Contacts of the helix formed by residues 227 - 237 (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 PRO 227 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136B PRO* 3.8 12.8 - - + -
225B PRO 4.3 2.2 - - - +
226B SER* 1.3 90.3 - - - +
228B LEU* 1.3 68.1 + - - +
229B TRP* 3.4 29.8 - - + +
230B MET* 2.8 16.7 + - + +
231B GLN 3.0 10.0 + - - -
244B ASN* 5.0 1.6 - - + -
383B LEU* 3.8 36.1 - - + -
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Residues in contact with LEU 228 (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 PHE* 5.7 1.1 - - + -
135B PHE* 3.6 46.2 - - + -
136B PRO* 4.6 2.6 - - + +
139B ALA* 4.2 12.7 - - + +
140B LEU* 3.8 18.2 - - + -
146B LEU* 4.2 14.4 - - + -
149B ALA* 3.7 37.0 - - + +
150B TRP* 4.1 15.7 - - + -
226B SER 3.7 0.4 + - - -
227B PRO* 1.3 70.2 - - - +
229B TRP* 1.3 56.2 + - + +
231B GLN* 2.9 5.7 + - - +
232B ARG* 2.6 37.5 + - - +
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Residues in contact with TRP 229 (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 ALA 5.6 0.2 + - - -
227B PRO* 3.5 28.8 - - + +
228B LEU* 1.3 76.3 - - + +
230B MET* 1.3 97.3 + - + +
232B ARG* 3.5 11.4 + - - +
233B ALA* 3.0 29.1 + - + +
251B TYR* 3.4 37.5 - + - -
375B ARG* 6.1 0.4 - - - -
379B LEU* 4.9 10.8 - - + -
383B LEU* 4.5 11.4 - - + +
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Residues in contact with MET 230 (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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226B SER* 3.6 22.7 - - - +
227B PRO* 2.8 18.8 + - + +
229B TRP* 1.3 116.8 - - + +
231B GLN* 1.3 68.4 + - - +
233B ALA* 3.2 4.4 + - - +
234B LEU* 2.8 38.0 + - + +
247B ASP* 3.9 25.6 - - - +
248B VAL* 4.2 6.3 - - + -
251B TYR* 4.1 21.3 - - + -
379B LEU* 5.3 2.9 - - + -
383B LEU* 3.8 19.7 - - + -
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Residues in contact with GLN 231 (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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133B LEU* 4.5 3.2 - - - +
134B GLU 2.6 31.7 + - - +
135B PHE* 3.5 23.5 - - - -
150B TRP* 4.1 12.8 - - + -
225B PRO* 5.3 0.2 - - - -
226B SER* 2.8 38.2 + - - +
227B PRO 3.0 5.4 + - - +
228B LEU* 2.9 8.6 + - - +
230B MET* 1.3 76.9 - - - +
232B ARG* 1.3 58.0 + - - +
234B LEU* 3.8 0.9 - - - +
235B PHE* 2.8 44.6 + - - +
241B PRO* 3.7 35.9 - - + +
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Residues in contact with ARG 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B SER* 3.0 27.5 + - - -
39B PHE* 3.8 6.8 - - + -
149B ALA 4.5 4.9 - - - -
150B TRP* 3.5 38.5 - - + +
151B PRO* 3.0 53.8 + - - +
152B GLU 3.0 15.6 + - - -
153B GLU* 3.4 23.3 + - - +
228B LEU 2.6 19.9 + - - +
229B TRP* 3.5 10.8 - - - +
231B GLN* 1.3 72.6 - - - +
233B ALA* 1.3 59.6 + - - +
235B PHE* 3.2 2.1 + - - +
236B ALA* 2.9 31.3 + - + +
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Residues in contact with ALA 233 (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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4B PRO* 5.6 0.4 - - - -
7B TRP* 3.3 41.8 - - + -
153B GLU* 5.7 2.2 - - - -
229B TRP* 3.0 18.9 + - + +
230B MET 3.7 2.9 - - - +
232B ARG* 1.3 76.6 - - - +
234B LEU* 1.3 58.2 + - - +
236B ALA* 3.3 7.8 + - - +
237B ALA* 2.9 28.8 + - - +
251B TYR* 3.9 13.5 - - + +
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Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B TRP* 4.7 0.7 - - + -
230B MET* 2.8 43.0 + - + +
231B GLN 3.8 2.7 - - - +
233B ALA* 1.3 72.7 - - - +
235B PHE* 1.3 62.3 + - - +
237B ALA* 3.0 10.2 + - - +
239B MET* 2.8 41.0 + - + +
240B ARG 5.6 0.4 - - - -
241B PRO* 4.3 10.8 - - + -
247B ASP* 3.8 33.9 - - + +
250B ASN* 4.1 9.6 - - + +
251B TYR* 3.9 29.6 - - + +
254B LEU* 4.0 20.0 - - + -
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Residues in contact with PHE 235 (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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39B PHE* 4.1 10.6 - - + -
120B PRO* 3.8 33.0 - - + -
125B VAL* 3.6 28.8 - - + +
126B GLY* 4.2 7.6 - - - -
127B GLU 5.5 0.4 - - - -
128B TYR* 5.7 0.7 - - + -
133B LEU* 3.6 22.9 - - + -
150B TRP* 3.8 17.7 - + + -
231B GLN* 2.8 27.3 + - - +
232B ARG 3.6 3.6 - - - +
234B LEU* 1.3 76.6 - - - +
236B ALA* 1.3 58.2 + - - +
238B GLY* 3.0 19.1 + - - -
239B MET 3.3 9.0 - - - -
240B ARG* 4.1 17.0 - - + -
241B PRO* 3.2 30.5 - - + -
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Residues in contact with ALA 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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2B ARG* 3.9 15.9 + - - +
4B PRO* 3.9 23.8 - - + -
38B VAL* 5.7 0.4 - - - -
39B PHE* 3.8 20.6 - - + -
153B GLU* 4.4 6.5 - - + +
155B VAL* 4.0 21.0 - - + +
232B ARG 2.9 17.6 + - - +
233B ALA* 3.5 7.6 - - - +
234B LEU 3.2 0.2 - - - -
235B PHE* 1.3 72.3 - - - +
237B ALA* 1.3 57.4 + - - +
238B GLY 2.9 9.1 + - - -
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Residues in contact with ALA 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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2B ARG* 3.7 26.8 - - + +
4B PRO* 4.2 6.0 - - + +
7B TRP* 3.9 10.1 - - + -
233B ALA 2.9 13.6 + - - +
234B LEU 3.0 9.6 + - - +
236B ALA* 1.3 76.2 - - - +
238B GLY* 1.3 61.1 + - - +
239B MET* 3.5 2.7 + - - +
254B LEU* 3.9 28.2 - - + +
355B GLU* 5.5 2.9 - - - +
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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