Contacts of the helix formed by residues 254 - 274 (chain A) in PDB entry 4BZ5
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 254 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A GLY 3.5 4.1 + - - +
253A ILE* 1.3 75.6 - - - +
255A ASP* 1.3 65.4 + - - +
256A LEU* 3.3 8.6 + - - +
257A ASP* 2.9 38.5 + - - +
258A TRP* 3.0 27.1 + - - +
296A ARG* 4.0 16.2 - - + +
297A LEU* 4.8 2.7 - - - -
393A PRO* 5.8 8.5 - - + +
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Residues in contact with ASP 255 (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 ASN* 1.3 75.5 - - - +
256A LEU* 1.3 55.0 + - - +
258A TRP* 3.8 3.0 - - - +
259A SER* 2.7 38.4 + - - -
296A ARG 4.2 2.2 + - - -
297A LEU* 3.3 8.1 - - - +
298A THR* 2.7 52.9 + - - +
300A PHE* 4.9 2.1 - - - +
316A LEU 3.4 19.5 + - - +
317A SER* 3.5 4.5 + - - -
318A GLY* 2.9 26.6 + - - +
393A PRO* 5.8 2.6 - - - +
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Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ASN* 3.3 9.6 + - - +
255A ASP* 1.3 79.0 - - - +
257A ASP* 1.3 64.9 + - - +
259A SER* 3.2 8.7 + - - -
260A ASN* 2.8 52.0 + - - +
316A LEU 5.6 0.2 - - - -
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Residues in contact with ASP 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ILE* 3.7 20.1 - - + +
254A ASN* 2.9 31.3 + - - +
256A LEU* 1.3 81.4 - - - +
258A TRP* 1.3 57.0 + - - +
260A ASN* 3.5 9.4 + - - +
261A ALA* 2.9 29.3 + - - +
404A ILE* 4.6 7.2 - - + +
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Residues in contact with TRP 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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185A LEU* 3.8 34.5 + - + -
208A VAL* 3.9 33.3 - - + +
249A LEU* 3.7 20.6 - - + -
253A ILE* 3.6 22.6 - - + +
254A ASN 3.0 20.1 + - - +
255A ASP 3.8 2.2 - - - +
257A ASP* 1.3 76.9 - - - +
259A SER* 1.3 64.6 + - - +
261A ALA* 3.2 4.7 + - - +
262A ILE* 3.1 53.4 + - + +
286A CYS* 4.7 2.2 - - - -
295A PHE* 4.1 16.2 - + - -
297A LEU* 3.7 22.6 - - + +
318A GLY* 3.1 43.5 - - - -
319A TYR* 4.6 3.6 - + - -
321A TYR* 5.4 0.2 - + - -
322A ALA* 4.1 0.2 - - + -
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Residues in contact with SER 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ASP 2.7 23.7 + - - -
256A LEU* 3.2 10.0 + - - -
258A TRP* 1.3 81.4 - - - +
260A ASN* 1.3 59.6 + - - +
262A ILE* 4.4 0.7 - - - -
263A GLY* 2.9 27.9 + - - -
316A LEU 4.4 2.9 + - - -
318A GLY* 3.5 14.9 - - - -
321A TYR* 3.3 49.0 + - - +
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Residues in contact with ASN 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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256A LEU* 2.8 46.9 + - - +
257A ASP* 3.9 10.1 + - - +
259A SER* 1.3 75.1 - - - +
261A ALA* 1.3 62.5 + - - +
264A PRO* 3.1 20.6 - - - +
321A TYR* 5.3 4.0 + - - -
404A ILE* 5.6 0.4 - - - -
408A HIS* 3.6 8.8 - - - -
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Residues in contact with ALA 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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247A LEU* 3.9 18.0 - - + +
249A LEU* 4.5 6.5 - - + -
257A ASP 2.9 18.4 + - - +
258A TRP* 3.5 8.3 - - - +
