Contacts of the helix formed by residues 246 - 267 (chain B) in PDB entry 4YCV
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 246 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B ASN* 2.8 13.8 + - - -
245B GLU* 1.3 80.0 - - - +
247B SER* 1.3 63.6 + - - +
248B ARG 3.4 0.4 - - - -
249B HIS* 3.1 18.4 + - - +
250B THR* 3.1 14.0 + - - -
567B LYS* 4.4 14.8 + - - -
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Residues in contact with SER 247 (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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240B ASP* 2.6 60.4 + - - -
241B LEU* 3.2 11.5 + - - -
244B ASN* 4.0 3.1 - - - +
245B GLU 4.3 1.1 + - - +
246B SER* 1.3 79.0 - - - +
248B ARG* 1.3 62.1 + - - +
250B THR* 3.0 13.7 + - - -
251B PHE* 3.0 35.4 + - - -
567B LYS* 6.2 0.7 - - - +
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Residues in contact with ARG 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PHE* 5.6 3.4 - - - -
317A GLY 5.8 1.3 - - - -
318A GLY* 4.2 12.0 + - - -
319A ILE* 4.4 24.9 - - + +
157B ASP* 2.9 18.5 + - - +
158B GLY* 2.8 40.0 - - - +
241B LEU* 3.7 35.7 - - + +
245B GLU* 4.6 11.8 - - - +
247B SER* 1.3 78.4 + - - +
249B HIS* 1.3 64.7 + - - +
251B PHE* 3.7 4.7 - - - +
252B VAL* 2.9 56.9 + - - +
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Residues in contact with HIS 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B GLU 4.3 7.6 + - - +
246B SER* 3.1 15.6 + - - +
248B ARG* 1.3 82.7 - - + +
250B THR* 1.3 68.4 + - - +
252B VAL* 3.6 8.7 - - + +
253B THR* 2.9 43.7 + - - -
565B THR* 6.4 0.4 - - + -
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Residues in contact with THR 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B SER* 3.1 10.1 + - - -
247B SER* 3.0 17.1 + - - +
249B HIS* 1.3 83.0 + - - +
251B PHE* 1.3 59.4 + - + +
253B THR* 3.1 7.2 - - - -
254B ARG* 2.9 23.6 + - - +
561B THR* 5.3 0.7 - - + -
565B THR* 3.8 31.3 + - + +
567B LYS* 3.4 26.3 + - - -
572B ASP 4.3 12.8 - - - +
573B VAL* 4.2 17.5 - - + -
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Residues in contact with PHE 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PHE* 4.1 8.9 - - + -
319A ILE* 6.3 2.0 - - + -
237B ARG* 3.5 26.7 - - - -
241B LEU* 3.9 15.0 - - + -
247B SER* 3.0 29.0 + - - +
248B ARG* 4.2 4.9 - - - +
249B HIS 3.3 0.2 - - - -
250B THR* 1.3 77.6 - - + +
252B VAL* 1.3 67.9 + - - +
254B ARG* 3.2 14.6 + - - +
255B THR* 3.0 25.1 + - - -
572B ASP 3.1 21.1 - - - -
573B VAL* 3.2 33.7 - - - -
574B ILE 3.8 8.3 - - - -
575B LEU* 3.5 46.0 - - + -
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Residues in contact with VAL 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PHE* 3.3 31.6 - - + -
319A ILE* 5.5 1.8 - - + -
248B ARG* 2.9 50.1 + - - +
249B HIS* 3.6 10.5 - - + +
251B PHE* 1.3 74.7 - - - +
253B THR* 1.3 63.5 + - - +
255B THR* 2.9 6.9 + - - -
256B LYS* 2.9 50.1 + - + +
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Residues in contact with THR 253 (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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249B HIS* 2.9 39.9 + - - -
250B THR 3.1 9.9 - - - -
252B VAL* 1.3 75.5 - - - +
254B ARG* 1.3 62.3 + - - +
256B LYS* 3.0 13.7 + - - +
