Contacts of the helix formed by residues 220 - 233 (chain G) in PDB entry 1MVW
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 220 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206G LYS 5.5 0.7 - - - +
213G LYS* 2.8 64.1 + - + +
214G MET 3.5 4.6 - - - +
217G THR* 2.8 39.8 + - - +
218G LEU 2.9 1.6 - - - -
219G GLU* 1.3 88.0 - - - +
221G GLN* 1.3 51.0 + - - -
222G ILE 3.0 1.3 - - - -
223G ILE* 2.7 7.5 + - - +
224G SER* 2.3 41.4 + - - +
340G ILE* 4.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 221 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206G LYS* 4.5 4.0 - - - +
216G GLY* 3.6 6.5 + - - +
217G THR* 2.6 38.4 + - - +
218G LEU* 2.4 47.1 - - + +
220G ASP* 1.3 69.7 - - - +
222G ILE* 1.3 63.8 + - - +
224G SER* 4.2 4.3 - - - -
225G ALA* 2.8 24.5 + - - +
340G ILE* 3.6 20.7 - - + +
341G LEU* 3.4 20.4 - - + +
448G GLN* 4.0 22.9 - - - +
449G LEU* 3.6 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 222 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193G ILE* 4.0 26.7 - - + +
197G ALA* 5.2 5.8 - - + -
218G LEU* 2.9 37.7 - - + -
219G GLU* 3.5 20.6 - - - +
221G GLN* 1.3 80.1 - - - +
223G ILE* 1.3 70.4 + - + +
225G ALA* 3.3 13.2 - - - +
226G ASN* 4.2 5.7 - - - +
250G ILE* 6.0 1.1 - - + -
252G ILE* 5.0 9.4 - - + -
260G LEU* 5.3 9.9 - - + -
262G SER 5.1 1.6 - - - +
263G ALA* 3.2 30.1 - - + -
449G LEU* 4.7 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 223 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193G ILE* 5.3 4.5 - - + -
194G GLN* 3.2 49.8 - - - +
197G ALA* 4.9 6.1 - - + -
219G GLU 2.8 25.1 - - - +
220G ASP* 2.7 8.6 + - - +
222G ILE* 1.3 86.0 - - + +
224G SER* 1.3 57.2 + - - +
225G ALA 2.6 16.8 + - - -
226G ASN* 2.9 35.5 + - - +
227G PRO* 3.2 5.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 224 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213G LYS 4.2 3.8 + - - -
220G ASP* 2.3 32.6 + - - -
221G GLN* 3.7 6.3 - - - -
223G ILE* 1.3 68.6 - - - +
225G ALA* 1.3 65.1 + - - +
227G PRO* 3.0 21.1 - - - +
228G LEU 3.9 0.3 + - - -
337G ALA* 3.7 17.2 - - - +
340G ILE* 3.8 25.0 - - - +
341G LEU* 3.4 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 225 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221G GLN 2.8 9.7 + - - +
222G ILE* 3.3 17.3 - - - +
223G ILE 2.6 5.3 + - - -
224G SER* 1.3 73.7 - - - +
226G ASN* 1.3 68.6 + - - +
228G LEU* 3.0 19.6 + - - +
229G LEU* 3.4 10.6 + - + +
265G ILE* 4.1 25.4 - - + -
341G LEU* 3.7 10.5 - - - -
445G ILE* 4.4 14.3 - - + +
449G LEU* 5.2 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 226 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190G MLY 4.1 31.2 - - + +
193G ILE* 5.6 8.3 - - - +
194G GLN* 6.0 0.2 + - - -
222G ILE 4.2 6.7 + - - +
223G ILE* 2.9 31.2 + - - +
225G ALA* 1.3 77.8 - - - +
227G PRO* 1.3 58.1 - - + +
228G LEU 2.8 11.6 + - - -
229G LEU* 3.0 8.8 + - - +
230G GLU* 2.8 33.5 + - + +
248G MLY 2.8 36.7 - - - -