259A SER 3.2 0.4 - - - -
260A ASN* 1.3 78.7 - - - +
262A ILE* 1.3 62.3 + - + +
264A PRO* 4.2 0.2 - - - +
265A ILE* 3.5 11.4 - - - +
404A ILE* 3.9 27.6 - - + -
408A HIS* 2.7 26.5 + - - -
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Residues in contact with ILE 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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185A LEU* 4.3 7.4 - - + -
206A PHE* 4.4 11.0 - - + -
208A VAL* 3.7 36.3 - - + -
247A LEU* 4.0 7.2 - - + -
249A LEU* 5.3 0.2 - - + -
258A TRP* 3.1 55.1 + - + +
259A SER* 3.9 4.3 - - - +
261A ALA* 1.3 79.2 - - + +
263A GLY* 1.3 69.8 + - - +
264A PRO 3.5 1.1 - - - -
265A ILE* 3.1 10.2 + - - +
266A LEU* 2.9 33.7 + - + +
321A TYR* 4.7 2.5 - - + -
322A ALA* 3.9 17.5 - - + -
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Residues in contact with GLY 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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259A SER 2.9 18.7 + - - -
262A ILE* 1.3 77.6 - - - +
264A PRO* 1.3 67.8 - - - +
266A LEU* 3.3 3.6 + - - +
267A ASP* 3.1 27.4 + - - +
321A TYR* 3.5 22.7 - - - -
325A LYS* 3.8 10.0 - - - +
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Residues in contact with PRO 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A SER 4.5 0.2 - - - +
260A ASN* 3.1 23.6 - - - +
261A ALA 4.2 2.0 - - - +
262A ILE 3.7 0.9 - - - -
263A GLY* 1.3 89.4 - - - +
265A ILE* 1.3 58.2 + - - +
267A ASP* 3.9 6.0 - - + +
268A SER* 3.0 30.8 + - - -
321A TYR* 5.2 0.9 - - - +
408A HIS* 4.1 9.0 - - + -
434A LEU* 3.7 29.5 - - + +
435A TYR* 3.5 29.9 + - + -
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Residues in contact with ILE 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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206A PHE* 3.6 28.7 - - + -
245A PHE* 5.8 0.4 - - + -
247A LEU* 3.9 15.7 - - + -
261A ALA 3.5 22.2 - - - +
262A ILE 3.1 6.8 + - - +
264A PRO* 1.3 74.1 - - - +
266A LEU* 1.3 61.2 + - - +
268A SER* 2.9 3.9 + - - +
269A LEU* 2.9 49.3 + - + +
408A HIS* 3.9 8.1 - - + -
411A ILE* 3.3 40.2 - - + -
435A TYR* 3.5 24.7 - - + +
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Residues in contact with LEU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A LEU* 5.5 0.2 - - + -
183A VAL* 3.8 39.3 - - + -
206A PHE* 3.9 17.7 - - + -
262A ILE* 2.9 40.0 + - + +
263A GLY* 3.7 6.3 - - - +
265A ILE* 1.3 75.7 - - - +
267A ASP* 1.3 63.7 + - - +
269A LEU* 3.3 7.2 + - + +
270A ASN 3.0 19.6 + - - -
321A TYR* 5.7 0.4 - - + -
322A ALA* 4.2 15.7 - - + -
325A LYS* 4.0 15.3 - - + -
326A ILE* 4.4 12.3 - - + -
329A TRP* 3.2 27.0 - - + -
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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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263A GLY 3.1 12.0 + - - +
264A PRO* 4.0 3.0 - - + +
266A LEU* 1.3 79.5 - - - +
268A SER* 1.3 62.7 + - - +
270A ASN* 3.5 2.9 + - - +
271A ILE* 3.1 30.8 + - + +
325A LYS* 2.6 38.9 + - - +
329A TRP* 3.4 23.0 + - - -
434A LEU* 3.8 24.9 - - + +
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Residues in contact with SER 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 PRO 3.0 13.1 + - - -