257B ILE* 2.8 38.2 + - + +
372B LEU* 4.3 19.1 - - + -
373B PHE* 5.9 1.6 - - + -
564B LEU* 5.1 5.2 - - + +
565B THR* 3.5 22.8 - - + +
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Residues in contact with ARG 254 (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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274A GLU* 3.4 22.4 + - - +
250B THR* 2.9 10.9 + - + +
251B PHE* 3.2 19.9 + - + +
253B THR* 1.3 73.8 - - - +
255B THR* 1.3 63.8 + - - +
257B ILE* 3.2 8.5 + - - +
258B ILE* 3.0 36.4 + - + +
327B LYS* 5.8 1.6 - - - +
343B THR* 3.4 22.2 + - - -
557B ILE* 4.9 4.6 - - - +
558B ASP* 2.7 40.3 + - - +
561B THR* 3.6 29.0 + - + +
573B VAL* 2.7 48.2 + - - +
574B ILE* 4.1 8.3 - - - +
575B LEU* 6.1 2.2 - - - -
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Residues in contact with THR 255 (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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271A PHE* 3.4 26.3 - - + -
272A GLU* 2.7 41.1 + - + +
273A VAL* 4.8 1.2 - - - +
251B PHE 3.0 6.8 + - - -
252B VAL 2.9 9.0 + - - -
254B ARG* 1.3 77.4 - - - +
256B LYS* 1.3 58.7 + - + +
258B ILE* 3.3 7.1 + - + +
259B ASN* 2.9 54.4 + - - +
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Residues in contact with LYS 256 (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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271A PHE* 6.2 0.2 - - + -
252B VAL* 2.9 39.1 + - + +
253B THR* 3.0 12.3 + - - +
255B THR* 1.3 73.1 - - + +
257B ILE* 1.3 60.4 + - - +
259B ASN* 3.8 9.4 - - - +
260B PHE* 2.9 32.1 + - - +
371B HIS* 5.2 10.5 - - + -
372B LEU* 4.3 21.8 - - + +
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Residues in contact with ILE 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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253B THR* 2.8 28.6 + - + +
254B ARG* 3.2 12.1 - - - +
256B LYS* 1.3 76.0 - - - +
258B ILE* 1.3 63.0 + - + +
260B PHE* 3.2 8.6 + - - +
261B LEU* 2.9 27.1 + - + +
364B PHE* 5.2 5.7 - - + -
368B LEU* 4.2 17.9 - - + -
372B LEU* 3.5 16.6 - - + +
557B ILE* 5.1 9.6 - - + -
560B ILE* 5.0 8.7 - - + -
561B THR* 4.6 17.3 - - + +
564B LEU* 3.4 39.7 - - + -
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Residues in contact with ILE 258 (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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272A GLU* 5.9 3.1 - - - +
274A GLU* 3.6 28.9 - - + +
254B ARG* 3.0 27.4 + - + +
255B THR* 3.9 6.3 - - - +
257B ILE* 1.3 73.2 - - + +
259B ASN* 1.3 63.3 + - - +
261B LEU* 3.2 8.3 + - - +
262B ARG* 2.9 50.6 + - - +
325B ILE* 4.3 18.1 - - + +
343B THR* 5.0 3.4 - - + -
557B ILE* 3.8 31.0 - - + -
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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
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262A ARG* 5.3 1.7 - - - -
266A ASN* 4.6 17.2 + - - +
272A GLU* 3.8 18.9 - - - +
255B THR* 2.9 45.1 + - - +
256B LYS* 3.8 7.9 - - - +
258B ILE* 1.3 77.4 - - - +
260B PHE* 1.3 55.3 + - - +
262B ARG* 3.3 10.2 + - - +
263B ASN* 2.3 49.7 + - - +
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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
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256B LYS 2.9 19.9 + - - +
