Contacts of the helix formed by residues 228 - 242 (chain B) in PDB entry 3RIG
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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157B ILE 5.1 2.2 + - - +
221B VAL* 5.2 3.2 - - + +
226B ASN 3.9 0.4 + - - -
227B LEU* 1.3 74.5 - - - +
229B PRO* 1.3 67.8 - - - +
230B ALA* 2.6 43.0 + - - +
231B ILE* 3.2 27.8 + - + +
232B LEU* 2.9 27.9 + - - +
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Residues in contact with PRO 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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226B ASN* 6.1 0.7 - - + -
227B LEU 3.4 8.3 - - - +
228B ASP* 1.3 90.9 - - - +
230B ALA* 1.3 61.3 + - - +
232B LEU* 3.2 9.5 + - + +
233B GLU* 3.0 33.0 + - + +
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Residues in contact with ALA 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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228B ASP* 2.6 18.5 + - - +
229B PRO* 1.3 73.9 - - - +
231B ILE* 1.3 62.3 + - + +
233B GLU* 3.2 24.9 + - - +
234B GLU* 3.3 19.4 + - + +
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Residues in contact with ILE 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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155B LEU* 4.7 14.4 - - + -
156B GLU* 3.9 23.1 - - + +
157B ILE* 3.8 36.1 - - + +
227B LEU* 6.0 0.9 - - + -
228B ASP* 3.2 30.6 + - + +
230B ALA* 1.3 77.9 - - + +
232B LEU* 1.3 60.2 + - + +
234B GLU* 3.3 10.5 + - - +
235B VAL* 3.0 26.6 + - + +
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Residues in contact with LEU 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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157B ILE* 5.9 0.2 - - + -
227B LEU* 4.0 40.6 - - + +
228B ASP 2.9 16.0 + - - +
229B PRO* 3.2 7.4 + - + +
231B ILE* 1.3 77.0 - - + +
233B GLU* 1.3 57.2 + - - +
235B VAL* 3.5 6.5 + - + +
236B ASP* 3.0 39.8 + - - +
256B PRO* 4.4 7.6 - - + -
260B PHE* 4.2 22.9 - - + -
7D ALA* 3.7 33.7 - - + -
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Residues in contact with GLU 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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229B PRO* 3.0 23.5 + - + +
230B ALA* 3.2 16.3 + - - +
232B LEU* 1.3 75.2 - - + +
234B GLU* 1.3 58.8 + - - +
236B ASP* 3.3 10.6 + - - +
237B ARG* 3.0 49.1 + - - +
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Residues in contact with GLU 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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155B LEU* 4.0 24.5 - - + +
230B ALA 3.3 17.0 - - - +
231B ILE* 3.5 9.4 - - - +
233B GLU* 1.3 72.4 - - - +
235B VAL* 1.3 65.6 + - - +
237B ARG* 2.4 40.6 + - - +
238B GLU* 3.0 30.9 + - + +
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Residues in contact with VAL 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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138B ILE* 4.1 11.4 - - + -
155B LEU* 4.1 15.9 - - + +
157B ILE* 3.9 28.0 - - + -
231B ILE* 3.0 21.6 + - + +
232B LEU* 3.6 11.9 - - + +
233B GLU 3.4 0.2 - - - -
234B GLU* 1.3 74.2 - - - +
236B ASP* 1.3 60.7 + - - +
238B GLU* 3.1 3.7 + - - +
239B LEU* 2.9 56.5 + - + +
260B PHE* 3.7 30.7 - - + -
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Residues in contact with ASP 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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232B LEU* 3.0 25.0 + - - +
233B GLU* 3.3 11.8 - - - +
234B GLU 3.2 0.2 - - - -
235B VAL* 1.3 77.3 - - - +
237B ARG* 1.3 66.9 + - - +
239B LEU* 4.0 5.6 - - - +
240B ALA* 2.9 27.9 + - - +
260B PHE* 5.6 2.4 - - - -
263B GLN* 4.7 12.4 + - - +
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Residues in contact with ARG 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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52B HIS* 5.4 0.7 - - - -
233B GLU* 3.0 26.4 + - - +
234B GLU* 2.4 56.8 + - - +
236B ASP* 1.3 77.2 - - - +
238B GLU* 1.3 67.5 + - + +
240B ALA* 4.5 1.1 - - - -
241B HIS* 3.1 40.2 + - + +
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Residues in contact with GLU 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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52B HIS* 2.7 40.1 + - - -
54B VAL* 3.6 14.7 - - + +
134B ARG* 2.7 33.2 + - - -
136B VAL* 3.6 20.6 - - + +
138B ILE* 4.4 6.1 - - + -
155B LEU* 4.3 8.7 - - + +
234B GLU* 3.0 20.9 + - - +
235B VAL 3.6 4.9 - - - +
237B ARG* 1.3 83.6 - - - +
239B LEU* 1.3 58.9 + - - +
242B CYS* 2.9 35.2 + - - +
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Residues in contact with LEU 239 (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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54B VAL* 4.0 10.8 - - + -
56B ILE* 4.1 2.2 - - + -
138B ILE* 4.0 18.4 - - + -
235B VAL* 2.9 33.0 + - + +
236B ASP* 4.1 4.9 - - - +
238B GLU* 1.3 77.3 - - - +
240B ALA* 1.3 57.1 + - - +
242B CYS* 3.6 9.2 - - - -
260B PHE* 3.6 40.8 - - + +
263B GLN* 3.8 27.4 - - + +
264B VAL* 3.8 26.0 - - + +
267B ARG* 2.8 26.4 + - - -
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Residues in contact with ALA 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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236B ASP 2.9 19.9 + - - +
237B ARG* 3.2 4.5 + - - +
239B LEU* 1.3 72.0 - - - +
241B HIS* 1.3 73.9 + - + +
267B ARG* 3.0 30.1 + - - +
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Residues in contact with HIS 241 (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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52B HIS* 4.0 19.6 + - + +
237B ARG* 3.1 36.0 + - + +
240B ALA* 1.3 93.0 + - + +
242B CYS* 1.3 69.1 + - - +
243B ASP* 3.7 1.9 + - - +
267B ARG* 3.8 3.8 + - - +
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Residues in contact with CYS 242 (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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52B HIS* 3.2 24.8 + - + +
54B VAL* 3.4 23.8 - - + -
238B GLU 2.9 21.2 + - - +
239B LEU* 3.6 16.8 - - - -
241B HIS* 1.3 82.1 - - - +
243B ASP* 1.3 58.4 + - - +
244B LEU 3.7 12.6 - - - +
245B CYS* 4.8 0.2 - - - -
264B VAL* 4.1 21.5 - - - -
267B ARG* 3.1 20.8 + - - -
269B VAL* 4.0 3.5 - - - +
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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