Contacts of the helix formed by residues 209 - 221 (chain j) in PDB entry 5M32
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 MET 209 (chain j).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207j SER 2.5 15.9 + - - +
208j LEU* 1.3 76.0 - - - +
210j PRO* 1.4 75.8 - - + +
211j TYR 3.4 1.4 + - - -
212j PHE* 3.6 2.4 + - - +
213j LEU* 3.3 19.6 + - - +
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Residues in contact with PRO 210 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207j SER 4.6 2.9 - - - +
208j LEU* 4.1 3.1 - - - +
209j MET* 1.4 93.8 - - + +
211j TYR* 1.3 65.1 + - + +
213j LEU* 3.2 9.3 + - + +
214j LEU* 2.9 27.2 + - - +
229j VAL* 6.1 0.2 - - - +
236j LYS* 4.3 26.9 - - + +
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Residues in contact with TYR 211 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181j LYS* 5.0 20.9 - - + +
185j VAL* 5.0 13.1 - - + +
208j LEU 5.5 0.2 - - - -
209j MET 3.5 0.2 - - - -
210j PRO* 1.3 83.7 - - + +
212j PHE* 1.3 59.9 + - - +
214j LEU* 3.3 8.2 + - - +
215j THR* 3.0 24.9 + - - -
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Residues in contact with PHE 212 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201j GLN* 6.3 2.9 - - + -
208j LEU* 4.1 11.8 + - - +
209j MET 3.6 7.8 + - - +
211j TYR* 1.3 76.3 - - - +
213j LEU* 1.3 58.7 + - - +
215j THR* 3.0 22.7 + - - -
216j GLN* 3.0 15.2 + - - +
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Residues in contact with LEU 213 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209j MET 3.3 11.5 + - - +
210j PRO* 3.2 13.6 + - + +
212j PHE* 1.3 79.0 - - - +
214j LEU* 1.3 57.1 + - - +
216j GLN* 3.6 4.1 + - - +
217j ALA* 2.9 27.2 + - - +
229j VAL* 5.1 6.7 - - + +
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Residues in contact with LEU 214 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210j PRO 2.9 13.5 + - - +
211j TYR* 3.3 8.7 + - - +
212j PHE 3.2 0.4 - - - -
213j LEU* 1.3 74.6 - - - +
215j THR* 1.3 60.5 + - - +
217j ALA* 3.5 8.9 - - + +
218j VAL* 3.0 28.2 + - - +
229j VAL* 5.0 10.5 - - + +
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Residues in contact with THR 215 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188j LEU* 5.5 13.2 - - - -
197j LEU* 5.5 11.7 - - - -
211j TYR 3.0 12.6 + - - -
212j PHE* 3.0 14.6 + - - -
214j LEU* 1.3 78.2 - - - +
216j GLN* 1.3 57.5 + - - +
218j VAL* 3.4 5.1 + - - +
219j ARG* 2.9 26.3 + - - +
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Residues in contact with GLN 216 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212j PHE 3.0 12.7 + - - +
213j LEU* 4.4 3.8 - - - +
215j THR* 1.3 73.9 - - - +
217j ALA* 1.3 59.4 + - - +
218j VAL 3.2 0.9 - - - -
219j ARG* 3.6 8.7 - - + -
220j THR* 2.9 30.1 + - - -
45s ASP* 3.5 32.3 - - + +
46s ASP* 5.2 3.8 - - + +
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Residues in contact with ALA 217 (chain j).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213j LEU 2.9 19.9 + - - +
214j LEU* 3.2 12.9 + - - +
216j GLN* 1.3 77.3 - - - +
218j VAL* 1.3 55.8 + - - +
220j THR* 4.7 2.1 - - - -
221j GLY* 3.3 16.9 + - - -
222j ASN 4.1 10.6 + - - +
225j LYS* 5.0 2.5 - - + +
226j PHE* 4.4 19.3 + - + +
229j VAL* 4.4 16.2 - - + -
249j LEU* 4.7 2.1 - - - +
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Residues in contact with VAL 218 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188j LEU* 6.0 5.6 - - + -
214j LEU 3.0 14.4 + - - +
215j THR* 4.0 5.2 - - - +
217j ALA* 1.3 75.6 - - - +
219j ARG* 1.3 63.3 + - - +
220j THR 3.2 2.2 - - - -
221j GLY* 3.2 16.6 + - - +
248j ARG* 6.1 0.7 - - + -
249j LEU* 4.3 17.0 - - + +
252j ASN* 4.5 12.6 - - - +
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Residues in contact with ARG 219 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193j ILE* 5.3 16.8 - - + -
194j PRO* 5.8 9.6 - - + -
215j THR 2.9 18.8 + - - +
216j GLN* 3.3 13.9 + - + +
218j VAL* 1.3 74.6 - - - +
220j THR* 1.3 60.5 + - - +
252j ASN* 6.0 0.5 - - - +
45s ASP* 5.6 3.6 - - + -
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Residues in contact with THR 220 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216j GLN 2.9 15.8 + - - -
217j ALA* 4.7 2.7 - - - -
218j VAL 3.6 0.7 - - - -
219j ARG* 1.3 78.5 - - - +
221j GLY* 1.3 62.9 + - - +
222j ASN* 3.9 3.6 - - - -
252j ASN* 5.6 2.3 - - - +
253j VAL* 5.6 3.6 - - - +
46s ASP* 4.3 22.0 - - - -
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Residues in contact with GLY 221 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217j ALA 3.3 11.6 + - - -
218j VAL 3.2 14.5 + - - -
220j THR* 1.3 80.6 - - - +
222j ASN* 1.3 61.2 + - - +
249j LEU* 3.5 32.1 - - - +
252j ASN* 5.2 3.1 - - - -
253j VAL* 4.5 11.8 - - - +
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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