Contacts of the helix formed by residues 226 - 236 (chain D) in PDB entry 5MR4
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 226 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159D ASN* 4.5 7.1 + - - +
224D CYS* 3.8 0.9 - - - +
225D GLN* 1.3 81.1 + - + +
227D GLN* 1.3 63.6 + - - +
228D ALA* 3.5 24.3 + - - +
229D CYS* 3.4 18.1 + - - +
230D ALA* 3.2 21.1 + - - +
314D PRO* 3.6 10.2 - - - +
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Residues in contact with GLN 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D ASP* 1.3 73.0 - - - +
228D ALA* 1.3 63.1 + - - +
230D ALA* 3.8 0.7 - - - +
231D GLU* 2.8 48.8 + - - +
312D SER* 2.5 42.5 + - - +
314D PRO* 3.9 6.6 - - + +
502D FMT 3.9 7.9 + - - +
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Residues in contact with ALA 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D ASN* 4.7 7.0 + - - +
226D ASP* 3.4 15.8 + - - +
227D GLN* 1.3 82.6 - - + +
229D CYS* 1.3 59.9 + - - +
231D GLU* 3.9 5.4 - - - +
232D ARG* 3.2 23.2 + - - +
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Residues in contact with CYS 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D ASN* 3.6 35.8 - - + +
161D CYS* 3.5 16.3 - - - -
223D SER 3.7 5.4 - - - -
224D CYS* 2.2 52.5 - - + -
225D GLN 4.7 0.4 - - - +
226D ASP* 3.4 23.0 + - - +
227D GLN 3.3 0.4 - - - -
228D ALA* 1.3 78.3 - - - +
230D ALA* 1.3 57.6 + - - +
232D ARG* 3.2 6.5 + - - +
233D ARG* 3.0 23.4 + - - +
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Residues in contact with ALA 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D CYS* 3.3 9.1 - - + -
226D ASP 3.2 13.0 + - - +
227D GLN 3.8 0.9 - - - +
229D CYS* 1.3 79.4 - - - +
231D GLU* 1.3 56.0 + - - +
233D ARG* 3.3 13.6 + - - +
234D ARG* 2.9 29.1 + - - +
309D TYR* 5.8 0.3 - - - +
311D ASP 4.9 0.5 - - - +
312D SER* 3.2 34.7 - - - +
313D SER 3.8 12.6 - - - +
314D PRO* 3.9 7.4 - - + -
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Residues in contact with GLU 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B LEU* 6.1 0.2 - - + -
181B SER* 2.9 33.4 + - - +
227D GLN* 2.8 36.3 + - - +
228D ALA* 3.9 6.3 - - - +
230D ALA* 1.3 71.3 - - - +
232D ARG* 1.3 64.8 + - - +
234D ARG* 2.7 37.2 + - - +
235D GLN* 3.0 36.6 + - - +
312D SER* 3.5 19.2 + - - -
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Residues in contact with ARG 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B SER* 4.7 1.0 + - - -
122B ASP* 5.4 2.0 - - - +
123B GLU* 2.8 30.3 + - - +
177B LEU* 3.1 55.1 + - + +
178B ASP 4.8 3.4 + - - -
183B TYR* 4.9 1.0 + - - -
159D ASN* 4.4 5.7 - - - +
161D CYS* 3.7 35.4 - - + +
162D LEU* 3.5 29.2 - - - +
165D ALA* 4.0 9.3 - - - +
178D ARG* 4.1 3.8 - - - +
228D ALA 3.2 11.5 + - - +
229D CYS 3.2 9.9 + - - +
231D GLU* 1.3 77.6 - - - +
233D ARG* 1.3 62.7 + - - +
235D GLN* 3.1 12.1 + - - +
236D THR* 3.3 12.3 + - - -
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Residues in contact with ARG 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D CYS* 3.7 16.8 - - - -
219D MET 4.3 2.2 - - - +
220D LEU* 3.6 10.1 - - - +
222D CYS* 3.1 36.4 + - - -
223D SER* 4.2 1.4 - - - +
224D CYS* 3.8 19.4 - - - +
229D CYS 3.0 7.6 + - - +
230D ALA* 3.5 14.8 + - - +
231D GLU 3.3 0.2 - - - -
232D ARG* 1.3 77.4 - - - +
234D ARG* 1.3 60.8 + - - +
236D THR* 2.8 25.6 + - - -
308D ASN* 4.9 1.2 - - - +
309D TYR* 3.6 47.7 - - + -
311D ASP 5.5 2.0 + - - -
313D SER 3.4 15.0 + - - -
314D PRO 3.2 26.5 + - - -
317D ILE* 3.7 27.8 - - - +
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Residues in contact with ARG 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D ALA 2.9 16.6 + - - +
231D GLU* 2.7 52.4 + - - +
233D ARG* 1.3 77.4 - - - +
235D GLN* 1.3 67.3 + - - +
236D THR 3.6 0.7 + - - -
237D ILE 4.4 0.9 + - - -
239D PRO* 3.4 35.8 - - - +
240D SER* 5.3 2.0 - - - +
244D GLU* 3.7 19.2 + - - -
308D ASN* 3.0 28.2 + - - +
309D TYR* 3.5 30.0 + - + +
310D VAL 5.0 2.0 + - - -
311D ASP* 3.7 36.2 - - - +
312D SER 4.1 0.2 - - - +
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Residues in contact with GLN 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B LEU* 4.3 10.9 - - + +
181B SER* 2.9 43.4 + - - +
183B TYR* 2.9 28.2 + - + +
231D GLU* 3.0 34.6 + - - +
232D ARG 3.1 6.7 + - - +
234D ARG* 1.3 83.9 + - - +
236D THR* 1.3 65.0 + - - +
237D ILE 3.2 2.9 - - - -
238D LEU* 2.8 19.2 + - - +
239D PRO* 3.5 20.2 - - - +
240D SER* 5.1 3.6 + - - -
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Residues in contact with THR 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B TYR* 3.6 9.8 + - - -
181D TYR* 2.6 42.4 + - + +
207D PHE* 5.4 2.2 - - + -
208D PHE* 5.1 7.4 - - + -
216D THR 5.7 0.2 - - - +
219D MET* 3.6 41.0 + - + +
220D LEU* 4.5 22.3 - - + +
232D ARG 3.3 9.0 + - - -
233D ARG* 2.8 19.9 + - - -
234D ARG 3.4 0.2 - - - -
235D GLN* 1.3 76.9 - - - +
237D ILE* 1.3 60.1 + - + +
238D LEU 3.4 0.7 + - - -
308D ASN* 6.0 0.2 - - - -
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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