Contacts of the helix formed by residues 247 - 262 (chain B) in PDB entry 3H11
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 GLY 247 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227B HIS* 5.0 0.8 - - - -
245B ARG 3.4 0.2 + - - -
246B ASN* 1.3 74.0 - - - +
248B THR* 1.3 62.8 + - - +
249B HIS* 3.1 5.7 - - - +
250B LEU* 3.3 17.4 + - - +
251B ASP* 3.5 7.2 + - - -
398B ARG* 4.8 3.1 - - - -
399B ASN 4.5 4.5 - - - -
400B PRO* 3.4 20.7 + - - -
403B GLY* 3.5 20.0 - - - -
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Residues in contact with THR 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B ASN* 2.5 32.7 + - - +
227B HIS* 3.7 26.7 - - + -
245B ARG* 2.9 57.1 + - - +
246B ASN 3.4 0.6 - - - -
247B GLY* 1.3 76.0 - - - +
249B HIS* 1.3 64.1 + - - +
250B LEU 3.2 0.2 - - - -
251B ASP* 3.2 12.5 + - - +
252B ALA 2.9 22.7 + - - -
300B LEU* 3.7 8.1 - - - +
398B ARG* 4.5 2.1 - - - +
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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
----------------------------------------------------------
225B ASN* 3.0 27.4 + - - +
227B HIS* 3.9 39.3 + + + -
247B GLY* 3.1 3.4 - - - +
248B THR* 1.3 77.0 - - - +
250B LEU* 1.3 59.2 + - - +
252B ALA* 3.3 3.2 + - - +
253B GLY* 2.9 25.5 + - - -
270B ASP* 4.6 11.4 + - + -
271B ASP* 5.6 2.9 - - - -
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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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247B GLY* 3.3 11.2 + - - +
248B THR 3.2 0.6 - - - -
249B HIS* 1.3 77.4 - - - +
251B ASP* 1.3 57.8 + - - +
253B GLY* 3.3 2.1 + - - -
254B ALA* 2.8 30.1 + - - +
400B PRO 4.8 4.3 - - - +
401B ALA* 3.1 35.2 - - - +
402B GLU* 3.7 13.0 - - - +
403B GLY* 3.9 2.2 - - - +
408B GLN* 3.7 11.9 + - - +
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Residues in contact with ASP 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ARG* 4.8 1.4 + - - -
247B GLY 3.5 5.3 + - - -
248B THR* 3.2 13.2 + - - +
249B HIS 3.1 0.4 - - - -
250B LEU* 1.3 80.2 - - - +
252B ALA* 1.3 56.4 + - - +
254B ALA* 3.1 2.6 + - - +
255B LEU* 2.9 35.7 + - - +
300B LEU* 4.1 10.9 - - + +
343B GLN* 4.4 1.7 - - - +
403B GLY* 3.4 0.7 - - - -
404B THR* 2.7 55.1 + - - +
407B ILE* 3.6 19.0 - - + +
408B GLN* 3.0 25.1 + - - +
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Residues in contact with ALA 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ILE* 4.0 9.5 - - + +
225B ASN* 3.8 29.8 - - + +
248B THR 2.9 15.1 + - - +
249B HIS* 3.3 6.0 + - - +
251B ASP* 1.3 76.4 - - - +
253B GLY* 1.3 57.3 + - - +
255B LEU* 3.8 5.5 - - - +
256B THR* 2.8 34.0 + - - +
268B PRO* 6.4 2.0 - - + -
270B ASP* 5.1 2.0 - - - +
300B LEU* 4.0 8.0 - - + +
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Residues in contact with GLY 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 14.6 + - - -
250B LEU* 3.7 3.4 - - - -
252B ALA* 1.3 76.0 - - - +
254B ALA* 1.3 63.8 + - - +
256B THR* 3.3 7.5 + - - -
257B THR* 3.0 26.1 + - - +
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Residues in contact with ALA 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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250B LEU 2.8 17.6 + - - +
251B ASP* 3.6 4.0 - - - +
253B GLY* 1.3 75.5 - - - +
255B LEU* 1.3 58.3 + - - +
257B THR* 3.3 9.2 - - - +
258B THR* 2.8 34.2 + - - +
407B ILE* 5.1 0.4 - - + -
408B GLN* 4.0 20.2 - - - +
411B CYS* 3.7 21.8 - - + -
