Contacts of the helix formed by residues 146 - 159 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A PRO* 4.5 6.9 - - + +
143A PRO* 3.0 44.2 + - + +
145A SER* 1.3 78.4 + - - +
147A GLN* 1.3 61.9 + - - +
148A SER 2.9 6.1 - - - -
149A SER* 2.9 25.1 + - - +
150A VAL* 4.1 0.7 + - - +
179A ARG* 3.1 36.9 + - - +
341A ASN* 3.7 25.4 + - - -
345A ASP* 4.0 9.0 + - + -
346A ARG 4.6 5.9 + - - -
347A LYS* 6.4 0.2 - - - -
351A TYR* 4.0 16.7 + - - +
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Residues in contact with GLN 147 (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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124A ARG* 4.3 10.6 + - - +
143A PRO 4.3 0.2 + - - -
144A TYR* 2.9 32.8 + - - +
146A HIS* 1.3 79.2 - - - +
148A SER* 1.3 57.9 + - - +
150A VAL* 2.9 21.5 + - - +
151A TRP* 3.0 28.6 + - + -
250A GLY* 3.5 16.5 - - - -
251A GLU* 2.8 39.5 + - - +
252A ARG* 5.4 0.4 - - - +
253A GLU* 5.1 2.0 + - - -
269A LEU* 3.8 22.6 - - + +
351A TYR* 3.9 23.1 + - + -
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Residues in contact with SER 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A SER 3.0 16.8 + - - -
147A GLN* 1.3 78.5 - - - +
149A SER* 1.3 51.2 + - - +
151A TRP* 3.0 26.2 + - - +
152A PHE* 2.6 35.3 + - - +
176A ALA* 4.5 4.0 - - - -
179A ARG* 4.0 12.8 - - - -
180A LEU* 3.2 32.7 - - - +
183A LEU* 3.2 11.1 - - - +
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Residues in contact with SER 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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146A HIS* 2.9 15.5 + - - +
148A SER* 1.3 75.1 - - - +
150A VAL* 1.3 59.0 + - - +
152A PHE* 3.1 5.3 + - - +
153A GLU* 2.8 35.1 + - - +
179A ARG* 2.7 33.4 + - - -
183A LEU* 3.6 15.1 - - - +
367A TYR* 4.0 17.0 - - - -
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Residues in contact with VAL 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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146A HIS 4.6 1.6 - - - +
147A GLN 2.9 8.2 + - - +
149A SER* 1.3 72.5 - - - +
151A TRP* 1.3 57.5 + - + +
153A GLU* 2.9 1.7 + - - -
154A MET* 2.6 40.4 + - + +
269A LEU* 3.8 26.7 - - + -
351A TYR* 3.4 35.4 - - + -
353A ILE* 4.5 10.1 - - + -
367A TYR* 3.5 46.0 - - + -
372A VAL* 5.1 2.7 - - + -
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Residues in contact with TRP 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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144A TYR 5.8 0.4 - - - -
145A SER* 5.5 1.1 - - - -
147A GLN* 3.0 24.2 + - + -
148A SER* 3.2 33.0 - - - +
150A VAL* 1.3 77.3 - - + +
152A PHE* 1.3 56.5 + - - +
154A MET* 2.9 4.7 + - - +
155A MET* 2.8 34.3 + - - +
165A LEU* 5.1 3.6 - - + -
176A ALA* 4.8 16.2 - - + -
180A LEU* 5.0 9.0 - - + -
220A ILE* 3.5 31.9 - - + -
221A LEU 3.7 18.2 - - - -
222A SER* 4.5 10.5 - - - -
248A LEU* 3.5 35.0 - - + +
249A VAL* 2.8 41.9 + - - -
250A GLY* 3.5 9.6 - - - -
253A GLU* 5.3 1.1 - - - -
269A LEU* 3.9 12.6 - - + +
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Residues in contact with PHE 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 SER 2.6 16.7 + - - +
