Contacts of the helix formed by residues 271 - 279 (chain B) in PDB entry 1B43
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 LEU 271 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B ILE* 4.2 14.8 - - + +
237B ASN* 5.0 10.5 - - + +
241B ILE* 4.0 24.5 - - + -
260B LEU* 3.5 41.4 - - + +
263B PHE* 4.0 19.5 - - + -
264B GLN* 2.8 25.6 + - + +
267B SER* 3.6 18.4 - - - +
269B VAL* 3.2 30.1 + - + +
270B ASP* 1.3 72.5 - - - +
272B TYR* 1.3 55.9 + - - +
274B ILE* 3.2 10.0 + - - +
275B LYS 3.1 20.8 + - - -
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Residues in contact with TYR 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B ASP* 2.4 30.5 + - - -
260B LEU* 4.0 17.3 + - + +
261B ALA* 3.2 38.0 + - + +
264B GLN* 2.8 30.0 + - + +
270B ASP* 4.4 2.9 - - - +
271B LEU* 1.3 70.9 - - - +
273B ALA* 1.3 58.0 + - - +
274B ILE 3.1 5.4 - - - -
275B LYS* 3.8 28.0 - - + +
276B GLU* 3.1 31.4 + - - +
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Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ASN* 3.8 23.5 - - - +
287A TYR 6.0 0.2 - - - +
85B PHE* 3.3 20.4 - - + -
86B LYS* 4.5 0.4 - - - +
270B ASP* 3.3 38.5 + - + +
271B LEU 3.2 1.0 - - - -
272B TYR* 1.3 76.9 - - - +
274B ILE* 1.3 57.0 + - - +
276B GLU* 3.5 21.6 - - - +
277B PHE* 3.3 12.0 - - - +
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Residues in contact with ILE 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PHE* 3.7 22.2 - - + -
230B ILE* 4.6 7.9 - - + -
234B THR* 4.0 5.4 - - - +
236B TYR* 3.4 34.3 - - + -
237B ASN* 3.7 14.6 - - + +
269B VAL* 3.4 27.1 - - + -
270B ASP 3.2 12.6 - - - +
271B LEU* 3.2 10.3 + - - +
272B TYR 3.1 0.6 - - - -
273B ALA* 1.3 78.6 - - - +
275B LYS* 1.3 65.0 + - - +
276B GLU 3.4 0.2 - - - -
277B PHE* 3.3 3.3 + - - +
278B PHE* 3.1 53.1 + - + -
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Residues in contact with LYS 275 (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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223B GLU* 2.8 45.9 + - - -
226B ILE* 4.0 11.5 - - + +
227B GLU* 3.9 17.6 + - + -
230B ILE* 3.5 26.2 - - + +
258B ASP* 5.8 0.8 + - - -
260B LEU* 4.1 6.7 - - + -
271B LEU 3.1 11.8 + - - +
272B TYR* 3.6 28.0 + - + +
274B ILE* 1.3 77.8 - - - +
276B GLU* 1.3 57.9 + - + +
278B PHE* 3.5 4.2 + - - +
279B LEU* 3.2 38.0 + - + +
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Residues in contact with GLU 276 (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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162A LYS* 5.1 1.4 + - - -
285A ASP* 3.4 47.4 - - + +
286A ASN* 4.6 0.8 + - + -
272B TYR 3.1 15.9 + - - +
273B ALA* 3.5 23.8 - - - +
275B LYS* 1.3 77.3 - - - +
277B PHE* 1.3 60.6 + - - +
279B LEU* 3.7 10.9 - - + +
280B ASN* 2.8 39.3 + - - +
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Residues in contact with PHE 277 (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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284A THR* 5.1 8.3 - - - -
286A ASN* 5.6 3.6 - - + -
83B PRO* 3.2 24.5 - - + -
85B PHE* 3.9 16.4 - + + -
150B SER* 3.7 8.7 - - - -
151B GLU* 3.5 14.4 - - + -
178B PHE* 3.6 17.9 - + - -
236B TYR* 3.3 37.9 - + - -
273B ALA 3.3 18.2 - - - +
274B ILE 3.5 5.6 - - - +
275B LYS 3.3 0.2 - - - -
276B GLU* 1.3 81.8 - - - +
278B PHE* 1.3 57.4 + + - +
280B ASN 4.4 4.0 - - - -
281B PRO* 2.9 36.9 - - + +
282B PRO* 3.5 30.5 - - + -
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Residues in contact with PHE 278 (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 VAL* 5.3 0.2 - - + -
174B ASP* 4.3 10.3 - - - -
177B LEU* 3.5 34.0 - - + +
178B PHE* 3.3 51.7 - + - -
222B ARG* 3.1 16.5 + - - -
226B ILE* 3.6 36.1 - - + -
230B ILE* 4.9 0.9 - - + -
234B THR* 3.8 23.1 - - + -
236B TYR* 3.3 22.9 - + - -
274B ILE* 3.1 41.9 + - + -
275B LYS 3.7 1.3 - - - +
276B GLU 3.3 0.2 - - - -
277B PHE* 1.3 80.6 - + - +
279B LEU* 1.3 58.4 + - - +
281B PRO* 3.6 2.1 - - - +
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Residues in contact with LEU 279 (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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178B PHE 5.2 0.2 - - - +
222B ARG* 3.4 35.4 + - + +
223B GLU* 4.2 24.5 - - + +
226B ILE* 3.8 19.5 - - + -
275B LYS* 3.2 43.4 + - + +
276B GLU* 3.7 7.9 - - - +
277B PHE 3.3 0.2 - - - -
278B PHE* 1.3 80.5 - - - +
280B ASN* 1.3 78.1 + - - +
281B PRO* 3.6 3.3 - - - +
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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