Contacts of the helix formed by residues 254 - 274 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B GLY 3.5 4.5 + - - +
253B ILE* 1.3 74.8 - - - +
255B ASP* 1.3 65.3 + - - +
256B LEU* 3.3 8.6 + - - +
257B ASP* 2.8 34.5 + - - +
258B TRP* 3.0 24.4 + - - +
296B ARG* 4.0 14.4 - - + +
297B LEU* 3.8 4.0 - - - -
393B PRO* 6.0 6.3 - - + -
394B HIS 5.4 2.6 + - - +
395B GLU* 3.4 32.7 + - - +
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Residues in contact with ASP 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ASN* 1.3 74.1 - - - +
256B LEU* 1.3 58.2 + - - +
258B TRP* 3.9 1.2 - - - +
259B SER* 2.8 34.6 + - - -
296B ARG 4.2 2.2 + - - -
297B LEU* 3.3 12.0 - - - +
298B THR* 2.7 52.6 + - - +
300B PHE* 4.9 1.4 - - - -
315B SER* 4.8 6.4 - - - +
316B LEU 3.4 19.1 - - - +
317B SER* 3.5 4.1 + - - -
318B GLY* 2.9 24.1 + - - +
393B PRO* 5.4 2.4 - - - +
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Residues in contact with LEU 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ASN* 3.3 10.3 + - - +
255B ASP* 1.3 79.2 - - - +
257B ASP* 1.3 65.5 + - - +
259B SER* 3.3 7.6 + - - -
260B ASN* 2.8 56.0 + - - +
315B SER 5.7 9.2 - - - +
316B LEU 5.6 0.4 - - - -
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Residues in contact with ASP 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B ILE* 3.6 20.6 - - + +
254B ASN* 2.8 31.2 + - - +
256B LEU* 1.3 83.6 - - - +
258B TRP* 1.3 58.5 + - - +
260B ASN* 3.5 8.1 + - - +
261B ALA* 2.9 28.8 + - - +
395B GLU* 4.2 8.1 - - - +
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Residues in contact with TRP 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU* 3.8 35.4 + - + -
208B VAL* 3.9 28.6 + - + +
249B LEU* 3.8 20.9 - - + -
253B ILE* 3.5 22.1 - - + +
254B ASN 3.0 18.7 + - - +
255B ASP 3.9 1.1 - - - +
257B ASP* 1.3 73.7 - - - +
259B SER* 1.3 66.9 + - - +
261B ALA* 3.3 4.2 + - - +
262B ILE* 3.1 56.2 + - + +
286B CYS* 4.7 1.8 - - - -
295B PHE* 4.1 14.7 - + - -
297B LEU* 3.6 26.4 - - + +
318B GLY* 3.1 43.1 - - - -
319B TYR* 3.9 4.9 - + - -
322B ALA* 4.0 1.1 - - + -
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Residues in contact with SER 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B ASP 2.8 25.5 + - - -
256B LEU* 3.5 10.3 - - - -
258B TRP* 1.3 80.1 - - - +
260B ASN* 1.3 60.8 + - - +
262B ILE* 4.6 1.6 - - - -
263B GLY* 2.9 32.2 + - - -
264B PRO* 4.3 0.2 - - - +
316B LEU 4.5 2.9 + - - -
318B GLY* 3.4 18.4 - - - -
321B TYR* 3.5 40.4 - - - +
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Residues in contact with ASN 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B LEU* 2.8 47.1 + - - +
257B ASP* 4.0 8.5 + - - +
259B SER* 1.3 79.6 - - - +
261B ALA* 1.3 60.8 + - - +
264B PRO* 3.3 22.1 - - - +
321B TYR* 5.1 6.3 + - - -
408B HIS* 4.0 6.6 + - - -
438B THR* 6.2 4.5 - - - -
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Residues in contact with ALA 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B LEU* 4.2 9.4 - - + -
249B LEU* 4.7 8.1 - - + -
253B ILE* 4.9 1.8 - - + -
257B ASP 2.9 18.4 + - - +
