Contacts of the helix formed by residues 228 - 236 (chain B) in PDB entry 6S1M
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 ASP 228 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B ALA 3.6 20.1 - - - +
11B HIS* 3.9 13.4 - - + +
12B THR* 3.6 12.9 + - - -
13B LEU* 3.2 34.8 + - + +
227B GLY* 1.3 72.3 - - - +
229B GLU* 1.3 85.2 + - - +
230B GLY 3.1 7.2 + - - +
231B GLU* 3.3 4.3 + - - +
232B GLN* 2.9 33.9 + - - +
35C ASN* 5.9 0.2 - - - +
96C ALA 4.5 14.1 - - - +
97C SER* 3.5 10.8 + - - +
98C ILE 4.9 3.2 - - - +
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Residues in contact with GLU 229 (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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9B ARG* 4.6 14.1 + - + -
10B ALA 5.2 4.0 - - - +
12B THR* 3.4 29.5 + - - +
13B LEU* 5.3 0.9 - - - +
21B ASN* 5.6 1.7 - - - +
22B ALA* 4.2 23.5 + - + +
24B PHE* 4.1 19.3 - - + -
228B ASP* 1.3 91.2 + - - +
230B GLY* 1.3 59.8 + - - +
232B GLN* 3.6 13.9 - - - +
233B CYS* 2.9 30.5 + - - +
35C ASN* 4.5 12.6 + - - +
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Residues in contact with GLY 230 (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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5B GLN 5.1 0.6 - - - +
6B ALA* 3.5 30.1 - - - -
9B ARG* 5.0 15.5 + - - +
10B ALA 5.7 0.2 + - - -
11B HIS* 5.9 2.1 - - - -
228B ASP* 3.1 7.1 + - - +
229B GLU* 1.3 76.6 - - - +
231B GLU* 1.3 56.3 + - - +
233B CYS* 3.3 5.1 + - - +
234B SER* 2.9 30.8 + - - -
96C ALA 5.1 1.8 - - - -
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Residues in contact with GLU 231 (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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2B PHE* 5.2 3.5 - - - -
6B ALA* 4.4 3.1 + - - -
221B VAL* 5.0 16.7 - - + +
226B LEU 4.0 14.9 - - - +
227B GLY* 4.0 3.6 - - - -
228B ASP 3.3 10.7 + - - +
230B GLY* 1.3 75.3 - - - +
232B GLN* 1.3 58.0 + - - +
234B SER* 3.1 8.4 + - - -
235B ALA* 2.9 33.1 + - - +
64C SER* 2.9 28.9 + - - -
75C HIS* 3.9 14.7 + - - -
77C VAL* 5.2 3.5 - - - +
96C ALA* 3.7 17.9 - - + +
97C SER* 3.3 29.2 - - - -
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Residues in contact with GLN 232 (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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22B ALA 5.4 0.2 - - - +
24B PHE* 3.7 25.7 - - + -
224B GLY* 4.2 16.4 + - - +
225B GLN 4.6 0.8 - - - -
226B LEU 4.0 12.4 + - - +
227B GLY 2.9 23.3 + - - +
228B ASP 2.9 22.4 + - - +
229B GLU* 3.5 7.9 + - - +
231B GLU* 1.3 74.8 - - - +
233B CYS* 1.3 64.0 + - - +
235B ALA* 4.6 3.1 - - - +
236B ALA* 3.4 21.7 + - - +
33C HIS* 5.6 0.4 - - - -
34C VAL* 5.8 1.6 - - - +
35C ASN* 3.2 31.9 + - - +
38C LYS* 4.2 3.8 - - - +
134C ALA* 4.1 21.6 - - + +
135C ILE* 4.1 6.5 - - + +
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Residues in contact with CYS 233 (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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5B GLN* 5.2 5.6 + - - -
9B ARG* 3.3 42.2 - - - +
24B PHE* 4.2 21.5 - - + -
229B GLU 2.9 20.5 + - - +
230B GLY 3.3 2.9 + - - +
232B GLN* 1.3 79.0 - - - +
234B SER* 1.3 58.4 + - - +
235B ALA 3.5 0.2 - - - -
236B ALA* 3.7 8.9 + - - +
237B HIS* 3.0 36.2 + - - -
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Residues in contact with SER 234 (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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2B PHE* 3.3 53.6 - - - -
5B GLN* 5.3 11.9 - - - -
6B ALA* 4.1 8.4 - - - +
195B PHE* 5.2 1.0 - - - -
230B GLY 2.9 17.5 + - - -
231B GLU* 3.1 13.5 + - - -
233B CYS* 1.3 76.3 - - - +
235B ALA* 1.3 60.3 + - - +
236B ALA 3.2 2.0 - - - -
237B HIS* 3.4 18.5 + - - +
238B VAL* 4.0 4.2 + - - +
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Residues in contact with ALA 235 (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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2B PHE* 4.4 5.6 - - + -
26B ARG* 2.7 28.8 + - - -
221B VAL* 3.5 33.7 - - + +
222B VAL* 4.3 9.1 - - + +
224B GLY* 5.7 0.4 - - - -
231B GLU 2.9 18.9 + - - +
232B GLN* 4.9 1.1 - - - -
234B SER* 1.3 74.3 + - - +
236B ALA* 1.3 53.8 + - - +
237B HIS 3.2 1.5 + - - -
238B VAL* 3.6 17.2 + - + +
135C ILE* 4.3 7.9 - - + -
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Residues in contact with ALA 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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24B PHE* 4.4 8.7 - - + -
25B ALA 3.9 15.0 - - - +
26B ARG* 3.6 14.9 + - - +
27B VAL* 3.5 25.2 + - - +
232B GLN 3.4 19.7 + - - +
233B CYS* 3.9 7.9 - - - +
234B SER 3.2 1.2 - - - -
235B ALA* 1.3 77.5 - - - +
237B HIS* 1.3 62.7 + - + +
238B VAL 3.4 0.6 + - - -
135C ILE* 3.9 18.1 - - + +
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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