250G ILE* 5.4 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 227 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190G MLY 6.2 2.2 - - - -
223G ILE* 3.2 9.9 - - + +
224G SER* 3.0 22.2 - - - +
226G ASN* 1.3 97.4 - - + +
228G LEU* 1.3 58.9 + - - +
230G GLU* 4.1 12.9 - - + +
231G ALA* 3.7 8.5 + - - +
333G ALA* 4.9 16.4 - - + +
334G THR* 3.8 19.2 + - - -
337G ALA* 4.8 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 228 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224G SER 3.9 5.1 + - - +
225G ALA 3.0 10.2 + - - +
226G ASN 2.8 3.2 + - - -
227G PRO* 1.3 73.5 - - - +
229G LEU* 1.3 70.4 + - + +
230G GLU 3.0 0.9 - - - -
231G ALA* 2.8 14.5 + - - +
232G PHE* 3.2 39.9 - - + -
334G THR* 4.2 10.8 - - + +
337G ALA* 4.6 5.8 - - + -
338G ILE* 3.5 30.3 - - + -
341G LEU* 4.5 8.5 - - + -
343G PHE* 4.1 21.8 - - + -
351G ILE* 5.9 0.2 - - + -
441G MET* 4.3 15.7 - - - -
445G ILE* 3.9 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 229 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225G ALA 3.4 13.4 + - - +
226G ASN* 3.0 9.2 + - - +
228G LEU* 1.3 83.4 - - + +
230G GLU* 1.3 53.2 + - + +
232G PHE* 3.1 3.0 + - - +
233G GLY* 2.4 39.2 + - - -
246G PHE* 4.0 20.8 - - + -
248G MLY 5.4 9.2 - - + +
265G ILE* 4.2 30.3 - - + -
267G THR* 5.6 0.2 - - - +
438G PHE* 3.9 23.0 - - + -
441G MET* 5.1 5.2 - - + -
442G VAL* 4.1 22.7 - - + +
445G ILE* 3.9 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 230 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186G THR* 3.6 12.4 - - + +
190G MLY 2.8 46.4 - - - +
226G ASN* 2.8 30.8 + - + +
227G PRO* 4.1 9.4 - - + +
229G LEU* 1.3 75.8 - - + +
231G ALA* 1.3 64.1 + - - +
232G PHE 3.1 0.4 - - - -
234G ASN* 2.9 46.0 + - + +
242G ASN* 2.6 31.9 + - - +
246G PHE* 6.1 0.9 - - + -
248G MLY 5.5 3.6 - - - -
286G HIS* 3.3 9.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 231 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227G PRO 3.7 5.2 + - - +
228G LEU 2.8 11.1 + - - +
230G GLU* 1.3 80.3 - - - +
232G PHE* 1.3 66.0 - - + +
286G HIS* 3.2 17.6 + - - -
287G ILE* 2.7 37.4 + - + +
290G GLN* 3.5 29.2 - - - +
334G THR* 3.8 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 232 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228G LEU* 3.2 44.4 + - + -
229G LEU* 3.1 5.2 + - - +
231G ALA* 1.3 81.1 - - + +
233G GLY* 1.3 58.5 + - - +
270G LEU* 5.0 0.3 - - - +
285G TYR* 2.8 22.0 - - - -
287G ILE* 3.0 38.8 - - + -
334G THR* 4.9 1.3 - - + -
338G ILE* 5.5 0.9 - - + -
351G ILE* 3.7 20.9 - - + -
355G THR* 3.8 19.3 - - - -
434G TYR* 2.8 37.0 + + + +
437G MET* 4.0 9.2 - - + -
438G PHE* 3.8 19.4 - - + -
441G MET* 3.8 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 233 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229G LEU 2.4 19.5 + - - -
232G PHE* 1.3 74.2 - - - +
234G ASN* 1.3 61.1 + - - +
245G ARG* 2.9 27.0 + - - -
246G PHE* 3.0 23.4 - - - -
270G LEU* 4.1 3.1 - - - -
285G TYR* 3.3 12.6 - - - -
438G PHE* 3.8 6.7 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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