Contacts of the helix formed by residues 237 - 246 (chain B) in PDB entry 4QOZ
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 LYS 237 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B PRO 5.9 0.6 + - - -
149B HIS* 5.0 8.1 - - + -
233B TRP* 2.9 71.8 + - + +
236B SER* 1.3 80.8 + - - +
238B PHE* 1.3 78.1 + - + +
239B LEU 3.6 0.9 - - - -
240B ASN 4.0 0.4 - - - -
241B ILE* 2.9 48.7 + - + +
146E GLU* 3.4 35.9 + - - +
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Residues in contact with PHE 238 (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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25A C 3.6 21.3 - - - -
26A A 3.9 27.6 - - - -
135B PHE* 4.3 9.9 - - + -
137B ALA* 3.8 17.9 - - + -
149B HIS* 3.5 50.5 - + + +
151B ILE* 3.9 17.5 - - + +
233B TRP* 2.9 41.9 + + + -
234B ASP* 3.5 18.2 - - - +
237B LYS* 1.3 84.1 - - + +
239B LEU* 1.3 58.5 + - - +
241B ILE* 4.0 2.3 - - + +
242B GLN* 2.9 32.1 + - - +
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Residues in contact with LEU 239 (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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135B PHE* 3.9 17.9 - - + -
151B ILE* 4.1 5.7 - - + +
154B PHE* 5.4 2.5 - - + -
203B PHE* 3.5 31.4 - - + -
207B LEU* 5.6 2.7 - - + -
234B ASP 2.9 20.5 + - - +
235B MET* 3.6 34.1 - - + +
238B PHE* 1.3 72.7 - - - +
240B ASN* 1.3 57.3 + - - +
242B GLN 3.9 0.2 - - - -
243B CYS* 2.9 45.7 + - - -
250B TYR* 3.7 16.8 - - + +
251B PRO* 4.4 10.3 - - + -
253B PHE* 6.3 0.7 - - + -
254B ALA* 3.8 11.4 - - + -
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Residues in contact with ASN 240 (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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235B MET 3.3 11.2 + - - +
236B SER* 2.9 31.4 + - - +
237B LYS 3.6 0.7 - - - +
239B LEU* 1.3 78.0 - - - +
241B ILE* 1.3 63.4 + - - +
243B CYS* 3.4 3.1 + - - +
244B GLN* 3.1 37.9 + - - +
250B TYR* 3.9 16.9 - - + +
322B MET* 3.4 24.4 - - - +
325B GLY* 4.5 6.6 + - - -
144E PRO* 6.2 0.4 - - - +
146E GLU* 3.6 17.0 + - + +
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Residues in contact with ILE 241 (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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147B PHE 5.5 4.0 - - - +
148B VAL* 4.4 8.1 - - + -
149B HIS* 3.7 31.4 - - + +
237B LYS* 2.9 42.8 + - + +
238B PHE* 4.0 3.1 - - - +
240B ASN* 1.3 70.3 - - - +
242B GLN* 1.3 66.5 + - - +
244B GLN* 3.0 10.7 + - - +
245B LEU* 2.9 34.2 + - + +
146E GLU* 3.8 30.5 - - + +
148E VAL* 4.2 14.4 - - + -
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Residues in contact with GLN 242 (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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149B HIS 5.0 1.5 + - - +
150B GLU* 3.4 19.5 + - - +
151B ILE* 3.1 38.7 + - + +
174B VAL* 5.8 0.2 - - - -
176B PRO* 5.9 0.9 - - - +
203B PHE* 3.4 42.9 - - + +
238B PHE 2.9 20.3 + - - +
239B LEU* 3.9 3.1 - - - +
241B ILE* 1.3 75.1 - - - +
243B CYS* 1.3 63.2 + - - +
245B LEU* 3.2 16.6 + - - +
246B SER* 2.9 45.6 + - - -
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Residues in contact with CYS 243 (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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203B PHE* 4.3 11.7 - - - -
207B LEU* 5.4 0.4 - - - -
239B LEU* 2.9 42.3 + - - +
240B ASN* 3.6 5.4 - - - +
242B GLN* 1.3 77.2 - - - +
244B GLN* 1.3 63.4 + - + +
246B SER* 3.2 3.2 + - - -
247B ARG 2.9 18.5 + - - -
248B LEU* 3.0 34.3 + - - +
249B LYS 4.4 4.0 - - - -
250B TYR* 4.3 10.5 - - + +
251B PRO* 4.0 24.2 - - - -
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Residues in contact with GLN 244 (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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240B ASN* 3.1 34.1 + - - +
241B ILE* 3.0 8.7 + - - +
243B CYS* 1.3 76.8 - - + +
245B LEU* 1.3 62.1 + - - +
247B ARG* 3.1 12.8 + - - +
248B LEU 5.0 1.3 - - - -
146E GLU 2.9 27.3 + - - -
147E PHE* 3.7 16.7 - - - +
148E VAL* 2.9 37.7 + - + +
178E ILE* 3.3 17.8 - - + +
179E ASN* 4.5 10.2 + - - +
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Residues in contact with LEU 245 (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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148B VAL* 4.0 11.0 - - + -
149B HIS 3.8 13.2 - - - +
150B GLU* 3.7 31.6 - - + +
177B GLU* 5.2 3.5 - - - +
178B ILE* 3.9 18.8 - - + -
241B ILE* 2.9 26.9 + - + +
242B GLN* 3.6 17.5 - - - +
244B GLN* 1.3 73.4 - - - +
246B SER* 1.3 59.3 + - - +
247B ARG* 3.2 15.8 + - - -
148E VAL* 4.4 12.6 - - + -
178E ILE* 3.9 33.2 - - + +
245E LEU* 4.0 9.9 - - + -
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Residues in contact with SER 246 (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 GLU* 5.5 7.1 + - - -
203B PHE* 3.9 11.0 - - - +
204B PRO* 4.0 22.8 - - - +
242B GLN* 2.9 38.5 + - - -
243B CYS 4.0 2.7 - - - -
245B LEU* 1.3 74.5 - - - +
247B ARG* 1.3 74.2 + - - +
248B LEU* 3.2 11.0 + - - -
347B PHE* 3.5 18.4 - - - -
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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