Contacts of the helix formed by residues 238 - 252 (chain B) in PDB entry 1IV4
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 238 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B TYR* 3.3 21.2 - - - +
220B LEU* 3.4 6.9 + - - -
221B CYS 3.0 15.6 + - - -
222B GLY* 2.8 30.1 + - - -
236B ASP* 2.9 24.7 + - - +
237B GLY* 1.3 71.8 - - - +
239B ALA* 1.3 62.4 + - - +
240B ALA 3.3 3.8 + - - -
241B MET* 3.0 30.0 + - + +
242B HIS* 3.0 29.4 + - - -
273B SER* 4.2 1.1 - - - +
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Residues in contact with ALA 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ASP* 3.4 24.0 - - - +
210B HIS* 4.3 3.1 - - + -
220B LEU* 4.3 4.7 - - + +
237B GLY 2.9 7.6 + - - +
238B ASP* 1.3 72.0 + - - +
240B ALA* 1.3 57.1 + - - +
243B ALA* 2.9 33.1 + - - +
342B VAL* 4.1 34.5 - - + +
344B ALA* 3.4 21.7 - - + +
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Residues in contact with ALA 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B LEU* 4.3 4.1 - - + +
221B CYS* 3.8 32.1 - - - +
238B ASP* 3.2 8.6 + - - +
239B ALA* 1.3 76.1 - - - +
241B MET* 1.3 66.1 + - - +
243B ALA* 4.0 0.9 - - - +
244B LEU* 3.0 31.7 + - + +
296B LEU* 4.0 9.1 - - + +
298B LEU* 3.8 18.4 - - + -
344B ALA* 3.9 10.4 - - - +
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Residues in contact with MET 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B CYS* 4.0 7.9 - - - -
222B GLY* 4.1 3.6 - - - +
238B ASP* 3.0 32.8 + - - +
240B ALA* 1.3 77.4 - - - +
242B HIS* 1.3 59.7 + - - +
244B LEU* 3.4 5.8 + - + +
245B THR* 2.7 34.2 + - - -
273B SER* 3.6 25.4 - - - +
274B GLU* 4.1 14.1 - - - +
277B LEU* 3.6 36.3 - - + +
316B LEU* 3.5 32.5 - - + -
319B LEU* 3.7 22.9 - - + -
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Residues in contact with HIS 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLU 5.1 0.2 - - - -
208B ASP* 2.9 21.1 + - + +
210B HIS* 3.3 6.9 + - - -
235B SER* 3.8 23.6 - - - -
238B ASP 3.0 20.1 + - - +
241B MET* 1.3 78.7 - - - +
243B ALA* 1.3 57.8 + - - +
245B THR* 3.2 7.1 + - - -
246B ASP* 2.9 33.7 + - - +
257B ILE* 3.7 24.4 - - + +
273B SER* 2.8 34.2 + - - -
276B PHE* 4.5 14.1 - + + -
1562B MG 2.0 30.8 - - - -
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Residues in contact with ALA 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B GLY* 3.6 17.1 - - - +
207B GLU 4.1 10.8 - - - +
208B ASP* 3.9 5.1 - - - +
239B ALA 2.9 18.0 + - - +
240B ALA 4.0 2.5 - - - +
242B HIS* 1.3 76.0 - - - +
244B LEU* 1.3 58.1 + - - +
246B ASP* 3.5 0.6 + - - -
247B ALA* 2.9 28.2 + - - +
296B LEU* 5.7 0.4 - - + -
344B ALA* 3.8 30.7 - - + +
346B ALA* 3.9 10.3 - - + +
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Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ALA 3.0 22.2 + - - +
241B MET* 3.8 9.2 - - + +
243B ALA* 1.3 73.6 - - - +
245B THR* 1.3 66.6 + - - +
247B ALA* 3.2 4.9 + - - +
248B LEU* 2.9 27.9 + - - +
277B LEU* 3.8 13.2 - - + -
294B ALA* 3.9 28.7 - - + -
296B LEU* 4.0 20.6 - - + -
316B LEU* 3.9 29.8 - - + -
320B MET* 3.9 17.0 - - + -
346B ALA* 3.9 17.0 - - + -
347B VAL 5.3 0.2 - - - +
348B VAL* 4.2 6.9 - - + +
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Residues in contact with THR 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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241B MET 2.7 22.1 + - - -
242B HIS* 3.6 6.1 - - - -
244B LEU* 1.3 77.6 - - - +
246B ASP* 1.3 63.6 + - - +
248B LEU* 3.1 7.9 + - - +
249B LEU* 3.0 27.6 + - + +
257B ILE* 3.4 23.6 - - + -
261B PHE* 3.9 11.0 - - + -
273B SER 4.7 0.7 + - - -
276B PHE* 3.9 15.2 - - + +
277B LEU* 3.3 27.3 + - - +
280B ALA* 3.9 18.8 - - + -
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Residues in contact with ASP 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A THR* 4.1 13.3 + - + +
