Contacts of the helix formed by residues 145 - 155 (chain B) in PDB entry 2P1Q
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 THR 145 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B SER* 1.3 71.0 - - - +
146B ASP* 1.3 61.3 + - - +
148B LEU* 3.3 14.9 + - + -
149B ALA* 2.8 24.8 + - - +
168B VAL* 4.5 4.0 - - + -
169B ASP 3.2 6.7 + - - +
170B ASP* 4.0 10.3 - - - +
171B VAL* 3.3 12.5 + - - +
172B SER* 3.1 42.0 + - - +
175B TRP* 3.3 30.9 - - + +
194B LEU* 4.8 1.6 - - + -
196B SER* 4.0 13.7 - - - +
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Residues in contact with ASP 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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119B ASP* 3.9 7.9 - - + +
123B GLU* 5.0 3.3 - - - +
144B SER* 3.0 13.5 + - - +
145B THR* 1.3 79.8 + - - +
147B GLY* 1.3 60.8 + - - +
149B ALA* 3.2 9.9 + - - +
150B ALA* 3.2 19.9 + - - +
171B VAL* 4.3 23.2 - - - +
172B SER* 5.8 1.7 - - - -
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Residues in contact with GLY 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ASP* 3.1 29.6 + - - -
122B LEU* 3.7 21.7 - - - +
123B GLU* 5.1 1.3 - - - -
144B SER 3.1 6.5 + - - -
146B ASP* 1.3 72.3 - - - +
148B LEU* 1.3 65.4 + - - +
150B ALA* 3.2 17.1 + - - +
151B ILE* 3.3 17.0 + - - +
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Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LEU* 4.1 6.5 - - + +
135B LEU* 5.5 0.7 - - + -
137B LEU* 5.2 1.8 - - + -
143B PHE* 4.1 16.8 - - + -
144B SER 3.3 10.4 + - - +
145B THR* 3.3 19.5 + - + +
147B GLY* 1.3 77.9 - - - +
149B ALA* 1.3 56.5 + - - +
151B ILE* 3.3 9.6 + - + +
152B ALA* 3.0 28.4 + - - +
161B LEU* 4.6 15.3 - - + +
163B LEU* 3.8 38.6 - - + -
168B VAL* 4.5 3.8 - - + -
175B TRP* 3.8 38.1 - - + +
194B LEU* 4.1 11.7 - - + -
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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 THR 2.8 16.3 + - - +
146B ASP* 3.2 15.6 + - - +
148B LEU* 1.3 71.8 - - - +
150B ALA* 1.3 57.1 + - - +
152B ALA* 3.5 1.2 + - - +
153B ALA* 2.9 32.2 + - - +
175B TRP* 3.7 22.4 - - + +
178B HIS* 3.7 25.9 - - + +
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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
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122B LEU 4.8 0.2 - - - +
123B GLU* 3.8 44.0 - - + +
126B ALA* 3.7 6.1 - - + +
146B ASP 3.2 6.2 + - - +
147B GLY 3.2 10.6 + - - +
149B ALA* 1.3 75.7 - - - +
151B ILE* 1.3 65.0 + - - +
153B ALA* 3.9 3.3 - - - +
154B THR* 3.1 32.0 + - - +
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Residues in contact with ILE 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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122B LEU* 3.6 41.7 - - + +
125B ILE* 4.0 21.5 - - + -
126B ALA* 4.4 1.3 - - - +
132B PHE* 4.8 0.9 - - + -
135B LEU* 4.4 10.8 - - + -
147B GLY 3.3 13.2 + - - +
148B LEU* 3.3 11.6 + - + +
150B ALA* 1.3 73.4 - - - +
152B ALA* 1.3 61.3 + - - +
155B CYS* 2.8 52.6 + - - +
158B LEU* 3.9 29.8 - - + -
161B LEU* 4.6 15.3 - - + -
179B PHE* 5.0 0.7 - - - -
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Residues in contact with ALA 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 LEU 3.0 16.2 + - - +
149B ALA 3.7 4.3 - - - +
151B ILE* 1.3 77.4 - - - +
153B ALA* 1.3 63.4 + - - +
154B THR 3.4 0.3 + - - -
155B CYS 4.4 4.3 + - - +
175B TRP* 3.8 21.5 - - + +
178B HIS* 3.9 2.5 - - + -
179B PHE* 3.5 61.6 - - + +
180B PRO* 3.6 5.4 - - - +
183B TYR* 5.7 0.2 - - - -
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Residues in contact with ALA 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 2.9 19.7 + - - +
150B ALA* 3.9 6.1 - - - +
151B ILE 3.3 0.2 - - - -
152B ALA* 1.3 77.8 - - - +
154B THR* 1.3 63.1 + - - +
178B HIS* 3.4 27.1 + - + +
180B PRO* 4.2 14.1 - - - +
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Residues in contact with THR 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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126B ALA* 3.4 33.8 - - + +
127B LYS* 4.5 5.2 - - + +
150B ALA* 3.1 19.1 + - - -
153B ALA* 1.3 85.2 - - - +
155B CYS* 1.3 61.7 + - - +
156B ARG* 2.9 17.2 + - - +
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Residues in contact with CYS 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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126B ALA* 3.8 29.6 - - - -
129B PHE 5.4 1.6 - - - -
130B LYS 5.9 1.8 - - - -
132B PHE* 3.9 31.9 - - + +
151B ILE* 2.8 33.0 + - - +
152B ALA 4.9 3.9 - - - +
153B ALA 3.9 0.2 - - - -
154B THR* 1.3 71.7 - - - +
156B ARG* 1.3 64.0 + - - +
157B ASN 3.2 2.9 - - - -
158B LEU* 3.2 35.2 + - + +
179B PHE* 5.3 0.5 - - - -
183B TYR* 3.9 7.1 - - - -
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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