Contacts of the helix formed by residues 146 - 158 (chain C) in PDB entry 4PE5
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 HIS 146 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142C PRO* 4.4 7.6 - - + -
143C PRO* 3.0 44.0 + - + +
145C SER* 1.3 78.6 + - - +
147C GLN* 1.3 61.5 + - - +
148C SER 2.9 5.8 - - - -
149C SER* 2.9 24.0 + - - +
150C VAL 4.1 0.7 + - - -
179C ARG* 3.1 35.1 + - - +
341C ASN* 3.9 21.7 + - - -
345C ASP* 4.0 9.1 + - - +
346C ARG 4.9 6.3 - - - -
351C TYR* 4.0 16.7 + - - +
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Residues in contact with GLN 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C ARG* 4.1 13.2 + - - +
143C PRO 4.3 0.4 + - - -
144C TYR* 2.8 34.1 + - - +
146C HIS* 1.3 78.8 - - - +
148C SER* 1.3 57.1 + - - +
150C VAL* 2.9 22.5 + - - +
151C TRP* 2.9 29.3 + - + -
250C GLY* 3.4 16.6 - - - -
251C GLU* 2.7 38.7 + - - +
252C ARG 5.4 0.2 - - - +
253C GLU* 4.9 3.0 + - - -
269C LEU* 3.9 22.8 - - + +
351C TYR* 3.9 20.8 + - + +
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Residues in contact with SER 148 (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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145C SER 3.0 16.3 + - - -
147C GLN* 1.3 78.4 - - - +
149C SER* 1.3 50.9 + - - +
151C TRP* 3.0 26.7 + - - +
152C PHE* 2.5 35.3 + - - +
176C ALA* 4.5 4.0 - - - -
179C ARG* 4.0 8.5 - - - -
180C LEU* 3.1 33.7 - - - +
183C LEU* 3.2 13.3 - - - +
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Residues in contact with SER 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C HIS* 2.9 13.0 + - - +
148C SER* 1.3 76.8 - - - +
150C VAL* 1.3 59.0 + - - +
152C PHE* 3.1 7.4 + - - +
153C GLU* 2.8 28.5 + - - +
179C ARG* 2.6 35.3 + - - -
183C LEU* 3.7 14.4 - - - +
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Residues in contact with VAL 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C HIS 4.7 1.3 - - - +
147C GLN 2.9 7.8 + - - +
149C SER* 1.3 75.0 - - - +
151C TRP* 1.3 57.8 + - - +
153C GLU* 2.9 6.6 + - + +
154C MET* 2.7 48.4 + - + +
269C LEU* 3.8 24.7 - - + -
351C TYR* 3.4 36.3 - - + -
353C ILE* 4.6 4.7 - - + -
367C TYR* 3.8 27.6 - - + -
372C VAL* 5.2 4.5 - - + -
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Residues in contact with TRP 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C TYR 5.7 0.4 - - - -
145C SER* 5.5 1.1 - - - -
147C GLN* 2.9 28.0 + - + -
148C SER* 3.2 30.3 - - - +
150C VAL* 1.3 76.7 - - - +
152C PHE* 1.3 51.1 + - - +
154C MET* 2.9 5.7 + - + +
155C MET* 2.7 39.7 + - - +
165C LEU* 5.2 4.0 - - + -
176C ALA* 4.8 15.3 - - + -
180C LEU* 5.0 7.6 - - + -
220C ILE* 3.5 32.3 - - + -
221C LEU 3.7 17.3 - - - -
222C SER* 4.4 11.4 - - - -
248C LEU* 3.5 35.4 - - + +
249C VAL* 2.8 42.3 + - - -
250C GLY* 3.4 10.5 - - - -
253C GLU* 5.2 1.1 - - - -
269C LEU* 3.8 13.3 - - + +
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Residues in contact with PHE 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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148C SER 2.5 16.2 + - - +
149C SER* 3.2 8.7 - - - +
151C TRP* 1.3 72.7 - - - +
153C GLU* 1.3 61.0 + - + +
155C MET* 3.0 19.9 + - + +
156C ARG* 2.8 31.8 + - + +
180C LEU* 4.8 2.7 - - + +
183C LEU* 3.1 59.2 - - + -
184C LEU* 4.3 13.0 - - + -
186C GLU* 6.1 0.7 - - + -
187C ARG* 4.7 14.1 - - + -
189C SER* 4.3 15.0 - - - -
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Residues in contact with GLU 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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149C SER 2.8 16.5 + - - +
150C VAL* 2.9 9.8 + - - +
152C PHE* 1.3 77.9 - - + +
154C MET* 1.3 51.8 + - - +
156C ARG* 3.0 11.0 + - + +
157C VAL* 2.5 35.3 + - - +
370C THR 5.0 11.4 - - - +
372C VAL* 3.7 22.7 - - + +
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Residues in contact with MET 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 VAL* 2.7 31.3 + - + +
151C TRP* 3.3 11.7 - - + +
153C GLU* 1.3 73.7 - - - +
155C MET* 1.3 59.4 + - - +
157C VAL* 3.4 8.9 - - + +
158C TYR* 2.7 36.7 + - + +
160C TRP* 3.8 23.8 - - + -
248C LEU* 3.6 28.5 - - + -
267C ILE* 4.3 6.5 - - + -
269C LEU* 4.6 5.2 - - + -
353C ILE* 4.3 32.8 - - + -
372C VAL* 4.7 8.3 - - - +
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Residues in contact with MET 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 TRP 2.7 19.4 + - - +
152C PHE* 3.2 22.9 - - + +
154C MET* 1.3 77.7 - - - +
156C ARG* 1.3 54.0 + - - +
159C ASN* 3.1 8.8 + - - -
160C TRP* 2.9 66.5 + - + +
161C ASN* 5.5 2.7 - - - -
163C ILE* 3.6 32.5 - - + -
180C LEU* 4.3 12.1 - - - -
184C LEU* 3.6 26.2 - - + -
189C SER* 5.1 5.6 - - - +
190C LYS 5.8 0.7 - - - +
220C ILE* 4.4 9.0 - - + -
248C LEU* 5.2 1.1 - - + -
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Residues in contact with ARG 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 PHE* 2.8 20.1 + - + +
153C GLU* 3.2 13.5 - - + +
155C MET* 1.3 78.0 - - - +
157C VAL* 1.3 65.0 - - - +
159C ASN* 3.5 9.1 + - - +
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Residues in contact with VAL 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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153C GLU 2.5 20.4 + - - +
154C MET* 3.0 14.5 + - + +
156C ARG* 1.3 76.8 - - - +
158C TYR* 1.3 57.9 + - + +
159C ASN* 3.4 3.5 + - - +
372C VAL* 4.8 17.9 - - + -
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Residues in contact with TYR 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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154C MET* 2.7 15.4 + - + +
157C VAL* 1.3 72.4 - - + +
159C ASN* 1.3 70.0 + - - +
160C TRP* 3.3 47.0 + - + +
381C TRP* 5.0 8.5 - - + -
388C LYS* 5.7 6.3 - - + +
389C PRO 5.4 1.2 - - - +
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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