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Residues in contact with LEU 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ILE* 3.9 16.2 - - + -
251B ASP 2.9 20.1 + - - +
252B ALA 3.8 3.1 - - - +
254B ALA* 1.3 76.5 - - - +
256B THR* 1.3 64.1 + - - +
258B THR* 4.4 0.9 - - - -
259B PHE* 3.0 51.2 + - + +
266B ILE* 4.6 0.2 - - - +
298B CYS* 4.0 29.4 - - + -
300B LEU* 4.0 29.4 - - + -
341B PHE* 5.7 0.2 - - + -
407B ILE* 3.8 20.2 - - + -
410B LEU* 4.7 8.7 - - + -
411B CYS* 3.5 20.9 - - - -
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Residues in contact with THR 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ILE* 3.5 16.4 - - - +
252B ALA* 2.8 23.2 + - - +
253B GLY* 3.5 8.7 - - - -
254B ALA 3.2 0.2 - - - -
255B LEU* 1.3 76.6 - - - +
257B THR* 1.3 63.6 + - - +
260B GLU* 3.0 49.7 + - - +
266B ILE* 3.8 17.5 - - + +
268B PRO* 5.3 4.2 - - - +
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Residues in contact with THR 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 GLY 3.0 16.3 + - - +
254B ALA* 3.3 15.7 - - - +
256B THR* 1.3 79.1 - - - +
258B THR* 1.3 64.2 + - - +
260B GLU* 4.2 6.6 - - - +
261B GLU* 3.0 37.8 + - - +
415B ARG* 3.3 23.7 + - - +
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Residues in contact with THR 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ALA* 2.8 24.1 + - - -
255B LEU* 3.8 3.8 - - - -
257B THR* 1.3 79.4 - - - +
259B PHE* 1.3 65.0 + - + +
261B GLU* 3.5 4.9 + - - +
262B LEU* 3.3 27.4 + - + +
411B CYS* 3.3 24.7 - - - +
414B LEU* 3.8 35.7 - - + -
415B ARG* 3.4 33.1 - - + +
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Residues in contact with PHE 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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221B CYS* 3.8 20.4 - - - -
255B LEU* 3.0 48.8 + - + +
258B THR* 1.3 75.5 - - + +
260B GLU* 1.3 63.9 + - - +
261B GLU 3.1 1.1 - - - -
262B LEU* 3.1 18.4 + - + +
263B HIS 3.2 0.3 + - - -
264B PHE* 2.9 37.1 + + + +
266B ILE* 3.7 16.2 - - + -
296B ILE* 3.4 27.4 - - + -
298B CYS* 4.6 3.6 - - - -
341B PHE* 3.8 22.7 - + - -
410B LEU* 5.6 0.2 - - + -
414B LEU* 3.5 28.9 - - + -
461B PHE* 3.9 17.3 - + - -
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Residues in contact with GLU 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 THR* 3.0 37.0 + - - +
257B THR* 4.2 5.3 - - - +
259B PHE* 1.3 76.1 - - - +
261B GLU* 1.3 63.3 + - + +
263B HIS* 3.0 17.5 + - - -
264B PHE 3.9 10.8 - - - +
266B ILE* 3.3 24.2 + - + +
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Residues in contact with GLU 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 THR* 3.0 21.8 + - - +
258B THR 3.6 4.9 - - - +
259B PHE 3.1 0.2 - - - -
260B GLU* 1.3 80.3 - - + +
262B LEU* 1.3 61.4 + - + +
263B HIS* 3.1 17.7 + - - -
415B ARG* 2.7 58.2 + - - +
463B SER* 4.6 8.3 + - - +
464B ASP* 4.7 5.7 + - - +
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Residues in contact with LEU 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B ARG* 3.3 19.4 + - - +
258B THR* 3.3 25.3 + - + +
259B PHE* 3.1 23.5 + - + +
261B GLU* 1.3 77.9 - - + +
263B HIS* 1.3 70.5 + - - +
264B PHE* 3.4 13.0 - - + -
414B LEU* 4.6 5.2 - - + +
415B ARG* 6.4 0.9 - - - -
418B CYS* 4.0 17.3 - - + -
461B PHE* 3.6 48.3 - - + +
462B PRO 4.4 3.7 - - - +
463B SER* 3.7 26.0 - - - +
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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