Contacts of the helix formed by residues 243 - 256 (chain B) in PDB entry 1B70
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 ASN 243 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B VAL* 3.8 20.8 - - + +
224B ALA 3.6 12.6 - - - +
225B PRO* 4.4 3.8 - - - -
226B SER 4.3 0.2 - - - -
242B ILE* 1.3 89.0 - - + +
244B ASN* 1.3 66.8 + - - +
245B VAL* 3.0 15.2 - - - +
246B VAL* 2.8 42.1 - - - +
247B ASP* 2.8 27.4 + - - -
324B VAL* 3.2 25.0 - - - +
325B ARG* 4.5 1.9 - - - -
326B GLU* 5.6 2.2 - - - +
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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
----------------------------------------------------------
222B ARG 3.3 19.6 + - - -
223B VAL* 3.6 7.4 - - - -
224B ALA* 2.6 41.4 + - - +
225B PRO 4.1 6.9 + - - +
226B SER* 3.2 20.5 + - - +
227B PRO* 5.0 0.7 - - + -
243B ASN* 1.3 71.8 + - - +
245B VAL* 1.3 70.9 + - - +
247B ASP* 3.6 1.2 - - - +
248B VAL* 2.9 36.0 + - - +
380B LEU* 5.4 0.7 - - - -
383B LEU* 2.8 41.7 + - + +
384B ALA* 3.7 6.2 - - - +
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Residues in contact with VAL 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B LEU* 4.7 11.7 - - + -
223B VAL* 4.0 17.7 - - + -
243B ASN* 3.0 8.6 - - - +
244B ASN* 1.3 87.8 + - - +
246B VAL* 1.3 69.0 + - - +
248B VAL* 3.2 12.5 + - - +
249B THR* 3.4 12.7 + - + +
262B ALA* 4.2 15.0 - - + -
324B VAL* 4.0 26.0 - - + -
331B ILE* 5.4 6.1 - - + -
380B LEU* 4.2 21.1 - - + +
384B ALA* 4.1 20.4 - - + -
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Residues in contact with VAL 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ILE* 4.2 23.3 - - + -
243B ASN* 2.8 32.9 - - - +
245B VAL* 1.3 73.2 - - - +
247B ASP* 1.3 64.1 + - - +
249B THR* 2.8 33.8 + - - +
250B ASN* 3.2 18.5 + - - +
262B ALA* 6.0 0.4 - - - -
323B GLU* 5.3 11.2 - - + +
324B VAL* 4.0 23.1 - - + +
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Residues in contact with ASP 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B SER* 2.8 41.3 + - - +
230B MET* 3.9 4.3 - - - -
234B LEU* 3.8 18.2 - - + +
240B ARG 4.3 1.2 - - - +
241B PRO* 3.2 17.2 - - - +
242B ILE* 2.7 32.5 + - - +
243B ASN* 2.8 25.1 + - - +
244B ASN 3.6 0.2 - - - +
246B VAL* 1.3 76.9 - - - +
248B VAL* 1.3 57.8 + - - +
250B ASN* 3.1 9.9 + - - +
251B TYR* 2.9 29.3 + - - +
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Residues in contact with VAL 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B MET* 4.4 4.9 - - + -
244B ASN 2.9 26.5 + - - +
245B VAL 3.4 8.3 - - - +
247B ASP* 1.3 76.5 - - - +
249B THR* 1.3 68.6 + - + +
250B ASN 3.1 0.3 + - - -
251B TYR* 3.2 7.2 + - - +
252B VAL* 3.0 32.6 + - + +
376B ALA* 4.0 25.8 - - + +
379B LEU* 4.0 18.4 - - + -
380B LEU* 4.1 19.3 - - + -
383B LEU* 4.2 24.7 - - + -
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Residues in contact with THR 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B VAL* 3.4 15.5 - - + +
246B VAL* 2.8 20.8 + - - +
248B VAL* 1.3 79.6 - - + +
250B ASN* 1.3 64.9 + - - +
252B VAL* 4.0 0.5 - - - +
253B MET* 3.1 26.7 + - - +
260B MET* 3.3 47.5 + - + +
261B HIS* 4.8 1.8 - - - -
262B ALA* 4.3 25.6 - - + +
333B LEU* 4.8 4.7 - - + -
380B LEU* 6.4 0.2 - - + -
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Residues in contact with ASN 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LEU* 4.1 14.5 - - + +
239B MET* 3.2 37.0 - - - +
240B ARG 5.2 5.9 + - - -
242B ILE* 5.8 1.8 - - - +
246B VAL* 3.6 25.9 + - - +
247B ASP* 3.1 13.1 + - - +
