Contacts of the helix formed by residues 151 - 156 (chain X) in PDB entry 2Q0Z
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 SER 151 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146X MSE 4.3 2.8 - - - +
149X LYS 3.8 1.0 + - - -
150X ASP* 1.3 77.4 - - - +
152X TYR* 1.3 64.8 + - - +
153X LEU* 3.0 27.2 + - - +
154X LYS* 3.1 21.1 + - - +
164X ILE* 3.4 34.1 - - - +
168X THR* 5.0 5.8 + - - -
173X GLU* 4.5 8.1 + - - -
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Residues in contact with TYR 152 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137X GLU* 5.6 1.6 + - - -
146X MSE 5.1 2.2 - - - -
148X SER 5.5 4.5 - - - -
150X ASP 4.5 7.6 - - - -
151X SER* 1.3 74.8 + - - +
153X LEU* 1.3 60.8 + - - +
154X LYS 3.1 2.0 + - - -
155X GLN* 2.8 37.8 + - - +
173X GLU* 4.0 21.1 + - + +
174X SER* 5.2 6.1 - - - -
175X VAL* 4.7 9.0 - - + +
207X TYR* 4.9 3.1 - - - +
307X MSE 3.8 26.0 - - + +
308X GLY* 3.4 41.3 - - - -
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Residues in contact with LEU 153 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151X SER* 3.0 15.8 - - - +
152X TYR* 1.3 74.8 - - - +
154X LYS* 1.3 59.3 + - - +
155X GLN 3.0 6.9 + - - -
156X LEU* 3.2 24.7 + - + +
159X PHE* 3.5 27.7 - - + +
164X ILE* 4.4 9.6 - - + +
167X CYS* 3.4 41.5 - - + -
168X THR* 5.9 0.4 - - - +
172X VAL* 3.7 16.4 - - + +
173X GLU* 4.0 6.5 - - - +
174X SER 3.8 22.2 - - - +
175X VAL* 4.1 3.8 - - + +
178X ILE* 3.7 24.9 - - + -
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Residues in contact with LYS 154 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92X LEU 3.7 15.0 + - - -
93X SER* 4.8 6.9 + - - +
94X ARG* 3.0 63.1 + - - +
145X ALA 3.6 7.6 - - - -
146X MSE 3.2 17.0 - - + -
147X TRP* 5.0 0.8 - - - -
150X ASP* 3.0 38.6 + - + +
151X SER 3.1 12.4 + - - +
153X LEU* 1.3 77.4 - - - +
155X GLN* 1.3 59.1 + - - +
156X LEU 3.4 5.6 + - - +
159X PHE* 5.0 6.4 - - - +
164X ILE* 3.9 24.2 - - + +
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Residues in contact with GLN 155 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94X ARG* 4.7 1.8 - - - +
144X GLN* 3.4 31.3 - - - +
146X MSE 3.1 21.3 - - + +
152X TYR* 2.8 22.4 - - - +
153X LEU 3.0 0.8 - - - -
154X LYS* 1.3 77.8 - - - +
156X LEU* 1.3 64.5 + - + +
157X PRO* 3.6 3.3 - - - +
175X VAL* 4.8 0.9 - - - +
203X PHE* 3.6 31.0 - - + -
207X TYR* 4.0 5.6 - - - -
247X PRO* 5.4 6.9 - - - +
306X TYR* 3.5 14.6 - - - +
307X MSE 2.8 51.9 + - - +
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Residues in contact with LEU 156 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153X LEU* 3.2 18.5 + - + +
154X LYS 4.1 4.5 - - - +
155X GLN* 1.3 78.0 - - + +
157X PRO* 1.3 75.2 - - + +
158X HIS 3.5 0.2 + - - -
159X PHE* 3.2 60.7 + - + +
175X VAL* 4.5 8.7 - - + -
178X ILE* 4.1 24.2 - - + -
200X VAL* 4.4 4.9 - - + -
203X PHE* 3.1 39.5 - - + -
204X CYS* 3.7 20.4 - - - -
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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