Contacts of the helix formed by residues 235 - 248 (chain B) in PDB entry 5I7L
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 ASP 235 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233B GLY 3.8 2.2 + - - -
234B LEU* 1.3 73.7 - - - +
236B ILE* 1.3 61.1 + - - +
237B THR* 2.7 45.2 + - - +
238B LEU* 3.0 23.0 + - + +
239B VAL* 2.9 24.6 + - - +
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Residues in contact with ILE 236 (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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173B ILE* 4.6 16.6 - - + +
234B LEU 3.2 6.4 + - - +
235B ASP* 1.3 71.5 + - - +
237B THR* 1.3 73.5 + - + +
239B VAL* 4.2 18.4 - - + -
240B HIS* 2.9 32.3 + - + +
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Residues in contact with THR 237 (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 ASP* 2.7 26.6 + - - +
236B ILE* 1.3 83.4 - - + +
238B LEU* 1.3 57.7 + - - +
240B HIS* 3.9 5.2 - - - +
241B ASP* 3.0 43.4 + - - -
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Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 3.8 21.3 - - + +
50B SER* 4.1 38.6 - - - +
51B LEU* 4.4 4.9 - - + +
54B ALA* 4.4 14.6 - - + -
234B LEU* 5.3 5.8 - - + -
235B ASP* 3.0 25.1 + - + +
237B THR* 1.3 80.0 + - - +
239B VAL* 1.3 65.6 + - - +
241B ASP* 3.7 2.8 - - - +
242B ILE* 2.9 51.9 + - + +
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Residues in contact with VAL 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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173B ILE* 4.1 17.0 - - + +
174B HIS* 4.5 0.2 - - - -
175B LEU* 4.0 27.8 - - + +
231B LEU 5.0 1.6 - - - +
234B LEU* 3.6 33.9 - - + +
235B ASP 2.9 18.9 + - - +
236B ILE* 3.6 16.4 - - + +
238B LEU* 1.3 74.7 - - - +
240B HIS* 1.3 56.0 + - - +
242B ILE* 3.1 6.5 + - - +
243B VAL* 2.6 53.0 + - + +
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Residues in contact with HIS 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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173B ILE* 5.0 15.0 - - + -
236B ILE* 2.9 25.8 + - + +
237B THR* 3.9 6.3 + - - +
239B VAL* 1.3 74.7 - - - +
241B ASP* 1.3 68.0 + - - +
243B VAL* 3.6 8.5 - - + +
244B ASN* 2.9 53.4 + - - +
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Residues in contact with ASP 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 3.6 26.8 - - + +
237B THR* 3.0 27.6 + - - +
238B LEU* 3.7 0.7 - - - +
240B HIS* 1.3 83.7 + - - +
242B ILE* 1.3 65.6 + - - +
244B ASN* 3.3 9.6 + - - +
245B MET* 3.1 26.5 + - - +
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Residues in contact with ILE 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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47B LEU* 4.0 20.9 - - + +
51B LEU* 3.8 37.2 - - + -
129B LEU* 4.2 6.1 - - + -
175B LEU* 4.0 20.6 - - + -
234B LEU* 5.4 0.2 - - + -
238B LEU* 2.9 44.4 + - + +
239B VAL 3.6 2.5 - - - +
241B ASP* 1.3 71.9 - - - +
243B VAL* 1.3 67.4 + - - +
245B MET* 3.3 4.1 + - - +
246B LEU* 3.0 33.3 + - + +
252B PHE* 3.8 21.3 - - + -
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Residues in contact with VAL 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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165B ALA* 4.1 15.0 - - + -
173B ILE* 3.9 31.2 - - + -
174B HIS 4.7 0.9 - - - +
175B LEU* 3.6 23.1 - - + -
239B VAL* 2.6 37.2 + - + +
240B HIS* 3.6 9.0 - - + +
242B ILE* 1.3 71.5 - - - +
244B ASN* 1.3 64.1 + - - +
246B LEU* 3.1 12.5 + - - +
247B ILE* 3.0 39.7 + - + +
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Residues in contact with ASN 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 HIS* 2.9 42.6 + - - +
241B ASP* 3.3 10.9 + - - +
243B VAL* 1.3 78.1 - - - +
245B MET* 1.3 64.5 + - + +
246B LEU 3.3 0.2 + - - -
247B ILE* 3.5 8.6 + - - +
248B HIS* 2.7 59.2 + - - -
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Residues in contact with MET 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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47B LEU* 3.5 23.8 - - + -
126B GLY 3.7 0.4 - - - +
241B ASP* 3.1 17.2 + - + +
242B ILE 3.9 2.0 - - - +
244B ASN* 1.3 78.0 - - + +
246B LEU* 1.3 60.6 + - - +
248B HIS* 3.8 2.0 - - - +
249B GLY 3.3 2.1 + - - -
250B LEU* 2.9 78.4 + - + +
251B GLN 3.8 16.6 - - - +
252B PHE* 3.8 17.3 - - + -
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Residues in contact with LEU 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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122B GLN* 4.3 2.7 - - - +
126B GLY 3.1 20.5 - - - +
127B HIS* 3.1 39.6 - - - +
128B ARG 4.3 2.5 - - - +
129B LEU* 4.3 24.7 - - + -
163B ILE 5.0 3.6 - - - +
165B ALA* 4.6 15.7 - - + +
175B LEU* 4.6 11.2 - - + -
242B ILE* 3.0 35.6 + - + +
243B VAL* 3.1 11.0 + - - +
245B MET* 1.3 73.3 - - - +
247B ILE* 1.3 58.8 + - + +
249B GLY 2.8 21.1 + - - -
252B PHE* 4.1 15.9 - - + -
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Residues in contact with ILE 247 (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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127B HIS* 3.5 15.3 + - - -
173B ILE* 6.0 1.6 - - + -
243B VAL* 3.0 35.7 + - + +
244B ASN* 3.6 12.1 - - - +
246B LEU* 1.3 75.3 - - + +
248B HIS* 1.3 78.4 + - + +
249B GLY 3.4 2.8 + - - -
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Residues in contact with HIS 248 (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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127B HIS* 4.6 1.1 - - - -
244B ASN* 2.7 47.9 + - - +
245B MET 3.7 0.4 + - - +
246B LEU 3.2 0.8 - - - -
247B ILE* 1.3 95.9 - - + +
249B GLY* 1.3 63.7 + - - +
250B LEU* 3.1 31.0 + - + +
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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