Contacts of the helix formed by residues 237 - 250 (chain D) in PDB entry 4U2M
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 237 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176D CYS* 3.4 20.2 - - - +
177D SER* 3.6 8.5 - - - -
209D LEU* 4.4 20.0 - - + -
212D PHE* 5.2 6.1 - - + -
213D MET* 2.9 41.3 - - + -
232D ALA* 2.9 11.2 + - + +
235D LEU* 3.0 39.9 - - + +
236D GLN* 1.3 78.0 - - - +
238D GLU* 1.3 64.9 + - - +
239D HIS 3.3 2.5 - - - -
240D VAL* 3.1 21.0 + - + +
241D VAL* 3.1 22.2 + - - +
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Residues in contact with GLU 238 (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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233D MET* 4.4 8.0 - - - +
236D GLN* 3.6 29.4 + - + +
237D MET* 1.3 72.9 - - - +
239D HIS* 1.3 69.2 + - + +
241D VAL* 3.1 21.7 + - - +
242D ASP* 2.9 31.8 + - - +
245D ARG* 5.9 0.3 + - - -
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Residues in contact with HIS 239 (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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196A ASN* 6.1 3.8 - - + -
3D PHE* 4.7 14.1 - + + -
9D HIS* 5.2 17.5 - + - -
237D MET 3.3 0.8 - - - -
238D GLU* 1.3 82.4 - - + +
240D VAL* 1.3 59.2 + - + +
242D ASP* 3.5 13.4 + - - +
243D THR* 2.9 30.4 + - - -
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Residues in contact with VAL 240 (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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3D PHE* 4.5 7.6 - - + -
209D LEU* 3.7 24.9 - - + -
212D PHE* 3.7 37.7 - - + -
218D LEU* 3.9 19.1 - - + -
228D VAL* 4.6 0.4 - - + -
232D ALA* 3.8 11.0 - - + -
237D MET* 3.1 21.1 + - + +
239D HIS* 1.3 76.3 - - + +
241D VAL* 1.3 64.7 + - - +
243D THR* 3.2 7.1 + - - -
244D CYS* 2.9 29.9 + - - -
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Residues in contact with VAL 241 (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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19C GLN* 4.4 1.3 - - - +
229D MET* 3.9 11.0 - - + +
232D ALA* 3.6 8.1 - - + +
233D MET* 3.5 48.9 - - + +
237D MET 3.1 15.4 + - - +
238D GLU* 3.4 22.2 - - - +
240D VAL* 1.3 74.8 - - - +
242D ASP* 1.3 64.3 + - - +
244D CYS* 3.1 8.9 + - - +
245D ARG* 3.0 48.2 + - - +
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Residues in contact with ASP 242 (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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189A LYS* 6.1 1.9 - - - -
238D GLU* 2.9 23.4 + - - +
239D HIS* 3.7 16.1 + - - +
241D VAL* 1.3 77.5 - - - +
243D THR* 1.3 61.5 + - - +
245D ARG* 2.5 40.0 + - - +
246D LYS* 3.0 42.9 + - - +
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Residues in contact with THR 243 (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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1D SER 5.2 7.0 - - - +
3D PHE* 3.4 31.1 - - + -
218D LEU* 4.3 12.1 - - + -
220D LEU* 4.6 7.4 - - + -
239D HIS 2.9 19.7 + - - -
240D VAL* 3.2 8.3 + - - -
242D ASP* 1.3 76.6 - - - +
244D CYS* 1.3 62.6 + - - +
246D LYS* 3.5 9.8 + - - +
247D PHE* 3.1 22.6 + - + +
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Residues in contact with CYS 244 (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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218D LEU* 4.8 0.7 - - - -
220D LEU* 4.0 17.9 - - - -
225D ILE* 3.2 21.7 - - + +
228D VAL* 3.9 17.3 - - - -
229D MET* 3.7 41.1 - - + -
240D VAL* 2.9 22.2 + - - -
241D VAL 3.4 8.3 - - - +
243D THR* 1.3 78.2 - - - +
245D ARG* 1.3 62.3 + - - +
247D PHE* 3.2 2.1 + - - -
248D ILE* 3.1 23.4 + - - +
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Residues in contact with ARG 245 (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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188A LEU* 3.8 28.6 - - - +
189A LYS* 6.1 3.2 - - - +
19C GLN* 2.2 49.3 + - - +
20C LEU* 4.2 9.4 - - + +
229D MET* 3.6 18.4 - - + -
241D VAL* 3.0 28.7 + - - +
242D ASP* 2.5 37.9 + - - +
244D CYS* 1.3 74.4 - - - +
246D LYS* 1.3 63.9 + - + +
248D ILE* 3.1 18.8 + - - +
249D LYS* 3.2 14.3 + - - +
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Residues in contact with LYS 246 (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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189A LYS* 5.2 13.4 - - - +
242D ASP* 3.0 35.3 + - - +
243D THR* 3.9 7.9 - - - +
245D ARG* 1.3 78.6 - - + +
247D PHE* 1.3 61.3 + - - +
248D ILE 3.2 0.5 + - - -
249D LYS* 3.4 8.4 + - - +
250D ALA* 3.3 21.8 + - - +
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Residues in contact with PHE 247 (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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220D LEU* 4.1 35.0 - - + -
221D ARG* 4.5 14.8 - - - -
222D GLU* 3.2 34.2 - - + +
225D ILE* 3.0 37.0 - - + -
243D THR* 3.1 17.0 + - + +
244D CYS 3.2 0.4 + - - -
246D LYS* 1.3 75.1 - - - +
248D ILE* 1.3 61.3 + - - +
250D ALA* 3.3 20.7 - - - +
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Residues in contact with ILE 248 (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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20C LEU* 3.8 43.1 - - + -
222D GLU* 6.1 0.9 - - - +
225D ILE* 3.9 25.6 - - + +
226D MET* 4.3 11.9 - - - -
229D MET* 4.2 11.0 - - - -
244D CYS 3.1 15.5 + - - +
245D ARG* 3.1 6.9 + - - +
247D PHE* 1.3 74.3 - - - +
249D LYS* 1.3 68.7 + - - +
250D ALA 3.0 10.7 + - - +
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Residues in contact with LYS 249 (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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245D ARG 3.2 8.7 + - - +
246D LYS* 3.7 10.5 - - - +
248D ILE* 1.3 80.1 - - - +
250D ALA* 1.3 57.7 + - + +
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Residues in contact with ALA 250 (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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222D GLU* 5.3 3.9 - - - +
246D LYS 3.3 12.9 + - - +
247D PHE* 3.3 15.6 - - - +
248D ILE 3.0 12.2 - - - +
249D LYS* 1.3 79.4 - - + +
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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