Contacts of the helix formed by residues 256 - 274 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A VAL* 3.4 22.9 + - - -
254A GLU 4.3 0.8 - - - +
255A GLU* 1.3 78.0 - - - +
257A LYS* 1.3 59.1 + - - +
258A LYS 3.1 2.0 - - - -
259A ASN* 3.3 9.8 + - - +
260A PHE* 2.9 29.8 + - - +
354A HIS* 2.9 35.9 + - - -
355A GLU 5.8 0.4 - - - -
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Residues in contact with LYS 257 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A VAL* 4.0 3.5 - - + +
253A GLY 3.5 16.2 + - - +
254A GLU* 4.1 11.7 - - + +
255A GLU 3.4 0.6 - - - -
256A SER* 1.3 78.8 - - - +
258A LYS* 1.3 57.1 + - - +
260A PHE* 3.8 0.7 - - - +
261A LEU* 3.0 49.9 + - + +
412A SER 4.3 5.9 + - - -
415A LEU* 3.7 44.6 + - + -
416A THR* 3.5 30.1 + - - +
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Residues in contact with LYS 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A GLU 3.9 11.7 + - - +
255A GLU* 3.6 16.5 + - - +
256A SER 3.1 0.2 - - - -
257A LYS* 1.3 80.9 - - - +
259A ASN* 1.3 65.4 + - - +
261A LEU* 3.8 3.2 - - - +
262A GLU* 3.0 59.9 + - + +
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Residues in contact with ASN 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A GLU* 2.6 39.3 + - - +
256A SER* 3.3 9.9 + - - +
258A LYS* 1.3 82.6 - - - +
260A PHE* 1.3 61.5 + - - +
262A GLU* 3.7 15.2 + - - +
263A LYS* 3.1 30.0 + - - +
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Residues in contact with PHE 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A LEU* 3.3 39.7 - - + -
256A SER 2.9 17.9 + - - +
257A LYS 3.8 2.0 - - - +
259A ASN* 1.3 76.5 - - - +
261A LEU* 1.3 71.6 + - + +
263A LYS* 2.9 12.9 + - - +
264A LEU* 2.7 53.1 + - + +
281A LEU* 4.4 14.8 - - + -
354A HIS* 3.6 28.0 + + + +
365A MET* 4.3 23.6 - - + -
411A MET* 4.4 6.3 - - + -
415A LEU* 3.3 37.9 - - + -
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Residues in contact with LEU 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A LYS* 3.0 36.4 + - + +
258A LYS* 4.0 3.8 - - - +
260A PHE* 1.3 91.3 - - + +
262A GLU* 1.3 57.2 - - + +
264A LEU* 3.7 23.0 - - + +
265A LYS* 3.0 27.4 + - - +
408A ASN* 3.9 10.3 + - - +
411A MET 4.5 0.2 - - - +
412A SER* 3.5 50.5 - - - +
415A LEU* 5.3 1.1 - - + -
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Residues in contact with GLU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A LYS* 3.0 55.8 + - + +
259A ASN* 4.0 12.3 + - - +
261A LEU* 1.3 77.2 - - + +
263A LYS* 1.3 62.7 + - - +
265A LYS* 3.6 11.7 + - + +
266A ARG* 3.5 23.5 + - - +
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Residues in contact with LYS 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A ASN* 3.8 40.4 + - - +
178A THR* 4.2 2.1 + - - +
179A LEU* 3.1 43.6 - - + +
259A ASN* 3.1 21.8 + - - +
260A PHE* 3.1 7.6 - - - +
262A GLU* 1.3 81.2 - - - +
264A LEU* 1.3 57.7 + - - +
266A ARG* 3.4 13.0 - - - +
267A ASP* 2.8 34.8 + - - +
351A MET 5.8 1.8 + - - -
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Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A LEU* 3.9 21.1 - - + -
260A PHE* 2.7 23.4 + - + +
261A LEU* 3.7 19.3 - - + +
263A LYS* 1.3 73.5 - - - +
265A LYS* 1.3 63.7 + - - +
267A ASP* 3.2 5.5 + - - -
268A VAL* 3.1 40.1 + - + +
281A LEU* 4.9 3.6 - - + -
367A ILE* 4.4 4.7 - - + -
407A PHE* 3.5 29.2 - - + -
408A ASN* 3.4 29.2 - - - +
411A MET* 3.7 26.2 - - + -
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Residues in contact with LYS 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A LEU 3.0 18.5 + - - +
262A GLU* 3.7 11.4 - - + +
263A LYS 3.4 0.2 - - - -
264A LEU* 1.3 75.8 - - - +
266A ARG* 1.3 58.0 + - + +
268A VAL* 4.3 1.2 - - - +
269A GLU* 3.0 44.0 + - - +
408A ASN* 3.2 16.1 - - - +
