Contacts of the helix formed by residues 155 - 159 (chain B) in PDB entry 3QXY
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 155 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B LEU* 3.5 23.5 - - + +
154B GLU* 1.3 80.4 + - - +
156B PRO* 1.3 65.5 - - + +
157B MET* 3.0 21.3 - - + -
158B PHE* 2.9 28.7 + - + +
159B TRP* 3.7 3.5 - - - -
218B ALA* 3.3 40.0 + - + +
221B MET* 4.5 7.4 - - + -
222B ALA* 3.6 11.3 - - + +
295B HIS 3.5 15.5 - - - +
296B MET* 2.8 32.0 + - - -
297B TYR 4.0 10.8 - - - -
298B GLY* 4.0 4.6 + - - -
6735B SAM 5.0 0.7 - - - -
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Residues in contact with PRO 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B GLU 3.4 4.0 - - - +
155B HIS* 1.3 83.8 - - + +
157B MET* 1.3 58.3 + - - +
158B PHE 3.0 1.3 - - - -
159B TRP* 3.0 34.7 + - + +
164B ARG* 3.0 38.8 + - - -
168B LEU* 4.1 7.2 - - + -
173B VAL* 3.8 25.8 - - + -
177B VAL* 4.3 3.6 - - + -
294B ILE* 3.0 35.2 - - + +
295B HIS* 4.0 8.3 - - - +
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Residues in contact with MET 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B HIS* 3.0 17.7 + - + -
156B PRO* 1.3 79.4 - - - +
158B PHE* 1.3 75.3 + - + +
159B TRP 4.1 0.7 - - - +
164B ARG* 3.7 8.4 + - - -
177B VAL* 3.8 28.6 - - + +
180B ASP* 5.7 6.3 - - + +
181B LEU* 4.0 20.8 - - + +
184B ILE* 3.6 28.5 - - + -
214B HIS* 3.9 30.1 - - + +
218B ALA* 4.0 11.0 - - - -
221B MET* 3.2 33.9 - - - +
295B HIS* 5.7 1.8 - - + +
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Residues in contact with PHE 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B LEU 5.7 0.4 - - - -
153B LEU* 3.9 32.5 - - + +
155B HIS* 2.9 21.3 + - + +
157B MET* 1.3 96.6 - - + +
159B TRP* 1.3 64.5 + - + +
160B PRO* 4.0 2.3 - - - +
214B HIS* 3.9 33.0 - + + -
215B GLN* 4.0 16.8 - - + -
218B ALA* 3.6 32.3 - - + -
450B ARG* 4.5 7.1 + - - +
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Residues in contact with TRP 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B GLU 3.5 8.4 + - - -
155B HIS 3.7 4.0 - - - -
156B PRO* 3.0 24.2 + - + +
157B MET 4.1 1.2 - - - +
158B PHE* 1.3 82.5 - - + +
160B PRO* 1.3 74.9 - - + +
161B GLU 3.4 0.7 + - - -
163B GLU* 4.3 8.7 - - + +
164B ARG* 2.8 42.3 + - + +
167B LEU* 3.8 20.6 - - + -
168B LEU* 3.7 22.4 - - + -
294B ILE* 4.0 23.3 - - + -
450B ARG* 3.5 51.0 - - + +
453B GLN* 3.7 10.3 - - - -
454B ALA* 4.7 1.8 - - + -
479B EDO 3.2 28.9 + - - -
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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