265A ILE* 2.9 12.1 + - - +
267A ASP* 1.3 77.3 - - - +
269A LEU* 1.3 58.1 + - - +
271A ILE* 3.4 3.2 + - - +
272A VAL* 3.0 34.7 + - - +
411A ILE* 5.4 0.7 - - - +
415A LEU* 3.4 12.0 - - - +
431A VAL* 3.6 26.7 - - - -
434A LEU* 3.4 11.4 - - - +
435A TYR* 2.8 25.7 + - - -
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Residues in contact with LEU 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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181A LEU* 4.1 16.8 - - + -
204A VAL* 4.4 1.1 - - + -
206A PHE* 3.8 31.6 - - + -
245A PHE* 4.0 35.7 - - + -
265A ILE* 2.9 40.2 + - + +
266A LEU* 3.7 7.4 - - + +
268A SER* 1.3 78.5 + - - +
270A ASN* 1.3 57.1 + - - +
273A ILE* 2.8 60.6 + - + +
411A ILE* 6.0 1.3 - - + -
415A LEU* 4.2 11.4 - - + -
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Residues in contact with ASN 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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181A LEU* 4.5 1.2 - - - +
266A LEU 3.0 6.7 + - - +
267A ASP* 3.8 4.5 + - - +
269A LEU* 1.3 77.1 - - - +
271A ILE* 1.3 63.4 + - - +
274A GLN* 2.9 29.3 + - - +
275A PRO* 3.5 22.4 - - - +
329A TRP* 3.4 68.9 - - + +
331A VAL* 4.4 5.2 - - - +
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Residues in contact with ILE 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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267A ASP* 3.1 24.1 + - + +
268A SER* 3.7 4.5 - - - +
269A LEU 3.3 0.2 - - - -
270A ASN* 1.3 84.7 - - - +
272A VAL* 1.3 62.8 + - + +
274A GLN* 3.5 16.6 - - - +
425A ILE 5.2 1.2 - - - +
426A TYR* 4.9 11.3 - - + +
427A ASP 5.8 1.1 - - - +
430A GLN* 3.6 33.7 - - + +
431A VAL* 4.0 18.8 - - + -
434A LEU* 3.7 27.8 - - + -
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Residues in contact with VAL 272 (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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268A SER 3.0 19.3 + - - +
271A ILE* 1.3 76.6 - - - +
273A ILE* 1.3 64.3 + - - +
274A GLN* 4.5 4.9 - - - +
415A LEU* 3.5 39.5 - - + -
418A TYR* 4.7 2.0 - - + -
419A ALA* 3.9 25.1 - - + -
424A LEU* 3.7 23.9 - - + +
425A ILE 5.0 3.5 - - - +
426A TYR* 3.7 37.2 - - + -
431A VAL* 3.9 8.5 - - + -
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Residues in contact with ILE 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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179A ARG* 2.9 42.4 + - + -
180A VAL 5.2 1.8 - - - +
181A LEU* 3.9 11.7 - - + -
204A VAL* 3.6 47.1 - - + -
269A LEU* 2.8 45.5 + - + +
272A VAL* 1.3 76.3 - - + +
274A GLN* 1.3 69.7 + - - +
275A PRO* 3.9 22.7 - - + -
415A LEU* 5.0 1.6 - - + -
418A TYR* 4.3 12.8 - - + +
424A LEU* 4.8 6.4 - - - +
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Residues in contact with GLN 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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179A ARG* 3.5 20.7 + - - +
270A ASN* 2.9 15.5 + - - +
271A ILE* 3.5 20.6 - - - +
272A VAL 4.5 3.3 - - - +
273A ILE* 1.3 79.2 - - - +
275A PRO* 1.3 71.9 - - - +
276A SER* 3.7 1.7 + - - -
425A ILE 4.6 10.8 - - - +
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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