Contacts of the helix formed by residues 148 - 161 (chain A) in PDB entry 3PII
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 CYS 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A CYS* 3.8 1.6 - - - -
61A HIS* 4.1 2.2 - - + -
62A GLU* 3.4 15.7 - - + +
144A ALA 4.3 0.2 + - - -
145A PRO 3.1 2.6 + - - -
146A ILE 3.2 0.2 - - - -
147A PHE* 1.3 81.1 - - - +
149A ALA* 1.3 63.3 + - - +
150A GLY 3.4 0.4 - - - -
151A VAL* 3.5 2.1 - - - +
152A THR* 2.8 39.6 + - - -
176A PHE* 4.6 8.5 - - - -
286A VAL* 5.1 0.7 - - - -
331A ARG* 3.8 4.9 - - - -
340A ZN 2.5 35.7 - - - -
600A BMD 2.8 33.2 - - - +
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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 PRO* 2.9 15.6 + - + +
148A CYS* 1.3 76.3 - - - +
150A GLY* 1.3 65.5 + - - +
153A THR* 3.0 24.8 + - - +
175A GLY 4.6 9.9 - - - +
176A PHE* 3.3 30.1 - - + -
179A VAL* 3.8 10.6 - - + +
331A ARG* 3.6 24.7 - - + +
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Residues in contact with GLY 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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145A PRO 3.2 7.9 + - - -
146A ILE* 3.3 22.4 - - - +
149A ALA* 1.3 76.0 - - - +
151A VAL* 1.4 51.0 + - - +
153A THR* 2.9 9.5 - - - +
154A TYR* 2.8 34.3 + - - +
179A VAL* 4.3 3.7 - - - +
183A TYR* 3.7 21.3 - - - -
306A THR* 6.3 0.2 - - - +
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Residues in contact with VAL 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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146A ILE 3.0 9.0 + - - +
147A PHE 3.5 21.8 - - - +
148A CYS* 3.5 10.3 - - - +
150A GLY* 1.4 65.6 - - - +
152A THR* 1.3 71.1 + - - +
153A THR 2.9 2.5 - - - -
154A TYR* 4.2 6.7 - - + -
155A LYS* 2.7 28.1 + - - +
286A VAL* 4.0 21.3 - - + +
287A GLY* 4.8 3.1 - - - +
288A THR 4.8 0.9 - - - +
291A ASP* 3.8 13.2 - - + +
292A LEU* 3.3 50.5 - - + +
295A ALA* 3.9 3.7 - - + +
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Residues in contact with THR 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 CYS* 2.8 33.1 + - - -
149A ALA 4.1 3.1 - - - -
151A VAL* 1.3 72.6 - - - +
153A THR* 1.3 57.6 + - - +
155A LYS* 3.9 1.6 - - - +
156A ALA* 3.0 27.7 + - - +
176A PHE* 4.4 13.0 - - + -
260A VAL* 3.6 35.1 - - + +
284A SER* 4.6 1.9 + - - -
285A ILE* 3.9 18.5 - - + +
286A VAL* 3.0 33.3 + - - +
600A BMD 5.4 0.2 - - - -
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Residues in contact with THR 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 3.0 14.3 + - - +
150A GLY 2.9 16.6 - - - +
151A VAL 2.9 0.4 - - - -
152A THR* 1.3 81.1 - - - +
154A TYR* 1.3 64.4 + - - +
156A ALA* 3.3 8.1 + - - +
157A LEU* 3.0 26.6 + - - +
176A PHE* 3.7 15.1 + - - +
179A VAL* 3.6 13.0 - - + -
180A ALA* 3.2 29.3 - - - +
183A TYR* 3.5 22.2 - - + -
235A VAL* 5.2 4.4 - - - +
237A THR* 5.1 2.8 - - - +
260A VAL* 5.3 2.6 - - - +
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Residues in contact with TYR 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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150A GLY 2.8 16.0 + - - +
151A VAL* 3.8 2.2 - - - +
153A THR* 1.3 78.6 - - - +
155A LYS* 1.3 57.2 + - - +
157A LEU* 2.7 27.5 + - - +
158A LYS* 3.0 34.2 + - + +
183A TYR* 3.7 35.7 - + + -
187A MET* 3.7 21.1 - - + -
291A ASP* 3.4 27.6 - - + -
294A GLU* 2.3 43.4 + - + +
295A ALA* 3.7 9.6 - - + -
298A PHE* 3.7 24.1 - + - -