149A SER* 3.2 9.0 - - - +
150A VAL 3.1 0.2 - - - -
151A TRP* 1.3 72.3 - - - +
153A GLU* 1.3 77.9 + - - +
155A MET* 3.0 18.9 + - + +
156A ARG* 3.0 45.4 + - + +
180A LEU* 4.8 2.9 - - + +
183A LEU* 3.1 57.4 - - + -
184A LEU* 4.1 19.7 - - + -
186A GLU* 6.3 0.2 - - + -
187A ARG* 4.7 13.7 - - + -
189A SER* 4.3 12.1 - - - -
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Residues in contact with GLU 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 SER* 2.8 17.7 + - - +
150A VAL 2.9 6.7 + - - +
152A PHE* 1.3 92.6 - - - +
154A MET* 1.3 50.7 + - - +
156A ARG* 2.4 52.3 + - - +
157A VAL* 2.5 34.3 + - - +
367A TYR* 3.6 26.0 + - + +
370A THR* 3.6 19.4 + - - +
371A HIS* 5.4 0.2 - - - -
372A VAL* 3.7 21.1 - - + +
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Residues in contact with MET 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 VAL* 2.6 20.0 + - + +
151A TRP* 2.9 14.1 + - - +
153A GLU* 1.3 71.7 - - - +
155A MET* 1.3 59.3 + - - +
157A VAL* 2.9 8.6 + - - -
158A TYR* 2.8 43.2 + - + +
160A TRP* 4.3 7.6 - - + -
248A LEU* 4.1 18.2 - - + -
353A ILE* 6.4 2.0 - - + -
372A VAL* 4.5 4.0 - - + +
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Residues in contact with MET 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 TRP 2.8 19.4 + - - +
152A PHE* 3.0 19.0 + - + +
154A MET* 1.3 74.8 - - - +
156A ARG* 1.3 51.9 + - + +
159A ASN* 2.5 39.2 + - - -
160A TRP* 3.2 50.8 + - + +
161A ASN* 5.3 2.2 - - - +
163A ILE* 3.6 37.9 - - + -
180A LEU* 4.7 4.0 - - - -
184A LEU* 3.8 21.8 - - + -
189A SER* 5.2 6.1 - - - +
190A LYS 5.8 1.1 - - - +
220A ILE* 4.5 9.9 - - + -
248A LEU* 5.4 1.1 - - + -
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Residues in contact with ARG 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 PHE* 3.0 44.9 + - + +
153A GLU* 2.4 43.5 + - - +
155A MET* 1.3 77.7 - - + +
157A VAL* 1.3 58.3 + - - +
158A TYR 2.9 6.1 + - - -
159A ASN* 3.5 17.1 + - - +
370A THR 4.8 3.0 + - - -
371A HIS* 5.9 1.6 - - - +
372A VAL* 5.8 1.8 - - - +
2E NAG 6.3 0.8 - - - +
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Residues in contact with VAL 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 GLU 2.5 18.5 + - - +
154A MET* 2.9 12.8 + - - +
156A ARG* 1.3 73.8 - - - +
158A TYR* 1.3 85.3 + - + +
159A ASN* 5.7 0.2 - - - -
372A VAL* 4.5 21.3 - - + -
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Residues in contact with TYR 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 MET* 2.8 30.9 + - + +
155A MET 3.3 0.9 - - - -
157A VAL* 1.3 102.5 - - + +
159A ASN* 1.3 74.2 + - - +
160A TRP* 3.3 48.1 + + + +
372A VAL* 5.7 4.8 - - + +
374A PRO* 5.3 10.4 - - + +
379A ILE* 3.2 24.1 - - + +
381A TRP* 4.0 26.9 - + - -
388A LYS* 4.8 11.2 - - + -
389A PRO 5.7 0.2 - - - +
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Residues in contact with ASN 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 MET 2.5 14.6 + - - -
156A ARG* 3.6 12.8 - - - +
158A TYR* 1.3 77.7 - - - +
160A TRP* 1.3 59.0 + - - +
161A ASN* 3.4 23.2 + - - +
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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