Contacts of the helix formed by residues 150 - 160 (chain A) in PDB entry 2PCB
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 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A LYS* 1.3 82.5 - - - +
151A ALA* 1.4 55.4 + - - +
152A GLY* 2.7 31.6 + - - -
153A TYR* 2.8 27.7 + - - +
154A VAL* 2.8 12.6 + - - +
237A SER* 3.5 7.6 - - - -
240A GLN* 4.8 10.5 - - - +
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Residues in contact with ALA 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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150A ASP* 1.4 73.0 - - - +
152A GLY* 1.3 52.6 + - - +
154A VAL* 3.7 2.7 - - - -
155A ARG* 2.8 32.9 + - - +
237A SER* 3.1 27.1 - - - +
240A GLN* 5.1 5.7 + - + +
241A ASP* 3.5 37.7 - - + +
244A TYR* 3.4 15.7 - - + -
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Residues in contact with GLY 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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150A ASP* 2.7 19.7 + - - -
151A ALA* 1.3 70.9 - - - +
153A TYR* 1.3 61.1 - - - -
155A ARG* 3.0 10.9 + - - +
156A THR* 2.9 33.9 + - - -
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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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144A LEU 4.4 2.1 + - - -
145A PRO* 3.4 18.9 - - + +
146A ASP* 3.1 55.3 + - - -
149A LYS* 3.4 43.5 - - + -
150A ASP* 2.8 18.5 + - - +
152A GLY* 1.3 71.2 - - - -
154A VAL* 1.3 69.6 + - + +
156A THR* 3.9 6.9 - - + -
157A PHE* 2.7 44.2 + + + +
234A THR* 4.7 0.4 - - + -
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Residues in contact with VAL 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 ASP 2.8 18.0 + - - +
151A ALA* 3.8 9.4 - - - +
153A TYR* 1.3 87.0 - - + +
155A ARG* 1.3 63.3 - - - +
157A PHE* 3.3 8.2 + - - +
158A PHE* 3.3 27.2 + - + -
168A VAL* 4.2 16.4 - - + -
172A MET* 4.6 7.6 - - + -
234A THR* 3.8 39.7 - - + +
237A SER* 4.8 0.7 - - - -
238A LEU* 4.7 6.1 - - + -
244A TYR* 3.8 14.3 + - + +
295A HEM 4.7 5.6 - - + -
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Residues in contact with ARG 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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151A ALA 2.8 24.5 + - - +
152A GLY* 3.4 11.0 - - - +
154A VAL* 1.3 69.5 - - - +
156A THR* 1.3 69.8 + - - +
157A PHE 3.5 0.2 + - - -
158A PHE* 3.5 5.1 + - - +
159A GLN* 3.4 31.7 + - - +
163A MET 4.9 1.9 - - - +
165A ASP* 2.9 31.7 + - - +
168A VAL* 5.9 0.4 - - - +
241A ASP* 2.4 47.4 + - - -
243A LYS* 2.9 33.5 - - - +
244A TYR* 2.7 27.7 + - - +
31C ARG* 6.1 1.3 - - - +
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Residues in contact with THR 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 GLY 2.9 15.7 + - - -
153A TYR* 3.9 7.0 - - + -
155A ARG* 1.3 83.6 - - - +
157A PHE* 1.3 64.1 + - - +
159A GLN* 3.1 36.1 + - + +
160A ARG* 4.1 2.4 + - - +
293C GLY 5.6 2.3 + - - -
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Residues in contact with PHE 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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51A TRP* 4.3 12.3 - + - -
55A GLY 4.2 3.4 - - - -
143A ARG 2.9 31.0 - - - -
144A LEU* 4.0 2.0 - - - -
145A PRO* 3.6 42.8 - - + -
153A TYR* 2.7 41.0 + + + +
154A VAL* 3.3 7.2 + - - +
156A THR* 1.3 73.4 - - - +
158A PHE* 1.3 84.9 + + + +
159A GLN 3.1 5.2 + - - -
160A ARG* 3.3 41.7 + - + +
161A LEU* 4.6 10.2 + - + +
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Residues in contact with PHE 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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51A TRP* 3.9 35.7 - + - -
154A VAL* 3.3 19.7 + - + +
155A ARG 3.5 2.4 + - - +
156A THR 3.3 0.6 - - - -
157A PHE* 1.3 90.8 - + + +
159A GLN* 1.3 63.1 + - - +
160A ARG 3.3 0.7 - - - -
161A LEU* 3.5 21.4 + - + +
163A MET* 2.8 53.6 + - + +
168A VAL* 3.7 31.4 - - + -
171A LEU* 4.4 16.6 - - + -
172A MET* 3.8 27.6 - - + -
269A LEU* 5.8 0.2 - - + -
295A HEM 3.9 17.7 - - + -
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Residues in contact with GLN 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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59A LYS* 3.1 25.2 + - - +
155A ARG* 3.4 22.5 + - - +
156A THR* 3.1 40.8 + - + +
158A PHE* 1.3 77.0 - - - +
160A ARG* 1.3 55.9 + - - +
161A LEU 3.0 7.4 + - - -
162A ASN* 3.0 12.9 + - - +
163A MET 4.3 8.9 - - - +
31C ARG* 3.5 36.7 + - - +
290C GLU* 6.3 3.6 - - + -
293C GLY 5.5 3.0 + - - -
294C LEU* 4.2 16.8 + - - -
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Residues in contact with ARG 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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55A GLY 3.0 25.7 + - - -
56A THR 3.9 2.2 - - - -
57A TRP* 2.6 28.2 + - - +
58A ASP* 3.2 37.7 - - - +
59A LYS* 3.2 28.4 + - - +
60A HIS* 3.9 14.1 - - + -
143A ARG* 2.9 40.6 + - - +
156A THR 4.1 2.8 + - - +
157A PHE* 3.3 28.2 + - + +
158A PHE 3.3 1.4 - - - -
159A GLN* 1.3 73.5 - - - +
161A LEU* 1.3 67.7 + - + +
162A ASN 3.7 0.9 - - - -
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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