163B LYS* 4.8 3.5 - - - +
164B PRO* 4.4 8.2 + - + -
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Residues in contact with LYS 155 (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 THR* 5.9 5.6 - - - +
151A VAL 2.7 21.1 + - - +
152A THR 3.9 0.7 - - - +
154A TYR* 1.3 74.9 - - - +
156A ALA* 1.3 66.3 + - - +
158A LYS* 3.1 14.7 + - + +
159A VAL* 2.9 38.5 + - + +
284A SER* 4.1 8.3 - - - +
286A VAL 3.3 20.4 - - - +
287A GLY* 4.1 3.4 - - - -
288A THR* 4.8 3.8 + - - -
291A ASP* 2.6 47.7 + - + +
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Residues in contact with ALA 156 (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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152A THR 3.0 21.5 + - - +
153A THR* 3.4 9.4 - - - +
154A TYR 3.2 0.2 - - - -
155A LYS* 1.3 74.1 - - - +
157A LEU* 1.3 63.0 + - - +
159A VAL* 3.1 7.5 + - - +
160A THR* 3.1 25.4 + - - +
235A VAL* 4.2 13.9 - - + -
258A VAL* 4.0 12.1 - - + +
260A VAL* 3.6 22.9 - - + -
284A SER* 4.1 9.8 + - - -
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Residues in contact with LEU 157 (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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153A THR 3.0 17.2 + - - +
154A TYR 2.7 11.3 + - - +
156A ALA* 1.3 75.3 - - - +
158A LYS* 1.3 62.6 + - - +
160A THR* 3.0 26.8 + - + -
161A GLY 3.8 0.5 + - - -
162A ALA* 4.6 4.3 + - - +
168A VAL* 4.1 15.7 - - + -
170A ILE* 4.8 3.4 - - + -
180A ALA* 3.7 12.8 - - + +
183A TYR* 3.6 17.7 - - + -
184A ALA* 3.5 42.6 - - + +
187A MET* 3.6 17.5 - - + +
189A LEU* 4.5 8.3 - - + +
235A VAL* 4.0 21.3 - - + -
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Residues in contact with LYS 158 (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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154A TYR* 3.0 37.1 + - + +
155A LYS* 3.6 16.2 - - + +
157A LEU* 1.3 75.0 - - - +
159A VAL* 1.3 58.9 + - + +
161A GLY* 3.0 21.1 + - - -
162A ALA 6.1 0.4 - - - -
187A MET* 3.6 18.5 - - + +
291A ASP* 2.8 30.0 + - - -
294A GLU* 2.9 28.2 + - - -
163B LYS* 4.7 15.8 - - + +
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Residues in contact with VAL 159 (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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155A LYS* 2.9 43.5 + - + +
156A ALA* 3.1 10.5 + - - +
158A LYS* 1.3 72.2 - - - +
160A THR* 1.3 61.6 + - - +
161A GLY* 2.8 7.9 + - - -
258A VAL* 3.9 13.9 - - + -
282A ILE* 3.8 41.4 - - + +
284A SER* 4.1 11.0 - - - +
280D LYS* 6.1 0.2 - - + -
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Residues in contact with THR 160 (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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156A ALA 3.1 18.3 + - - +
157A LEU* 3.0 22.4 + - + +
159A VAL* 1.3 74.5 - - - +
161A GLY* 1.3 57.3 + - - +
162A ALA* 2.9 28.9 + - - +
168A VAL* 4.4 3.0 - - + +
232A HIS 5.4 0.5 - - - +
233A ALA* 3.5 26.6 - - + +
234A ALA 5.1 0.7 - - - +
235A VAL* 4.0 15.0 - - + -
256A ALA* 4.1 15.8 - - - +
258A VAL* 3.8 19.5 - - + -
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Residues in contact with GLY 161 (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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158A LYS 3.0 15.0 + - - -
159A VAL 2.8 6.8 - - - -
160A THR* 1.3 79.3 + - - +
162A ALA* 1.3 64.3 + - - +
163A LYS* 3.7 4.9 + - - +
166A GLU* 4.4 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