Contacts of the helix formed by residues 254 - 274 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252C GLY 3.5 4.1 + - - +
253C ILE* 1.3 75.0 - - - +
255C ASP* 1.3 67.3 + - - +
256C LEU* 3.3 8.7 + - - +
257C ASP* 2.9 39.4 + - - +
258C TRP* 3.0 24.8 + - - +
296C ARG* 3.9 13.9 - - + +
297C LEU* 3.9 4.5 - - - -
393C PRO* 6.0 6.7 - - + -
394C HIS 5.5 6.3 + - - +
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Residues in contact with ASP 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C ASN* 1.3 75.0 - - - +
256C LEU* 1.3 55.7 + - - +
258C TRP* 3.4 1.4 + - - +
259C SER* 2.7 38.2 + - - -
296C ARG 4.1 2.5 + - - -
297C LEU* 3.3 11.7 - - - +
298C THR* 2.7 53.4 + - - +
300C PHE* 5.0 1.0 - - - -
315C SER* 4.0 14.1 + - - +
316C LEU 3.3 16.7 - - - +
317C SER* 3.5 4.3 + - - -
318C GLY* 2.9 25.4 + - - +
393C PRO* 5.3 2.6 - - - +
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Residues in contact with LEU 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C ASN* 3.3 11.0 + - - +
255C ASP* 1.3 78.7 - - - +
257C ASP* 1.3 66.4 + - - +
259C SER* 3.2 8.5 + - - -
260C ASN* 2.8 56.9 + - - +
315C SER* 4.2 14.5 + - - +
316C LEU 5.6 0.4 - - - -
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Residues in contact with ASP 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C ILE* 3.7 20.5 - - + +
254C ASN* 2.9 27.9 + - - +
256C LEU* 1.3 87.7 - - - +
258C TRP* 1.3 57.7 + - - +
260C ASN* 3.5 7.6 + - - +
261C ALA* 2.9 29.5 + - - +
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Residues in contact with TRP 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C LEU* 3.7 35.7 - - + -
208C VAL* 3.9 27.7 + - + +
249C LEU* 3.7 20.9 - - + -
253C ILE* 3.5 21.2 - - + +
254C ASN 3.0 18.9 + - - +
255C ASP 3.8 1.1 - - - +
257C ASP* 1.3 73.2 - - - +
259C SER* 1.3 67.6 + - - +
261C ALA* 3.3 4.3 + - - +
262C ILE* 3.1 55.7 + - + +
286C CYS* 4.7 1.4 - - - -
295C PHE* 4.1 15.5 - + - -
297C LEU* 3.6 28.7 - - + -
318C GLY* 3.2 43.5 - - - -
319C TYR* 3.8 4.9 - + - -
322C ALA* 4.1 1.6 - - + -
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Residues in contact with SER 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C ASP 2.7 24.2 + - - -
256C LEU* 3.4 10.7 - - - -
258C TRP* 1.3 82.9 - - - +
260C ASN* 1.3 60.3 + - - +
262C ILE* 4.7 1.1 - - - -
263C GLY* 2.9 32.4 + - - -
316C LEU 4.5 2.9 + - - -
318C GLY* 3.5 18.0 + - - -
321C TYR* 3.5 41.5 - - - +
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Residues in contact with ASN 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C LEU* 2.8 46.2 + - - +
257C ASP* 4.0 8.4 + - - +
259C SER* 1.3 79.1 - - - +
261C ALA* 1.3 62.0 + - - +
264C PRO* 3.3 21.7 - - - +
321C TYR* 5.0 6.5 + - - -
408C HIS* 4.0 7.2 + - - -
438C THR* 5.4 8.9 - - - +
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Residues in contact with ALA 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C LEU* 4.2 9.5 - - + +
249C LEU* 4.7 9.4 - - + -
253C ILE* 4.9 1.8 - - + -