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Residues in contact with ARG 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A PHE* 3.6 26.7 - - + -
173A GLU* 3.2 25.4 + - - +
174A CYS* 3.9 20.1 + - - +
177A ASN* 4.9 8.2 + - - +
178A THR* 5.3 0.4 - - - -
262A GLU 3.5 11.8 + - - +
263A LYS* 3.4 21.1 - - - +
265A LYS* 1.3 78.4 - - + +
267A ASP* 1.3 62.6 + - - +
269A GLU* 3.7 12.7 - - - +
270A PHE* 3.1 25.3 + - - +
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Residues in contact with ASP 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A PHE* 3.2 24.0 - - - -
178A THR* 3.5 11.7 - - - +
179A LEU* 3.2 36.2 + - - +
180A LEU* 4.1 11.2 - - + -
263A LYS* 2.8 25.5 - - - +
264A LEU* 3.2 3.9 + - - +
266A ARG* 1.3 76.2 - - - +
268A VAL* 1.3 57.3 + - - +
269A GLU 2.9 3.8 - - - -
270A PHE* 2.7 22.5 + - - +
271A LEU* 2.8 19.2 + - - +
367A ILE* 3.6 17.3 - - + -
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Residues in contact with VAL 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A LEU* 3.1 30.4 + - + +
265A LYS 4.6 1.3 - - - +
267A ASP* 1.3 73.9 - - - +
269A GLU* 1.3 55.8 + - - +
271A LEU* 3.9 9.9 - - - +
272A ALA* 3.0 26.9 + - - +
279A TYR* 3.1 28.1 + - + +
367A ILE* 4.1 6.1 - - + -
404A SER* 3.3 33.7 + - - +
407A PHE* 3.4 29.8 - - + -
408A ASN* 4.9 4.7 - - + +
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Residues in contact with GLU 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A LYS* 3.0 42.9 + - - +
266A ARG* 3.7 12.0 - - - +
267A ASP 2.9 0.4 - - - -
268A VAL* 1.3 77.8 - - - +
270A PHE* 1.3 59.1 + - - +
272A ALA* 3.3 7.7 + - + +
273A GLN* 2.9 30.4 + - - +
404A SER* 5.0 2.7 - - - -
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Residues in contact with PHE 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ILE* 5.9 0.2 - - + -
166A LYS* 3.9 12.8 - - + -
167A TYR* 3.4 35.4 - + + -
170A PHE* 3.5 42.0 - + + -
180A LEU* 3.8 21.8 - - + -
266A ARG 3.1 15.1 + - - +
267A ASP 2.7 8.1 + - - +
269A GLU* 1.3 74.8 - - - +
271A LEU* 1.3 81.5 + - + +
273A GLN* 3.1 32.3 + - + +
274A LEU* 3.3 35.2 + - + +
276A ILE* 5.1 0.4 - - + -
370A ILE* 5.5 2.0 - - + -
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Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU* 3.5 30.7 - - + -
267A ASP 2.8 17.9 + - - +
268A VAL* 3.9 6.1 - - - +
270A PHE* 1.3 90.8 - - + +
272A ALA* 1.3 61.4 + - - +
274A LEU* 3.3 2.9 + - - +
275A LYS 3.3 19.9 + - - -
276A ILE* 3.3 42.0 + - + -
279A TYR* 3.7 45.8 - - + -
367A ILE* 4.1 12.6 - - + -
370A ILE* 4.0 10.3 - - + -
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Residues in contact with ALA 272 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268A VAL 3.0 11.5 + - - +
269A GLU* 3.3 9.2 - - + +
270A PHE 3.1 0.2 - - - -
271A LEU* 1.3 76.0 - - - +
273A GLN* 1.3 66.3 + - - +
274A LEU 3.1 8.1 + - - +
275A LYS* 3.9 3.3 + - - +
276A ILE 4.9 4.0 - - - -
279A TYR* 5.8 0.4 - - - -
400A PRO* 4.4 12.8 - - - +
401A GLU* 3.6 29.8 - - - +
404A SER* 2.9 30.1 - - - +
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Residues in contact with GLN 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A LYS* 5.2 7.9 + - + +
269A GLU* 2.9 12.0 + - - +
270A PHE* 3.2 26.1 - - + +
272A ALA* 1.3 76.0 - - - +
274A LEU* 1.3 65.2 + - + +
401A GLU* 4.1 5.8 + - - -
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Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ASN 5.5 0.9 - - - +
163A ILE* 3.7 26.0 - - + -
166A LYS* 3.3 43.7 - - + +
270A PHE* 3.3 37.3 + - + +
271A LEU 3.6 4.3 - - - +
272A ALA 3.1 4.5 - - - +
273A GLN* 1.3 85.0 - - + +
275A LYS* 1.3 65.9 + - - +
276A ILE* 3.4 30.7 - - + -
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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