258B TRP* 3.5 9.4 - - - +
259B SER 3.2 0.4 - - - -
260B ASN* 1.3 77.6 - - - +
262B ILE* 1.3 63.5 + - + +
264B PRO* 4.0 0.2 - - - +
265B ILE* 3.5 10.4 - - - +
404B ILE* 3.4 31.0 - - + -
408B HIS* 3.1 24.6 - - - -
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Residues in contact with ILE 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU* 4.1 8.1 - - + -
206B PHE* 4.3 11.9 - - + -
208B VAL* 3.7 35.0 - - + -
247B LEU* 4.1 9.0 - - + -
258B TRP* 3.1 55.3 + - + +
259B SER* 4.1 3.6 - - - +
261B ALA* 1.3 79.6 - - + +
263B GLY* 1.3 63.0 + - - +
264B PRO 3.5 0.2 - - - -
265B ILE* 3.2 7.8 + - - +
266B LEU* 2.8 43.1 + - + +
321B TYR* 5.6 1.3 - - + -
322B ALA* 3.8 16.6 - - + -
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Residues in contact with GLY 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B SER 2.9 16.5 + - - -
262B ILE* 1.3 79.0 - - - +
264B PRO* 1.3 67.0 - - - +
266B LEU* 3.3 1.1 + - - -
267B ASP* 3.1 22.2 + - - +
321B TYR* 4.1 7.2 - - - -
325B LYS* 3.4 34.8 - - - +
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Residues in contact with PRO 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B SER 4.3 0.2 - - - +
260B ASN* 3.3 23.8 - - - +
261B ALA 4.0 2.0 - - - +
262B ILE 3.7 0.7 - - - -
263B GLY* 1.3 87.8 - - - +
265B ILE* 1.3 64.1 + - - +
267B ASP* 3.6 0.8 + - + +
268B SER* 2.8 30.3 + - - -
321B TYR* 5.7 1.1 - - - +
408B HIS* 4.3 5.8 - - + -
434B LEU* 3.6 21.3 - - + +
435B TYR* 3.4 34.9 - - + +
438B THR* 5.6 6.7 - - - +
440B MET* 6.4 2.2 - - - -
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Residues in contact with ILE 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B PHE* 3.8 23.6 - - + -
247B LEU* 4.1 16.2 - - + -
261B ALA 3.5 17.0 - - - +
262B ILE 3.2 7.7 + - - +
264B PRO* 1.3 75.6 - - - +
266B LEU* 1.3 65.4 + - - +
268B SER* 3.2 5.6 + - - -
269B LEU* 2.9 36.6 + - + +
404B ILE* 5.7 0.2 - - + -
408B HIS* 3.7 14.6 - - + +
411B ILE* 3.5 49.4 - - + -
412B LEU* 5.7 0.7 - - + -
435B TYR* 3.6 16.2 - - - +
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Residues in contact with LEU 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B LEU* 5.4 0.4 - - + -
183B VAL* 3.8 36.8 - - + -
206B PHE* 3.9 20.0 - - + -
262B ILE* 2.8 48.5 + - + +
263B GLY* 3.7 3.6 - - - +
265B ILE* 1.3 72.5 - - - +
267B ASP* 1.3 62.8 + - - +
269B LEU* 3.3 8.3 + - + +
270B ASN 3.0 18.7 + - - -
321B TYR* 6.4 0.4 - - + -
322B ALA* 4.4 14.4 - - + +
325B LYS* 4.3 11.7 - - + -
326B ILE* 4.4 13.9 - - + -
329B TRP* 3.2 28.6 - - + -
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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
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263B GLY 3.1 12.6 + - - +
264B PRO 3.9 0.4 - - - +
266B LEU* 1.3 76.0 - - - +
268B SER* 1.3 57.9 + - - +
270B ASN* 3.4 2.8 + - - +
271B ILE* 3.0 33.9 + - + +
325B LYS* 2.8 37.5 + - - +
328B SER* 5.4 0.3 + - - -
329B TRP* 3.0 27.2 + - - +
434B LEU* 3.2 29.7 - - + +
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Residues in contact with SER 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B PRO 2.8 22.9 + - - -
