Contacts of the helix formed by residues 326 - 337 (chain G) in PDB entry 2D11
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 326 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325G MET* 1.3 76.1 - - - +
327G TRP* 1.3 70.9 + - + +
328G ASN* 3.2 26.3 + - - +
329G ARG* 2.9 31.6 + - - +
330G LYS* 3.1 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 327 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C PHE* 3.8 23.3 - + - -
244C GLU* 3.2 43.6 + - + +
245C ILE* 4.3 3.8 - - + -
257C ILE* 3.3 44.4 - - + -
259C PRO* 3.7 29.5 - - + +
261C ASP* 5.9 2.2 - - + +
264C ALA* 3.9 24.2 - - + +
265C PRO* 3.5 22.0 - - + +
267C PHE* 3.9 17.7 - + + -
325G MET 5.3 0.2 - - - -
326G ASP* 1.3 79.0 + - + +
328G ASN* 1.3 60.7 + - - +
330G LYS* 3.7 21.1 - - + +
331G ARG* 3.2 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 328 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C ALA* 5.2 2.3 - - - +
265C PRO* 3.2 31.8 - - - +
326G ASP* 3.0 22.2 + - - +
327G TRP* 1.3 75.1 - - - +
329G ARG* 1.3 63.9 + - - +
331G ARG* 3.5 7.4 + - - +
332G GLU* 3.2 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 329 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325G MET* 4.1 21.4 - - + +
326G ASP* 2.9 16.4 + - - +
328G ASN* 1.3 75.8 - - - +
330G LYS* 1.3 64.5 + - - +
332G GLU* 3.5 26.3 + - - +
333G ILE* 3.0 59.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 330 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C ILE* 3.6 22.7 - - + +
239C GLY* 3.1 30.6 + - - +
240C PHE* 3.8 22.6 - - + -
241C PRO* 4.6 1.2 - - - +
244C GLU* 2.8 30.3 + - - -
267C PHE* 4.2 3.5 - - + -
323G PRO 5.7 1.3 - - - -
325G MET* 3.4 47.5 + - + +
326G ASP 3.1 9.5 + - - +
327G TRP* 3.7 26.7 - - + +
329G ARG* 1.3 77.5 - - - +
331G ARG* 1.3 56.3 + - - +
333G ILE* 4.8 0.9 - - - -
334G PHE* 3.0 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 331 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C LYS* 5.0 13.3 - - - +
265C PRO* 3.6 30.9 - - - +
266C ASP 3.3 29.5 + - - +
267C PHE* 4.3 17.0 - - + -
268C VAL* 4.6 17.6 - - - +
327G TRP* 3.2 10.0 + - + +
328G ASN* 3.6 9.9 - - - +
329G ARG 3.3 0.2 - - - -
330G LYS* 1.3 78.5 - - - +
332G GLU* 1.3 49.8 + - - +
334G PHE* 3.4 8.1 + - - +
335G SER* 2.4 44.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 332 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328G ASN 3.2 12.1 + - - +
329G ARG* 3.5 36.6 + - - +
331G ARG* 1.3 76.3 - - - +
333G ILE* 1.3 63.5 + - + +
335G SER* 3.4 9.8 - - - -
336G ASN* 2.9 44.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 333 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C LYS 5.3 2.2 - - - +
238C ILE* 3.9 12.3 - - + -
325G MET* 3.7 29.4 - - + -
329G ARG* 3.0 56.4 + - - +
330G LYS 3.9 2.5 - - - +
332G GLU* 1.3 73.9 - - + +
334G PHE* 1.3 65.6 + - - +
336G ASN* 3.4 8.8 + - - +
337G PHE* 3.2 50.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 334 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C ILE* 4.1 13.9 - - + -
209C LYS 3.5 22.0 - - - -
210C ASN* 2.9 47.6 + - - +
211C LYS 4.8 0.7 - - - -
216C LEU* 3.5 25.6 - - + -
227C ILE* 4.0 14.4 - - + -
238C ILE* 3.7 4.2 - - + +
267C PHE* 3.5 28.9 - + + -
268C VAL 3.3 22.0 - - - -
269C PHE* 3.6 13.7 - - + -
270C TYR* 5.8 0.7 - + - -
330G LYS 3.0 18.4 + - - +
331G ARG* 3.5 5.8 - - - +
333G ILE* 1.3 78.8 - - - +
335G SER* 1.3 59.5 + - - +
336G ASN 3.4 0.3 + - - -
337G PHE* 3.5 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 335 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C ASN* 2.8 24.6 + - - -
211C LYS* 6.5 0.2 - - - -
212C LYS* 5.0 6.6 - - - +
331G ARG* 2.4 41.8 + - - +
332G GLU* 3.4 11.6 - - - -
334G PHE* 1.3 75.6 - - - +
336G ASN* 1.3 62.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 336 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332G GLU* 2.9 33.7 + - - +
333G ILE* 3.9 8.6 - - - +
334G PHE 3.3 0.4 - - - -
335G SER* 1.3 77.4 - - - +
337G PHE* 1.3 69.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 337 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C ASN* 3.2 9.4 + - - -
212C LYS* 5.1 1.2 - - - +
214C THR* 2.7 39.1 + - - +
216C LEU* 4.1 33.2 - - + -
227C ILE* 4.5 6.1 - - + -
228C TYR 6.1 0.2 - - - -
229C GLU* 3.7 33.2 - - + -
237C LYS* 3.6 35.0 - - + -
238C ILE* 3.7 15.7 - - + -
333G ILE* 3.2 42.0 + - + -
334G PHE* 3.6 16.6 - + - +
335G SER 3.4 1.2 - - - -
336G ASN* 1.3 82.4 - - + +
----------------------------------------------------------
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