Contacts of the helix formed by residues 256 - 273 (chain B) in PDB entry 1BO1
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 SER 256 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252B VAL* 3.2 30.9 + - - +
253B GLY* 5.0 0.2 - - - -
254B GLU 4.3 1.2 - - - +
255B GLU* 1.3 79.0 - - - +
257B LYS* 1.3 58.5 + - - +
258B LYS 3.1 2.0 - - - -
259B ASN* 3.3 9.3 + - - +
260B PHE* 2.9 29.6 + - - +
354B HIS* 3.4 18.9 + - - -
355B GLU 6.1 0.2 - - - -
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Residues in contact with LYS 257 (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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252B VAL* 3.4 13.3 - - + +
253B GLY 3.2 23.6 + - - +
254B GLU* 4.5 6.3 - - + -
255B GLU 3.6 0.2 - - - -
256B SER* 1.3 77.4 - - - +
258B LYS* 1.3 57.3 + - - +
260B PHE* 3.8 0.8 - - - +
261B LEU* 3.0 45.7 + - + +
412B SER 4.3 7.1 + - - -
415B LEU* 2.8 59.4 + - + -
416B THR* 3.5 18.1 + - - +
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Residues in contact with LYS 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B GLU 3.7 18.8 + - - +
255B GLU* 3.8 6.9 + - - +
256B SER 3.1 0.2 - - - -
257B LYS* 1.3 81.9 - - - +
259B ASN* 1.3 64.1 + - - +
261B LEU* 3.8 4.3 - - - +
262B GLU* 3.0 60.0 + - + +
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Residues in contact with ASN 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B GLU* 2.6 35.2 + - - +
256B SER* 3.3 8.9 + - - +
258B LYS* 1.3 83.1 - - - +
260B PHE* 1.3 64.1 + - - +
262B GLU* 3.7 16.9 + - - +
263B LYS* 3.4 28.6 + - - +
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Residues in contact with PHE 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LEU* 3.6 36.1 - - + +
256B SER 2.9 17.1 + - - +
257B LYS* 3.8 3.8 - - - +
259B ASN* 1.3 76.7 - - - +
261B LEU* 1.3 69.1 + - + +
263B LYS* 2.9 30.6 + - + +
264B LEU* 3.2 16.1 + - + +
281B LEU* 4.4 12.1 - - + -
354B HIS* 3.5 29.4 - + + +
365B MET* 3.7 39.0 - - + -
411B MET* 5.3 4.7 - - + -
414B ILE* 6.4 1.3 - - + -
415B LEU* 3.1 34.5 - - + -
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Residues in contact with LEU 261 (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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257B LYS* 3.0 29.6 + - + +
258B LYS* 4.0 3.6 - - - +
260B PHE* 1.3 88.1 - - + +
262B GLU* 1.3 57.7 + - + +
264B LEU* 3.4 28.6 - - + +
265B LYS* 3.1 26.0 + - - +
408B ASN* 4.1 7.0 + - - +
411B MET 3.9 7.6 - - - +
412B SER* 3.8 46.9 - - - +
415B LEU* 3.7 13.7 - - + -
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Residues in contact with GLU 262 (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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258B LYS* 3.0 54.9 + - + +
259B ASN* 4.0 12.8 + - - +
260B PHE 3.2 0.2 - - - -
261B LEU* 1.3 74.3 - - + +
263B LYS* 1.3 70.8 + - - +
265B LYS* 3.5 15.6 + - + +
266B ARG* 3.6 12.5 + - - +
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Residues in contact with LYS 263 (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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177B ASN* 2.9 46.7 + - - +
178B THR* 4.7 6.8 + - - +
179B LEU* 3.7 34.1 - - + +
259B ASN* 3.4 20.4 + - - +
260B PHE* 2.9 12.0 + - - +
262B GLU* 1.3 74.6 - - - +
264B LEU* 1.3 68.2 + - - +
266B ARG* 2.7 39.0 + - - +
267B ASP* 3.2 11.0 + - - +
351B MET* 5.2 10.1 - - - +
354B HIS* 5.9 2.8 + - - -
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Residues in contact with LEU 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LEU* 4.2 15.4 - - + +
260B PHE* 3.2 11.5 + - + +
261B LEU* 3.4 22.9 - - + +
263B LYS* 1.3 79.4 - - - +
265B LYS* 1.3 61.3 + - - +
267B ASP* 3.2 6.9 + - - -
268B VAL* 3.1 42.1 + - + +
281B LEU* 4.9 2.7 - - + -
367B ILE* 4.1 10.3 - - + -
407B PHE* 3.4 28.7 - - + -
408B ASN* 3.4 28.5 - - - +
411B MET* 3.7 28.7 - - + -
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Residues in contact with LYS 265 (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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261B LEU 3.1 14.0 + - - +
262B GLU* 3.7 15.5 - - + +