257C ASP 2.9 18.7 + - - +
258C TRP* 3.5 9.2 - - - +
259C SER 3.2 0.2 - - - -
260C ASN* 1.3 79.1 - - - +
262C ILE* 1.3 62.7 + - + +
264C PRO* 4.1 0.3 - - - +
265C ILE* 3.5 11.3 - - - +
404C ILE* 3.5 29.4 - - + -
408C HIS* 3.2 23.2 - - - -
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Residues in contact with ILE 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C LEU* 4.0 11.4 - - + -
206C PHE* 4.3 11.2 - - + -
208C VAL* 3.7 34.8 - - + -
247C LEU* 4.2 8.5 - - + -
258C TRP* 3.1 54.7 + - + +
259C SER* 4.2 3.1 - - - +
261C ALA* 1.3 81.1 - - + +
263C GLY* 1.3 63.0 + - - +
264C PRO 3.5 0.2 - - - -
265C ILE* 3.2 7.9 + - - +
266C LEU* 2.8 43.0 + - + +
321C TYR* 5.6 1.6 - - + -
322C ALA* 3.9 16.6 - - + -
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Residues in contact with GLY 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C SER 2.9 17.1 + - - -
262C ILE* 1.3 79.5 - - - +
264C PRO* 1.3 66.4 - - - +
266C LEU* 3.3 1.3 + - - -
267C ASP* 3.1 20.9 + - - +
321C TYR* 4.1 7.2 - - - -
325C LYS* 3.4 34.7 - - - +
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Residues in contact with PRO 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C SER 4.3 0.7 - - - +
260C ASN* 3.3 24.5 - - - +
261C ALA 4.1 2.0 - - - +
262C ILE 3.7 0.9 - - - -
263C GLY* 1.3 90.1 - - - +
265C ILE* 1.3 53.4 + - - +
267C ASP 3.5 0.2 + - - -
268C SER* 2.7 36.9 + - - -
321C TYR* 5.6 1.3 - - - +
408C HIS* 4.3 6.7 - - + -
434C LEU* 3.5 22.1 - - + +
435C TYR* 3.3 34.3 - - + +
438C THR* 5.3 12.6 - - + +
440C MET* 6.3 2.0 - - - -
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Residues in contact with ILE 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C PHE* 3.7 24.2 - - + -
245C PHE* 5.9 0.2 - - + -
247C LEU* 4.0 15.9 - - + -
261C ALA 3.5 19.3 - - - +
262C ILE 3.2 6.8 + - - +
264C PRO* 1.3 74.5 - - - +
266C LEU* 1.3 61.1 + - - +
268C SER* 3.3 5.7 + - - -
269C LEU* 2.9 42.6 + - + +
404C ILE* 5.7 0.4 - - + -
408C HIS* 3.8 12.6 - - + +
411C ILE* 3.5 48.5 - - + -
412C LEU* 5.7 0.4 - - + -
435C TYR* 3.6 16.8 - - - +
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Residues in contact with LEU 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C LEU* 5.5 0.2 - - + -
183C VAL* 3.9 26.5 - - + -
206C PHE* 3.8 30.5 - - + -
262C ILE* 2.8 44.5 + - + +
263C GLY* 3.6 4.3 - - - +
265C ILE* 1.3 76.1 - - - +
267C ASP* 1.3 62.9 + - - +
269C LEU* 3.3 8.1 + - + +
270C ASN 3.0 18.7 + - - -
321C TYR* 6.4 0.2 - - + -
322C ALA* 4.3 15.3 - - + +
325C LYS* 4.3 10.3 - - + -
326C ILE* 4.4 14.8 - - + -
329C TRP* 3.2 28.4 - - + -
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Residues in contact with ASP 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C GLY 3.1 12.8 + - - +
264C PRO 3.9 0.4 - - - +
266C LEU* 1.3 76.2 - - - +
268C SER* 1.3 55.4 + - - +
270C ASN* 3.4 3.1 + - - +
271C ILE* 3.0 33.7 + - + +
325C LYS* 2.8 38.8 + - - +
328C SER* 5.3 0.2 + - - -
329C TRP* 3.0 26.4 + - - +
434C LEU* 3.1 32.5 - - + +