257B ILE 3.5 3.6 - - - +
259B ASN* 1.3 77.0 - - - +
261B LEU* 1.3 58.1 + - - +
263B ASN* 3.9 5.1 - - + +
264B PHE* 2.9 55.9 + + - +
364B PHE* 4.1 12.3 - + - -
367B GLN* 4.0 13.5 - - + -
368B LEU* 3.5 55.0 - - + -
371B HIS* 3.9 37.9 - + + +
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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 ILE* 2.9 14.1 + - + +
258B ILE* 3.2 8.9 + - - +
260B PHE* 1.3 76.0 - - - +
262B ARG* 1.3 59.4 + - - +
264B PHE* 3.2 5.8 + - + +
265B LEU* 2.9 45.0 + - + +
325B ILE* 4.1 8.7 - - + -
345B CYS* 3.6 26.2 - - + -
360B TRP* 4.2 7.0 - - + -
364B PHE* 3.7 33.0 - - + -
555B LEU* 3.7 17.3 - - + -
557B ILE* 3.6 27.8 - - + -
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Residues in contact with ARG 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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259A ASN* 5.6 2.7 - - - -
262A ARG* 3.2 47.5 - - - +
272A GLU* 3.9 7.7 + - - -
258B ILE* 2.9 37.4 + - - +
259B ASN* 3.7 8.9 + - - +
261B LEU* 1.3 76.2 - - - +
263B ASN* 1.3 62.0 + - - +
265B LEU* 3.8 2.4 - - - +
266B ASN* 2.9 43.3 + - - +
272B GLU* 2.4 42.1 + - - -
323B TYR* 3.7 18.5 + - + +
325B ILE* 4.2 24.7 + - + +
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Residues in contact with ASN 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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259B ASN* 2.3 47.1 + - - +
260B PHE* 3.9 6.3 - - + +
262B ARG* 1.3 76.5 - - - +
264B PHE* 1.3 58.8 + - - +
266B ASN* 3.7 11.0 + - - +
267B GLU* 2.9 43.7 + - + +
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Residues in contact with PHE 264 (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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260B PHE* 2.9 40.6 + + + +
261B LEU* 3.3 8.7 - - + +
263B ASN* 1.3 77.7 - - - +
265B LEU* 1.3 62.5 + - + +
267B GLU* 3.8 9.4 + - - +
268B ARG* 3.2 58.8 + - - +
360B TRP* 3.8 30.7 - + - -
363B ASP* 4.2 5.4 - - + -
364B PHE* 3.7 48.5 - + + -
367B GLN* 3.3 27.8 - - - -
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Residues in contact with LEU 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* 2.9 27.8 + - + +
262B ARG 3.8 3.6 - - - +
264B PHE* 1.3 76.3 - - + +
266B ASN* 1.3 64.3 + - - +
268B ARG* 2.9 13.1 + - - -
270B PHE* 3.2 48.4 + - + +
323B TYR* 3.5 41.7 - - + -
345B CYS* 4.0 19.1 - - - -
347B PHE* 4.4 8.1 - - + -
360B TRP* 3.4 36.3 - - + +
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Residues in contact with ASN 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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259A ASN* 4.5 19.9 + - - +
262B ARG* 2.9 32.6 + - - +
263B ASN* 3.7 11.9 + - - +
265B LEU* 1.3 76.6 - - - +
267B GLU* 1.3 62.2 + - + +
269B GLY* 3.1 14.7 + - - -
270B PHE 3.9 11.3 + - - +
272B GLU* 5.0 1.5 + - - +
323B TYR* 2.2 34.2 + - - -
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Residues in contact with GLU 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 ASN* 2.9 26.2 + - + +
264B PHE* 4.0 9.7 - - - +
265B LEU 3.2 0.2 - - - -
266B ASN* 1.3 76.2 - - + +
268B ARG* 1.3 67.8 + - - +
269B GLY 3.3 1.5 + - - -
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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