Contacts of the helix formed by residues 230 - 240 (chain B) in PDB entry 6AHU
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 230 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268A G 3.2 1.6 - - - -
138B HIS* 5.9 0.7 + - - -
226B PRO* 4.3 17.4 - - - +
228B VAL* 3.1 26.7 + - - +
229B LYS* 1.3 76.7 + - - +
231B HIS* 1.3 60.0 + - - +
232B ARG 3.4 1.3 - - - -
233B ALA* 3.6 21.0 - - - +
234B CYS* 3.1 35.9 + - - -
640B ARG* 5.5 6.4 + - - -
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Residues in contact with HIS 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A G 2.4 84.3 + + + +
230B SER* 1.3 71.8 - - - +
232B ARG* 1.3 59.3 + - + +
234B CYS* 3.9 8.5 + - - +
235B TYR* 4.1 8.5 + - - +
645B LYS* 4.1 27.2 + - + +
649B VAL* 4.7 18.8 - - + -
653B TYR* 5.2 4.1 + + - -
971B ASP* 4.7 7.1 + - - -
972B PHE* 5.5 2.2 - + - -
974B MET* 3.9 25.4 - - + +
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Residues in contact with ARG 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A G 3.2 27.9 + - - +
28A G 3.0 46.9 + - - +
29A G 6.5 0.2 - - - -
71A U 5.0 2.2 + - - -
267A U 4.4 16.7 - - - +
268A G 3.3 41.2 + - - +
269A A 5.1 5.5 - - - -
270A G 2.9 33.4 + - - -
231B HIS* 1.3 79.9 - - + +
233B ALA* 1.3 62.7 + - - +
234B CYS 3.4 0.2 - - - -
235B TYR* 3.8 3.2 + - - +
236B ARG* 3.3 31.2 + - - +
974B MET* 3.8 27.2 - - + +
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Residues in contact with ALA 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A U 4.1 15.9 + - - +
268A G 4.7 0.2 + - - -
229B LYS 5.2 0.2 - - - +
230B SER* 3.3 27.7 + - - +
231B HIS 3.2 1.0 - - - -
232B ARG* 1.3 77.3 - - - +
234B CYS* 1.3 60.3 + - - +
236B ARG* 3.4 6.9 + - - +
237B ALA* 2.9 30.7 + - - +
640B ARG* 3.4 34.2 + - + +
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Residues in contact with CYS 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B PRO* 5.5 6.5 - - - -
230B SER* 3.1 32.3 + - - +
231B HIS* 4.3 5.4 - - - +
232B ARG 3.4 0.2 - - - -
233B ALA* 1.3 74.6 - - - +
235B TYR* 1.3 62.8 + - - +
237B ALA* 3.5 1.2 + - - -
238B MET* 3.3 23.0 + - - +
243B LEU* 3.4 16.4 - - + +
640B ARG* 5.5 5.2 - - - -
641B VAL 5.0 2.9 - - - -
642B GLY* 4.1 17.9 - - - -
646B GLU* 3.7 33.8 - - + +
649B VAL* 5.8 2.7 - - + -
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Residues in contact with TYR 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A G 4.6 7.6 - - - -
30A C 4.5 11.3 + - - -
231B HIS 4.1 5.5 + - - +
232B ARG 3.8 3.0 + - - +
233B ALA 3.4 0.2 - - - -
234B CYS* 1.3 78.1 - - - +
236B ARG* 1.3 66.0 + - - +
238B MET* 3.2 16.5 + - + +
239B THR* 3.4 35.5 + - + +
611B ARG* 3.9 5.5 + - - -
614B TRP* 3.3 39.6 + + - -
649B VAL* 6.2 5.8 - - + +
653B TYR* 4.4 17.7 - + + -
974B MET* 3.5 54.2 + - + -
975B ALA* 3.3 25.2 - - + +
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Residues in contact with ARG 236 (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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28A G 2.8 38.8 + - - -
29A G 2.9 15.2 + - - -
266A G 3.3 61.8 - - - +
267A U 3.2 26.6 + - - -
232B ARG* 3.3 24.7 + - - +
233B ALA* 3.8 7.9 - - - +
234B CYS 3.3 0.2 - - - -
235B TYR* 1.3 83.0 - - + +
237B ALA* 1.3 56.7 + - - +
238B MET 3.2 2.8 + - - -
239B THR* 4.8 2.5 - - - -
240B ASN* 3.8 20.6 + - + +
241B ARG* 3.5 27.5 + - + +
640B ARG* 5.9 4.0 - - - +
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Residues in contact with ALA 237 (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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233B ALA 2.9 18.8 + - - +
234B CYS 3.5 4.7 + - - +
235B TYR 3.2 0.2 - - - -
236B ARG* 1.3 74.8 - - - +
238B MET* 1.3 56.0 + - - -
241B ARG* 3.0 34.3 - - + +
242B CYS 3.0 27.9 - - - +
243B LEU* 3.3 13.6 + - + +
638B GLY 6.0 0.4 - - - +
640B ARG* 4.6 19.1 - - + +
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Residues in contact with MET 238 (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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234B CYS 3.3 15.5 - - - +
235B TYR* 3.2 11.5 + - + +
237B ALA* 1.3 79.2 - - - +
239B THR* 1.3 64.4 + - + +
240B ASN 3.6 0.4 - - - -
241B ARG 4.0 2.9 - - - -
243B LEU* 4.6 3.1 - - + -
435B ILE* 3.7 31.4 - - + +
436B GLY* 4.0 3.8 - - - -
437B PRO* 3.3 17.5 - - - +
614B TRP* 3.6 51.3 - - + +
615B GLY* 4.5 4.5 - - - -
616B SER* 5.6 0.2 + - - -
646B GLU* 4.1 16.8 - - - +
649B VAL* 5.6 4.7 - - - +
650B HIS* 3.4 34.1 - - + +
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Residues in contact with THR 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A C 5.6 1.2 + - - -
235B TYR* 3.4 38.5 + - + +
236B ARG* 4.6 1.7 + - - -
238B MET* 1.3 78.4 - - - +
240B ASN* 1.3 79.2 + - - +
437B PRO* 3.4 16.7 - - - +
611B ARG* 4.4 7.0 - - - +
614B TRP* 3.5 35.4 - - + +
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Residues in contact with ASN 240 (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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266A G 5.7 2.2 + - - -
236B ARG* 3.8 18.8 + - + +
239B THR* 1.3 94.5 + - - +
241B ARG* 1.3 69.0 + - + +
437B PRO* 4.2 9.7 - - - +
438B LEU* 3.7 17.0 - - - +
27G PRO* 4.9 14.4 - - - +
28G SER* 5.0 5.4 - - - -
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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