263B LYS 2.9 0.2 + - - -
264B LEU* 1.3 78.3 - - - +
266B ARG* 1.3 58.8 + - + +
268B VAL* 4.3 1.4 - - - +
269B GLU* 3.0 42.7 + - - +
408B ASN* 3.4 16.1 - - - +
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Residues in contact with ARG 266 (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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170B PHE* 3.8 26.8 - - + -
173B GLU 3.6 21.8 + - - -
174B CYS* 3.9 19.3 + - - +
177B ASN* 4.8 13.5 + - - +
178B THR* 5.3 0.9 - - - -
262B GLU 3.6 5.6 + - - +
263B LYS* 2.7 38.9 + - - +
265B LYS* 1.3 75.3 - - + +
267B ASP* 1.3 65.0 + - - +
269B GLU* 3.7 13.9 - - - +
270B PHE* 3.0 25.5 + - - +
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Residues in contact with ASP 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B PHE* 3.4 23.2 - - - -
178B THR* 3.6 11.8 - - - +
179B LEU* 3.3 30.5 + - - +
180B LEU* 4.1 12.8 - - + -
263B LYS* 3.7 15.9 - - - +
264B LEU 3.2 4.3 + - - +
266B ARG* 1.3 77.4 - - - +
268B VAL* 1.3 56.5 + - - +
269B GLU 2.9 3.4 - - - -
270B PHE* 2.7 24.1 + - - +
271B LEU* 2.8 18.2 + - - +
367B ILE* 3.3 27.4 - - + +
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Residues in contact with VAL 268 (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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264B LEU* 3.1 41.2 + - + +
265B LYS 4.6 1.6 - - - +
267B ASP* 1.3 73.7 - - - +
269B GLU* 1.3 56.6 + - - +
271B LEU* 3.7 8.2 + - - +
272B ALA* 3.0 26.2 + - - +
279B TYR* 2.7 32.1 - - + +
367B ILE* 4.1 6.5 - - + +
404B SER* 3.1 35.4 + - - +
407B PHE* 3.6 15.3 - - + -
408B ASN* 5.0 4.5 - - + +
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Residues in contact with GLU 269 (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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265B LYS* 3.0 44.0 + - - +
266B ARG* 3.7 12.5 - - - +
267B ASP 2.9 0.2 - - - -
268B VAL* 1.3 77.4 - - - +
270B PHE* 1.3 59.0 + - - +
272B ALA* 3.3 9.0 + - + +
273B GLN* 2.9 26.0 + - - +
404B SER* 5.4 1.3 - - - -
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Residues in contact with PHE 270 (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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163B ILE* 5.9 0.9 - - + -
166B LYS* 3.9 7.9 - - + -
167B TYR* 3.4 36.3 - + + -
170B PHE* 3.6 41.7 - + + -
180B LEU* 3.9 18.8 - - + -
266B ARG 3.0 15.9 + - - +
267B ASP 2.7 12.6 + - - +
269B GLU* 1.3 69.1 - - - +
271B LEU* 1.3 82.9 + - + +
273B GLN* 2.9 40.6 + - - +
274B LEU* 3.3 32.1 + - + +
370B ILE* 4.9 3.4 - - + -
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Residues in contact with LEU 271 (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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180B LEU* 3.8 22.4 - - + -
267B ASP 2.8 17.1 + - - +
268B VAL* 3.9 8.5 - - - +
270B PHE* 1.3 90.9 - - + +
272B ALA* 1.3 58.0 + - - +
274B LEU* 2.7 36.8 - - - +
276B ILE* 3.4 22.3 + - + -
279B TYR* 3.5 44.9 - - + -
367B ILE* 4.2 7.0 - - + -
370B ILE* 3.6 31.0 - - + -
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Residues in contact with ALA 272 (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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268B VAL 3.0 12.7 + - - +
269B GLU* 3.3 11.0 - - + +
270B PHE 3.1 0.2 - - - -
271B LEU* 1.3 72.9 - - - +
273B GLN* 1.3 62.5 + - - +
274B LEU 2.9 6.7 + - - -
275B LYS* 3.8 8.2 + - - +
276B ILE 5.3 1.1 - - - +
279B TYR* 6.0 0.2 - - - -
400B PRO 5.7 0.4 - - - -
401B GLU* 3.4 36.1 - - - +
404B SER* 3.1 26.7 - - - +
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Residues in contact with GLN 273 (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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166B LYS* 2.9 46.1 + - - +
269B GLU 2.9 11.9 + - - +
270B PHE* 2.9 27.5 + - - +
272B ALA* 1.3 75.3 - - - +
274B LEU* 1.3 71.8 + - - +
275B LYS 4.1 0.4 + - - -
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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
------------------------------------------------------------
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