Contacts of the helix formed by residues 150 - 160 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149C LYS* 1.3 83.4 - - - +
151C ALA* 1.4 66.6 + - - +
152C GLY* 3.2 17.2 + - - -
153C TYR* 3.1 15.8 + - - +
154C VAL* 3.0 21.7 + - - +
234C THR* 4.6 2.0 - - - +
237C SER* 3.9 15.5 - - - -
240C GLN* 5.0 5.6 - - - +
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Residues in contact with ALA 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C ASP* 1.4 72.6 + - - +
152C GLY* 1.3 49.4 + - - +
154C VAL* 3.2 3.5 + - - +
155C ARG* 2.5 40.7 + - - +
237C SER* 3.3 18.4 - - - -
240C GLN* 5.6 1.1 - - + -
241C ASP* 3.6 39.0 - - + +
244C TYR* 3.8 16.1 + - + -
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Residues in contact with GLY 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C ASP* 3.2 9.8 + - - -
151C ALA* 1.3 69.1 - - - +
153C TYR* 1.3 58.3 + - - +
155C ARG* 2.8 10.6 + - - +
156C THR* 2.7 41.0 + - - -
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Residues in contact with TYR 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C LEU 4.1 2.1 + - - -
145C PRO* 2.9 33.9 - - + +
146C ASP* 2.9 40.7 + - + -
149C LYS* 3.4 42.4 - - + -
150C ASP* 3.1 18.7 + - - +
152C GLY* 1.3 73.1 - - - +
154C VAL* 1.3 68.6 + - + +
156C THR* 4.1 5.1 - - + -
157C PHE* 2.8 39.3 + + + +
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Residues in contact with VAL 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C ASP 3.0 17.8 + - - +
151C ALA* 3.7 5.8 - - - +
153C TYR* 1.3 81.2 - - + +
155C ARG* 1.3 72.4 + - - +
157C PHE* 4.5 2.7 - - - -
158C PHE* 3.3 34.2 + - + +
168C VAL* 4.4 7.9 - - + -
172C MET* 4.4 10.8 - - + -
234C THR* 3.8 39.9 - - + +
237C SER* 5.1 0.7 - - - +
238C LEU* 5.1 3.6 - - + -
244C TYR* 3.9 19.5 + - + +
295C HEM 4.1 10.1 - - + -
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Residues in contact with ARG 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C ALA 2.5 28.1 + - - +
152C GLY* 3.5 6.2 - - - +
154C VAL* 1.3 77.5 - - - +
156C THR* 1.3 71.2 + - - +
158C PHE* 3.0 11.3 + - - +
159C GLN* 3.2 20.8 + - + +
163C MET 5.6 0.3 - - - +
165C ASP* 3.0 38.3 + - - +
168C VAL* 5.9 0.7 - - - -
241C ASP* 3.5 35.1 + - - -
243C LYS* 4.3 7.1 - - - +
244C TYR* 3.1 24.2 + - - +
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Residues in contact with THR 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C GLY* 2.7 25.4 + - - -
153C TYR* 4.1 4.7 - - + +
155C ARG* 1.3 79.8 - - - +
157C PHE* 1.3 65.2 + - - +
159C GLN* 3.2 30.8 + - + +
160C ARG* 3.8 3.3 + - - +
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Residues in contact with PHE 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C TRP* 4.1 8.3 - + - -
55C GLY 3.9 9.2 - - - -
142C GLY 5.5 0.4 - - - -
143C ARG 2.5 31.0 - - - -
144C LEU 3.8 1.1 - - - -
145C PRO* 3.4 43.3 - - + -
153C TYR* 2.8 42.7 + + + +
154C VAL* 4.1 4.5 - - - +
155C ARG 3.1 0.4 + - - -
156C THR* 1.3 75.0 - - - +
158C PHE* 1.3 80.5 + + - +
160C ARG* 3.0 43.7 + - - +
161C LEU* 3.9 23.1 + - + +
295C HEM 6.4 0.2 - - + -
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Residues in contact with PHE 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C TRP* 3.8 36.1 - + - -
154C VAL* 3.3 27.3 + - + +
155C ARG 3.0 3.9 + - - +
157C PHE* 1.3 92.6 - + + +
159C GLN* 1.3 56.4 + - - +
161C LEU* 2.9 31.6 + - + +
162C ASN 3.0 7.4 + - - -
163C MET* 3.4 23.2 + - + +
168C VAL* 3.7 34.8 - - + -
171C LEU* 4.5 15.9 - - + -
172C MET* 4.0 9.0 - - + -
295C HEM 3.6 40.6 - - + -
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Residues in contact with GLN 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C LYS* 2.9 29.7 + - - +
155C ARG* 3.2 18.1 + - + +
156C THR* 3.3 27.8 - - + +
157C PHE 3.1 2.0 - - - -
158C PHE* 1.3 76.8 - - - +
160C ARG* 1.3 55.9 + - - +
161C LEU 3.0 0.2 - - - -
162C ASN* 2.8 17.0 + - - +
163C MET 4.4 10.0 + - - +
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Residues in contact with ARG 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C GLY 2.7 27.4 + - - -
56C THR 3.1 15.1 + - - -
57C TRP* 2.9 23.7 + - - +
58C ASP* 3.8 25.5 - - - +
59C LYS* 3.2 31.7 + - - +
60C HIS* 5.2 7.2 - - + +
142C GLY 4.7 0.6 + - - -
143C ARG* 2.5 42.9 + - - +
156C THR 3.8 2.2 + - - +
157C PHE* 3.0 29.6 + - - +
159C GLN* 1.3 78.5 - - - +
161C LEU* 1.3 67.5 + - - +
162C ASN 3.2 0.7 - - - -
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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