Contacts of the helix formed by residues 246 - 258 (chain B) in PDB entry 3H60
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 GLN 246 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243B THR* 3.1 17.3 + - - +
244B HIS 3.0 10.1 + - - +
245B GLY* 1.4 72.4 - - - +
247B PHE* 1.3 65.0 + - - +
248B TYR 3.3 2.9 - - - -
249B ASP* 2.9 32.0 + - + +
250B LEU* 3.0 19.6 + - - +
276B GLY* 4.9 6.0 - - - +
278B PHE* 5.0 3.1 - - - -
282B VAL* 3.8 4.3 - - - +
448B ALA* 3.6 18.1 - - + +
449B PRO 2.9 16.3 - - - +
450B ASN 4.4 1.3 + - - -
451B TYR* 3.6 21.4 - - - +
452B CYS* 3.4 28.3 - - - +
453B ASP* 5.1 1.3 - - - +
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Residues in contact with PHE 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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195B MET* 3.8 8.7 - - - -
198B TYR* 3.4 32.8 - + + -
199B LYS* 3.7 9.6 - - - -
245B GLY 3.1 5.1 + - - -
246B GLN* 1.3 76.3 - - - +
248B TYR* 1.3 75.1 + + - +
250B LEU* 3.3 7.9 + - + +
251B LEU* 3.0 65.8 + - + +
278B PHE* 3.5 26.9 - - + +
281B GLU* 3.7 22.4 - - + -
282B VAL* 3.6 15.0 - - + -
285B THR* 3.5 25.4 - - + -
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Residues in contact with TYR 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B TYR 3.2 13.4 + - - -
199B LYS* 2.8 49.4 + - + -
201B GLN* 3.7 5.7 - - - +
246B GLN 3.3 0.8 - - - -
247B PHE* 1.3 86.4 - + - +
249B ASP* 1.3 58.3 + - - +
251B LEU* 3.6 10.0 + - + +
252B ASN 3.1 19.8 + - - -
278B PHE* 3.8 29.3 - + - -
479B VAL* 3.2 20.0 - - + +
480B PRO 3.7 20.4 - - - +
481B HIS* 3.5 22.7 - - + -
482B PRO* 3.2 30.8 - - + +
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Residues in contact with ASP 249 (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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246B GLN* 2.9 37.9 + - + +
248B TYR* 1.3 78.0 - - - +
250B LEU* 1.3 59.2 + - - +
252B ASN* 3.2 7.7 + - - +
253B ILE* 2.9 32.4 + - - +
447B SER 5.0 2.0 - - - +
449B PRO* 3.5 32.2 - - + +
476B PHE* 4.2 3.4 - - + -
477B THR 4.6 1.0 - - - +
478B ALA* 3.5 6.7 - - - +
479B VAL* 3.2 33.8 + - - +
481B HIS* 5.7 4.2 - - - -
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Residues in contact with LEU 250 (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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243B THR* 4.7 9.8 - - + +
246B GLN 3.0 12.2 + - - +
247B PHE* 3.4 14.6 - - + +
249B ASP* 1.3 74.1 - - - +
251B LEU* 1.3 65.6 + - + +
253B ILE* 3.2 14.1 + - + +
254B PHE* 3.1 35.5 + - + -
268B PHE* 3.6 37.5 - - + -
282B VAL* 4.0 37.9 - - + +
285B THR* 4.4 14.4 - - + -
286B LEU* 4.1 13.5 - - + -
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Residues in contact with LEU 251 (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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195B MET* 4.0 32.3 - - + +
199B LYS* 4.0 30.1 - - + -
247B PHE* 3.0 59.3 + - + +
248B TYR* 3.8 13.2 - - + +
250B LEU* 1.3 77.0 - - + +
252B ASN* 1.3 62.1 + - - +
254B PHE* 3.2 10.0 + - + +
255B GLU* 3.0 36.9 + - + +
285B THR* 5.6 0.4 - - + -
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Residues in contact with ASN 252 (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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248B TYR 3.1 14.6 + - - +
249B ASP* 3.4 11.4 + - - +
250B LEU 3.1 0.8 - - - -
251B LEU* 1.3 74.0 - - - +
253B ILE* 1.3 65.7 + - - +
255B GLU* 3.1 18.4 + - - +
256B LEU* 2.9 60.5 + - - +
476B PHE* 4.0 7.5 - - - +
477B THR 3.7 21.2 + - - -
479B VAL* 3.6 24.3 - - + +
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Residues in contact with ILE 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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240B CYS* 4.2 23.1 - - - -
243B THR* 4.6 3.1 - - + -
249B ASP 2.9 19.8 + - - +
250B LEU* 3.2 15.7 + - + +
252B ASN* 1.3 75.2 - - - +
254B PHE* 1.3 61.7 + - + +
256B LEU* 3.3 7.8 + - - +
257B ASN* 2.9 30.2 + - + +
266B TYR* 4.0 25.6 - - + +
268B PHE* 4.4 11.0 - - + -
447B SER* 4.2 16.4 - - - +
461B TYR* 4.2 14.1 - - + -
476B PHE* 3.5 31.9 - - + -
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Residues in contact with PHE 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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195B MET* 4.2 17.0 - - - -
250B LEU* 3.1 41.3 + - + -
251B LEU* 3.2 8.9 + - + +
253B ILE* 1.3 78.3 - - + +
255B GLU* 1.3 58.5 + - + +
258B GLY* 2.8 37.5 + - - +
259B LEU* 3.6 19.2 + - + +
260B PRO* 3.8 29.2 - - + -
266B TYR* 3.6 25.8 - + - -
268B PHE* 4.0 19.7 - + - -
285B THR* 4.4 7.9 - - + -
286B LEU* 4.7 3.8 - - + -
289B PHE* 3.8 21.8 - + - -
297B PHE* 4.6 2.0 - + - -
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Residues in contact with GLU 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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199B LYS* 5.3 6.9 + - - +
251B LEU* 3.0 23.9 + - - +
252B ASN* 3.1 23.3 + - - +
254B PHE* 1.3 78.5 - - + +
256B LEU* 1.3 65.3 + - + +
257B ASN 3.4 0.3 + - - -
258B GLY* 4.0 2.9 + - - -
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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
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252B ASN* 2.9 41.6 + - - +
253B ILE* 3.9 3.1 - - - +
255B GLU* 1.3 78.1 - - + +
257B ASN* 1.3 58.2 + - - +
461B TYR* 3.7 23.4 + - + +
475B GLN 5.1 1.3 - - - +
476B PHE* 3.4 38.4 - - + -
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Residues in contact with ASN 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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236B LYS* 4.8 1.9 + - - -
238B THR* 3.0 26.9 + - - +
253B ILE* 2.9 16.2 + - + +
256B LEU* 1.3 78.0 - - - +
258B GLY* 1.3 54.3 + - - +
264B ASN* 2.8 30.0 + - - +
266B TYR* 2.9 27.2 + - - +
461B TYR* 3.5 22.8 + - + +
463B HIS* 2.7 31.1 + - - -
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Residues in contact with GLY 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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254B PHE* 2.8 20.1 + - - +
255B GLU 4.0 3.6 + - - -
256B LEU 3.6 1.2 - - - -
257B ASN* 1.3 78.4 - - - +
259B LEU* 1.3 65.8 + - - -
264B ASN* 3.3 3.7 - - - +
266B TYR* 2.7 27.5 + - - -
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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
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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