132A LYS* 3.5 27.5 + - - +
205B TYR 4.7 0.2 - - - -
206B GLY* 4.1 13.5 - - - -
207B GLU 3.9 3.6 + - - +
242B HIS 2.9 14.7 + - - +
243B ALA* 3.9 4.5 - - - +
245B THR* 1.3 75.9 - - - +
247B ALA* 1.3 58.0 + - - +
249B LEU* 3.3 4.4 + - - +
250B SER* 2.8 33.0 + - - -
256B ASP* 3.2 16.6 - - - +
257B ILE* 2.7 45.2 + - - +
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Residues in contact with ALA 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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204B GLY* 3.4 18.6 - - - +
205B TYR 3.9 4.0 - - - +
206B GLY* 3.6 21.2 - - - +
243B ALA 2.9 18.6 + - - +
244B LEU* 3.5 6.7 - - - +
245B THR 3.2 0.2 - - - -
246B ASP* 1.3 76.8 - - - +
248B LEU* 1.3 62.1 + - - +
250B SER* 3.3 0.7 + - - -
251B ALA 3.0 17.8 + - - -
346B ALA* 3.9 7.4 - - + +
348B VAL* 3.6 25.7 - - + +
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Residues in contact with LEU 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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244B LEU 2.9 13.0 + - - +
245B THR 3.5 4.7 - - - +
247B ALA* 1.3 73.7 - - - +
249B LEU* 1.3 65.7 + - - +
251B ALA* 3.2 15.5 + - - +
252B TYR 3.7 0.9 + - - -
277B LEU* 3.6 30.7 - - + -
280B ALA* 4.3 16.2 - - + -
281B MET* 3.9 20.2 - - + +
284B VAL* 3.6 27.9 - - + +
291B LEU* 4.0 32.8 - - + -
320B MET* 3.8 8.7 - - + -
348B VAL* 4.2 14.6 - - + -
350B LEU* 4.4 11.4 - - + +
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Residues in contact with LEU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B THR* 3.0 31.8 + - + +
246B ASP* 3.8 3.8 - - - +
248B LEU* 1.3 76.5 - - - +
250B SER* 1.3 63.2 + - - +
252B TYR* 3.0 4.9 + - - -
253B GLY 3.0 3.6 + - - -
254B LEU* 3.0 45.2 + - + +
255B GLY 3.6 14.4 - - - +
256B ASP* 3.7 31.2 - - - +
257B ILE 3.9 4.0 - - - +
260B LEU* 3.9 29.4 - - + -
261B PHE* 4.3 4.5 - - + -
280B ALA* 3.8 24.2 - - + +
283B LEU* 4.4 1.1 - - + -
284B VAL* 4.9 0.4 - - + -
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Residues in contact with SER 250 (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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93A GLN* 4.4 3.6 - - - +
95A SER* 2.7 28.6 + - - -
96A LEU 4.5 0.3 + - - -
125A ASP 4.8 0.3 - - - +
127A ILE 4.5 0.2 - - - -
128A GLY* 2.9 41.9 + - - -
129A LEU 5.1 0.4 - - - +
130A THR* 4.2 8.1 - - - +
203B ILE 4.7 0.6 - - - +
205B TYR 4.0 10.6 + - - -
246B ASP 2.8 18.8 + - - -
247B ALA 3.6 4.9 - - - -
249B LEU* 1.3 77.8 - - - +
251B ALA* 1.3 61.9 + - - +
253B GLY* 3.0 12.1 + - - +
255B GLY 4.3 6.2 + - - +
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Residues in contact with ALA 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLN* 3.0 17.4 - - - +
125A ASP 4.3 0.2 - - - -
202B ARG* 3.1 20.2 + - + -
203B ILE 3.4 25.1 - - - +
204B GLY* 3.9 0.4 - - - -
247B ALA 3.0 12.6 + - - +
248B LEU 3.5 10.5 - - - +
249B LEU 3.1 0.4 - - - -
250B SER* 1.3 77.6 - - - +
252B TYR* 1.3 61.3 + - + +
253B GLY 3.6 0.2 - - - -
348B VAL* 4.5 0.2 - - + -
350B LEU* 3.7 29.8 - - + -
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Residues in contact with TYR 252 (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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125A ASP* 3.4 27.7 - - + +
202B ARG* 3.3 42.9 + - - -
248B LEU 3.7 0.2 + - - -
249B LEU 3.0 2.8 + - - +
251B ALA* 1.3 82.8 - - + +
253B GLY* 1.3 63.9 + - - +
254B LEU* 3.2 32.8 + - + +
284B VAL* 3.6 21.3 - - + -
287B ARG* 4.0 33.5 + - + -
288B GLY 4.1 1.2 - - - -
289B ALA* 3.0 44.9 + - + +
350B LEU* 4.3 9.5 - - + +
351B ASP* 4.0 9.0 + - - -
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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