265B ILE* 3.6 4.5 - - - -
267B ASP* 1.3 73.6 - - - +
269B LEU* 1.3 67.5 + - - +
271B ILE* 3.3 5.1 + - - +
272B VAL* 3.0 29.8 + - - +
412B LEU* 4.0 11.9 - - - -
415B LEU* 3.7 16.8 - - - -
431B VAL* 3.7 12.7 - - - +
434B LEU* 3.5 14.8 - - - +
435B TYR* 3.5 14.9 - - - -
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Residues in contact with LEU 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B LEU* 4.0 18.4 - - + -
204B VAL* 4.6 1.8 - - + -
206B PHE* 3.8 41.3 - - + -
245B PHE* 4.0 32.5 - - + -
265B ILE* 2.9 33.5 + - + +
266B LEU* 3.5 8.5 - - + +
268B SER* 1.3 76.9 - - - +
270B ASN* 1.3 57.1 + - - +
273B ILE* 2.9 55.3 + - + +
411B ILE* 5.7 0.7 - - + -
415B LEU* 4.0 15.7 - - + +
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Residues in contact with ASN 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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181B LEU* 4.5 1.5 - - - +
266B LEU 3.0 9.9 + - - +
267B ASP 3.8 4.2 + - - +
268B SER 3.2 0.2 - - - -
269B LEU* 1.3 76.7 - - - +
271B ILE* 1.3 62.3 + - - +
274B GLN* 2.9 40.2 + - - +
275B PRO* 3.4 25.3 - - - +
329B TRP* 3.4 63.6 + - + +
331B VAL* 4.1 7.2 - - - +
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Residues in contact with ILE 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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267B ASP* 3.0 22.8 + - + +
268B SER* 3.3 6.0 + - - +
270B ASN* 1.3 80.8 - - - +
272B VAL* 1.3 65.0 + - + +
274B GLN* 3.3 24.6 + - - +
425B ILE 5.4 0.9 - - - +
427B ASP* 4.7 7.2 - - + +
430B GLN* 3.8 55.9 - - + +
431B VAL* 4.3 13.0 - - + +
434B LEU* 3.7 23.8 - - + -
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Residues in contact with VAL 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B SER 3.0 16.5 + - - +
271B ILE* 1.3 78.5 - - + +
273B ILE* 1.3 66.6 + - + +
274B GLN* 4.5 3.1 - - - +
415B LEU* 3.7 37.2 - - + -
418B TYR* 5.0 3.1 - - + -
419B ALA* 3.9 28.7 - - + -
424B LEU* 4.0 12.7 - - + +
425B ILE 4.4 16.1 - - - +
426B TYR* 4.0 21.3 - - + -
427B ASP 5.2 0.7 - - - +
431B VAL* 4.3 13.9 - - + -
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Residues in contact with ILE 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ARG* 3.6 37.3 + - + -
180B VAL 5.2 1.3 - - - +
181B LEU* 4.0 13.2 - - + -
204B VAL* 3.5 43.1 - - + -
245B PHE* 5.2 0.4 - - + -
269B LEU* 2.9 37.1 + - + +
272B VAL* 1.3 76.3 - - - +
274B GLN* 1.3 70.7 + - - +
275B PRO* 4.1 15.9 - - + -
415B LEU* 4.4 9.0 - - + -
418B TYR* 4.2 15.7 - - + +
424B LEU* 4.7 6.3 - - - +
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Residues in contact with GLN 274 (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 GLN 5.5 1.7 - - - +
179B ARG* 5.0 2.9 - - - +
270B ASN* 2.9 38.5 + - - +
271B ILE* 3.3 22.6 + - - +
272B VAL 4.5 2.9 - - - +
273B ILE* 1.3 80.4 - - - +
275B PRO* 1.3 71.7 - - - +
276B SER* 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
------------------------------------------------------------
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