Contacts of the helix formed by residues 175 - 187 (chain B) in PDB entry 4RQO
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 THR 175 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B PHE* 3.8 1.6 - - - -
174B ALA* 1.3 89.3 - - + +
176B ALA* 1.3 63.8 + - - +
177B THR* 3.9 2.5 - - - -
178B GLU* 2.9 27.9 + - - +
179B LEU* 3.0 17.3 + - - +
329B LEU* 3.6 12.5 - - - +
426B ASP* 3.4 21.2 + - - +
429B ILE* 5.9 0.9 - - - -
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Residues in contact with ALA 176 (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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175B THR* 1.3 70.6 - - - +
177B THR* 1.3 59.1 - - - +
179B LEU* 3.4 1.5 - - - +
180B LEU* 3.2 15.9 + - - +
329B LEU* 3.7 14.6 - - + +
370B GLU* 2.6 41.5 - - - +
425B LEU* 3.8 29.6 - - + -
426B ASP* 2.8 22.9 + - - +
429B ILE* 5.0 0.8 - - + +
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Residues in contact with THR 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B THR* 4.0 3.6 - - - -
176B ALA* 1.3 75.6 - - - +
178B GLU* 1.3 64.8 + - - +
180B LEU* 3.3 12.1 + - + +
181B LYS* 3.0 40.5 + - - +
370B GLU* 5.2 0.2 - - - -
424B SER* 5.2 2.3 + - - -
426B ASP* 2.5 24.1 + - - +
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Residues in contact with GLU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B PRO 3.6 18.7 - - - +
173B PHE* 3.7 9.3 - - + -
174B ALA* 4.0 5.9 + - - +
175B THR* 2.9 26.4 + - + +
177B THR* 1.3 75.3 - - - +
179B LEU* 1.3 56.1 + - - +
181B LYS* 3.3 15.4 + - + +
182B LEU* 3.0 57.7 + - + +
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Residues in contact with LEU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B PHE* 3.9 42.9 - - + +
175B THR 3.0 12.9 + - - +
176B ALA* 3.4 8.7 - - - +
178B GLU* 1.3 76.5 - - - +
180B LEU* 1.3 62.2 + - - +
182B LEU* 3.5 3.8 + - - +
183B CYS* 3.1 33.9 + - - -
190B ILE* 4.1 39.7 - - + -
193B LEU* 4.4 12.8 - - + -
325B ALA* 4.5 4.7 - - + -
326B ILE* 4.4 7.2 - - + -
329B LEU* 4.1 18.2 - - + -
370B GLU* 3.7 14.4 - - - +
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Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ALA 3.2 6.1 + - - +
177B THR* 3.3 10.5 + - + +
179B LEU* 1.3 75.6 - - - +
181B LYS* 1.3 66.0 + - - +
183B CYS* 3.2 2.3 + - - +
184B LYS* 3.0 29.8 + - + +
190B ILE* 5.1 3.1 - - + -
366B ILE* 2.9 42.1 - - + +
367B GLU* 4.6 18.4 - - + +
370B GLU* 3.1 46.9 - - + +
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Residues in contact with LYS 181 (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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177B THR* 3.0 34.1 + - - +
178B GLU* 3.6 15.9 - - + +
180B LEU* 1.3 76.6 - - - +
182B LEU* 1.3 65.5 + - + +
184B LYS* 3.7 6.1 - - - +
185B LYS* 3.1 30.8 + - + +
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Residues in contact with LEU 182 (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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171B TYR* 4.2 23.3 - - + +
172B PRO* 3.7 23.3 - - + +
173B PHE* 4.2 8.3 - - + -
178B GLU* 3.0 38.3 + - - +
179B LEU* 4.0 1.3 - - - +
181B LYS* 1.3 80.8 - - + +
183B CYS* 1.3 63.4 + - - +
185B LYS* 3.4 10.0 + - + +
186B HIS* 3.0 49.2 + - + +
193B LEU* 4.0 16.7 - - + +
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Residues in contact with CYS 183 (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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179B LEU* 3.1 28.0 + - - +
180B LEU* 3.2 5.4 + - - +
182B LEU* 1.3 76.1 - - - +
184B LYS* 1.3 52.8 + - - +
186B HIS 3.7 0.2 - - - -
187B HIS* 2.8 30.8 + - - -
188B LEU* 2.9 26.3 + - - +
189B THR 3.6 23.3 - - - -
190B ILE* 4.0 11.9 - - - -
193B LEU* 3.9 17.5 - - - -
366B ILE* 3.7 24.9 - - + -
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Residues in contact with LYS 184 (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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180B LEU* 3.0 17.7 + - + +
181B LYS* 3.7 7.4 - - - +
183B CYS* 1.3 79.0 - - + +
185B LYS* 1.3 62.3 + - - +
186B HIS 3.4 0.3 + - - -
187B HIS* 3.4 22.6 + - - +
366B ILE* 5.5 10.0 - - + +
367B GLU* 3.0 31.2 + - - +
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Residues in contact with LYS 185 (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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181B LYS* 3.1 21.7 + - + +
182B LEU* 3.4 11.5 + - + +
184B LYS* 1.3 79.4 - - - +
186B HIS* 1.3 87.4 + - + +
187B HIS* 3.5 12.4 + - - -
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Residues in contact with HIS 186 (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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171B TYR* 3.2 48.5 + + + +
182B LEU* 3.0 30.8 + - + +
185B LYS* 1.3 109.0 + - + +
187B HIS* 1.3 74.0 + - - +
188B LEU* 3.4 28.3 - - + +
193B LEU* 5.9 0.2 - - - +
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Residues in contact with HIS 187 (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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183B CYS 2.8 13.9 + - - -
184B LYS* 3.4 13.3 + - - +
185B LYS* 3.5 16.5 + - - -
186B HIS* 1.3 78.6 - - - +
188B LEU* 1.3 61.9 + - - +
192B GLU* 4.5 2.4 - - - +
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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