
147B ALA* 3.8 5.4 - - - +
149B VAL* 1.3 73.0 - - - +
151B LEU* 1.3 59.2 + - - +
153B GLN* 3.7 13.8 - - - +
154B GLU* 2.9 31.0 + - - +
157B MET* 5.8 0.3 - - - +
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Residues in contact with LEU 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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138B ASP* 3.4 27.6 - - + +
139B ASP* 4.3 0.7 - - - -
141B HIS* 3.6 20.2 - - + +
142B LEU* 3.6 12.1 - - + -
147B ALA 2.9 18.4 + - - +
148B ALA 3.6 5.4 - - - +
150B ALA* 1.3 77.1 - - - +
152B MET* 1.3 62.6 + - - +
154B GLU* 3.2 10.0 + - + +
155B GLU* 3.0 42.1 + - + +
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Residues in contact with MET 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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135B LEU* 3.9 25.5 - - + +
136B TYR 3.1 27.4 - - - +
138B ASP* 3.8 20.0 - - - +
139B ASP* 4.3 9.0 - - + +
148B ALA 3.0 20.2 + - - +
149B VAL* 3.9 1.8 - - - +
151B LEU* 1.3 74.0 - - - +
153B GLN* 1.3 67.2 + - - +
155B GLU* 3.2 26.8 + - - +
156B ALA* 2.9 23.6 + - - +
169B ILE* 5.5 1.3 - - + -
173B ARG* 4.5 2.0 - - - +
190B ILE* 3.7 39.5 - - + -
194B ILE* 3.7 10.1 - - + +
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Residues in contact with GLN 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 VAL* 2.7 40.1 + - + +
150B ALA* 3.7 12.5 - - - +
152B MET* 1.3 72.4 - - - +
154B GLU* 1.3 57.5 + - - +
156B ALA* 3.1 3.3 + - - +
157B MET* 2.8 43.0 + - + +
193B GLY* 3.0 39.7 + - - +
194B ILE* 4.2 6.0 - - + +
196B GLU* 4.2 10.7 + - - +
197B VAL* 3.3 25.8 - - + +
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Residues in contact with GLU 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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150B ALA 2.9 19.5 + - - +
151B LEU* 3.5 12.0 - - + +
153B GLN* 1.3 76.9 - - - +
155B GLU* 1.3 60.0 + - - +
157B MET* 3.4 19.5 + - - +
158B GLN* 2.9 63.1 + - - +
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Residues in contact with GLU 155 (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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28B ARG* 3.2 49.8 + - - +
29B SER 5.2 0.2 - - - +
132B ASP* 4.5 1.7 - - - +
135B LEU* 3.7 9.5 - - + +
138B ASP* 2.5 43.6 - - - +
151B LEU* 3.0 26.2 + - + +
152B MET* 3.2 24.6 + - - +
154B GLU* 1.3 80.4 - - - +
156B ALA* 1.3 59.2 + - - +
158B GLN* 3.2 24.5 + - - +
159B GLY* 3.3 5.7 + - - -
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Residues in contact with ALA 156 (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 LEU* 3.9 11.3 - - + +
152B MET 2.9 12.5 + - - +
153B GLN 3.5 7.4 - - - +
155B GLU* 1.3 73.4 - - - +
157B MET* 1.3 66.5 + - - +
159B GLY 2.9 12.3 + - - -
160B TYR* 2.9 10.4 + - - +
167B PHE* 3.5 25.3 - - + -
194B ILE* 3.9 28.0 - - + -
197B VAL* 4.3 10.3 - - + -
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Residues in contact with MET 157 (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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150B ALA 5.8 0.2 - - - +
153B GLN* 2.8 28.8 + - + +
154B GLU* 3.5 28.3 - - - +
156B ALA* 1.3 71.3 - - - +
158B GLN* 1.3 63.2 + - - +
160B TYR* 3.4 10.4 - - - +
161B ALA* 2.9 24.4 + - - +
197B VAL* 3.4 34.4 - - + +
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Residues in contact with GLN 158 (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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28B ARG* 2.9 38.0 + - - +
154B GLU* 2.9 47.2 + - - +
155B GLU* 3.2 9.0 - - - +
156B ALA 3.1 0.4 - - - -
157B MET* 1.3 77.7 - - - +
159B GLY* 1.3 60.8 + - - +
161B ALA* 3.5 13.6 + - - +
162B LYS* 3.6 24.4 + - - +
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Residues in contact with GLY 159 (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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28B ARG* 5.5 0.6 - - - +
132B ASP* 3.7 18.6 - - - -
155B GLU 3.3 4.6 + - - -
156B ALA 2.9 7.3 + - - -
158B GLN* 1.3 76.0 - - - +
160B TYR* 1.3 64.8 + - - +
162B LYS* 2.8 22.6 + - - -
163B GLY 3.2 0.5 + - - -
164B GLN* 3.1 28.9 + - - +
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Residues in contact with TYR 160 (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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156B ALA 2.9 11.2 + - - +
157B MET* 3.2 14.6 + - - +
159B GLY* 1.3 75.5 - - - +
161B ALA* 1.3 59.6 + - - +
163B GLY* 2.9 16.3 + - - -
164B GLN 3.3 20.6 + - - -
165B ARG* 2.9 56.3 + - - -
167B PHE* 4.1 11.7 - + + -
197B VAL* 4.9 10.3 - - + -
198B ALA* 3.9 21.7 + - - -
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Residues in contact with ALA 161 (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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157B MET 2.9 16.2 + - - +
158B GLN* 3.6 10.1 - - - +
159B GLY 3.1 0.2 - - - -
160B TYR* 1.3 78.4 - - - +
162B LYS* 1.3 61.0 + - + +
163B GLY 3.3 1.1 + - - -
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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