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Residues in contact with SER 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264C PRO 2.7 22.2 + - - -
265C ILE* 3.7 4.5 - - - -
267C ASP* 1.3 72.5 - - - +
269C LEU* 1.3 66.2 + - - +
271C ILE* 3.3 5.9 + - - +
272C VAL* 3.0 30.0 + - - +
412C LEU* 4.0 12.1 - - - -
415C LEU* 3.7 16.2 - - - -
431C VAL* 3.7 13.1 - - - +
434C LEU* 3.6 10.2 - - - +
435C TYR* 3.5 18.0 - - - -
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Residues in contact with LEU 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C LEU* 4.0 19.3 - - + -
204C VAL* 4.6 0.4 - - + -
206C PHE* 3.8 41.7 - - + -
245C PHE* 4.1 24.9 - - + -
265C ILE* 2.9 30.3 + - + +
266C LEU* 3.6 7.0 - - + +
268C SER* 1.3 76.1 - - - +
270C ASN* 1.3 55.8 + - - +
273C ILE* 2.9 61.8 + - + +
411C ILE* 5.8 1.3 - - + -
415C LEU* 3.9 21.3 - - + -
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Residues in contact with ASN 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C LEU* 4.5 1.7 - - - +
266C LEU 3.0 9.8 + - - +
267C ASP 3.7 4.0 + - - +
269C LEU* 1.3 75.2 - - - +
271C ILE* 1.3 69.2 + - - +
274C GLN* 2.9 33.8 + - - +
275C PRO* 3.3 26.7 - - - +
329C TRP* 3.3 60.4 + - + +
331C VAL* 4.2 8.5 - - - +
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Residues in contact with ILE 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C ASP* 3.0 23.0 + - + +
268C SER* 3.7 6.1 - - - +
270C ASN* 1.3 83.4 - - - +
272C VAL* 1.3 66.4 + - + +
274C GLN* 3.4 21.3 - - - +
425C ILE 5.4 0.3 - - - +
427C ASP* 4.6 8.3 - - + +
430C GLN* 3.9 56.3 - - + +
431C VAL* 4.3 12.3 - - + +
434C LEU* 3.7 23.6 - - + -
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Residues in contact with VAL 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268C SER 3.0 17.1 + - - +
271C ILE* 1.3 79.4 - - + +
273C ILE* 1.3 66.8 + - + +
274C GLN* 4.5 3.1 - - - +
415C LEU* 3.7 36.3 - - + +
418C TYR* 5.0 3.4 - - + -
419C ALA* 3.9 28.5 - - + -
424C LEU* 3.9 13.6 - - + +
425C ILE 4.4 17.6 - - - +
426C TYR* 4.1 17.9 - - + -
427C ASP 5.1 1.1 - - - +
431C VAL* 4.3 15.3 - - + -
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Residues in contact with ILE 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C ARG* 3.8 37.2 - - + -
180C VAL 5.2 1.3 - - - +
181C LEU* 4.1 9.4 - - + -
204C VAL* 3.6 34.5 - - + -
245C PHE* 5.2 0.2 - - + -
269C LEU* 2.9 54.2 + - + +
272C VAL* 1.3 74.6 - - - +
274C GLN* 1.3 69.8 - - - +
275C PRO* 4.1 17.3 - - + -
415C LEU* 4.3 8.5 - - + -
418C TYR* 4.2 17.5 - - + +
424C LEU* 4.7 6.8 - - - +
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Residues in contact with GLN 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C GLN 5.7 1.2 - - - -
179C ARG* 5.0 2.6 - - - -
270C ASN* 2.9 35.6 + - - +
271C ILE* 3.4 19.9 - - - +
272C VAL 4.5 3.1 - - - +
273C ILE* 1.3 78.9 + - - +
275C PRO* 1.3 71.7 - - - +
276C SER* 3.6 3.1 - - - -
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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