248B VAL 3.1 0.8 - - - -
249B THR* 1.3 85.3 + - - +
251B TYR* 1.3 68.0 + - - +
253B MET* 2.9 12.8 + - - +
254B LEU* 2.9 28.3 + - - +
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Residues in contact with TYR 251 (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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7B TRP* 3.2 52.0 + + - -
11B TYR* 4.3 1.6 + - - -
229B TRP* 3.4 32.0 - + - -
230B MET* 4.1 25.1 - - + -
233B ALA* 3.9 17.6 - - + +
234B LEU* 3.9 12.9 - - + +
247B ASP 2.9 12.9 + - - +
248B VAL* 3.5 9.0 - - - +
250B ASN* 1.3 75.1 - - - +
252B VAL* 1.3 58.2 + - + +
254B LEU* 3.0 6.8 + - - +
255B GLU* 2.9 35.8 + - - +
375B ARG* 3.9 20.4 + - - -
379B LEU* 4.5 13.9 - - + -
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Residues in contact with VAL 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B VAL* 3.0 23.6 + - + +
249B THR 4.1 0.4 - - - +
251B TYR* 1.3 74.1 - - + +
253B MET* 1.3 66.4 + - - +
255B GLU* 4.0 7.0 - - - +
256B ARG* 2.9 46.2 + - + +
258B GLN 4.1 0.2 - - - +
260B MET* 3.2 27.1 - - + -
372B ALA 4.4 4.3 - - - +
375B ARG* 4.0 14.8 - - + +
376B ALA* 4.2 10.8 - - + -
379B LEU* 3.7 27.6 - - + -
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Residues in contact with MET 253 (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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168B LEU 4.2 0.2 - - - +
239B MET* 3.6 30.7 - - + -
249B THR 3.1 17.7 + - - +
250B ASN* 2.9 17.0 + - - +
252B VAL* 1.3 76.5 - - - +
254B LEU* 1.3 76.3 + - + +
256B ARG 2.4 19.3 - - - +
257B ALA* 3.7 4.2 - - - -
258B GLN 3.2 16.7 + - - +
259B PRO* 3.4 35.4 - - + -
260B MET 4.8 0.7 - - - +
355B GLU* 3.9 23.1 - - + -
356B ALA* 4.3 6.5 - - - -
359B ARG* 3.7 15.9 + - - +
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Residues in contact with LEU 254 (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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1B MET* 4.1 7.2 - - + +
7B TRP* 3.7 20.4 - - + -
168B LEU 3.9 3.6 - - - +
169B GLY* 3.2 4.8 - - - -
170B LEU* 2.9 29.8 + - + +
234B LEU* 4.0 8.7 - - + -
237B ALA* 3.9 28.0 - - + +
239B MET* 4.0 20.2 - - - -
250B ASN 2.9 14.3 + - - +
251B TYR 3.4 6.3 - - - +
253B MET* 1.3 94.9 - - + +
255B GLU* 1.3 57.9 + - - +
355B GLU* 4.9 4.9 - - - +
359B ARG* 3.6 23.6 - - - +
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Residues in contact with GLU 255 (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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7B TRP* 4.6 3.6 - - + -
11B TYR* 3.1 27.5 + - + +
169B GLY* 3.1 2.6 - - - -
170B LEU* 3.0 10.4 + - - +
171B LEU* 2.9 42.5 + - + +
172B GLY 4.1 0.2 + - - -
187B PRO* 3.6 11.0 - - - +
251B TYR* 2.9 16.3 + - + +
252B VAL* 3.1 12.1 + - - +
254B LEU* 1.3 77.1 - - - +
256B ARG* 1.3 92.6 + - - +
375B ARG* 2.8 40.6 + - - +
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Residues in contact with ARG 256 (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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169B GLY* 4.0 1.1 - - - -
171B LEU* 4.3 19.1 - - + +
175B ARG* 5.9 5.2 - - - +
186B GLU* 5.6 1.6 - - - +
187B PRO* 3.8 20.4 + - - +
252B VAL* 2.9 31.1 - - + +
253B MET 2.4 27.6 - - - +
255B GLU* 1.3 101.7 + - + +
257B ALA* 1.3 54.1 + - - +
258B GLN* 2.7 17.7 + - + +
368B GLY 5.6 0.4 - - - -
371B PRO* 4.3 24.4 + - - +
372B ALA* 4.2 17.7 - - - +
375B ARG* 3.9 20.9 - - - +
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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