Contacts of the helix formed by residues 320 - 332 (chain G) in PDB entry 4D1Q
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 ASN 320 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271G SER* 4.4 3.2 + - - -
274G LEU* 3.8 12.3 - - - +
318G ARG 3.3 2.0 + - - -
319G TRP* 1.3 76.0 - - - +
321G SER* 1.3 66.2 + - - +
322G THR* 3.2 4.7 - - - -
323G TYR* 3.0 33.9 + - - +
324G THR* 3.4 6.6 + - - -
364G LEU* 3.2 35.8 + - - +
367G PHE* 4.0 2.4 - - - -
368G GLU* 3.2 47.1 + - - +
371G PHE* 4.0 19.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 321 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313G SER 5.2 1.2 - - - +
314G GLU* 3.3 37.0 + - - -
316G PRO* 4.2 13.9 + - - +
318G ARG* 3.4 23.0 + - - -
319G TRP 3.2 3.7 - - - -
320G ASN* 1.3 73.6 + - - +
322G THR* 1.3 74.0 + - - +
324G THR* 2.9 20.6 + - - -
325G MET* 3.3 11.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 322 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278G PHE* 4.8 23.8 - - + -
288G ILE* 4.5 18.8 - - + -
314G GLU* 4.7 16.7 + - - +
320G ASN* 4.6 1.4 - - - -
321G SER* 1.3 83.3 + - - +
323G TYR* 1.3 65.6 + - - +
325G MET* 3.0 7.4 + - - +
326G LEU* 2.9 53.0 + - + +
364G LEU* 5.1 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 323 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B SER* 5.4 1.7 - - - -
320G ASN* 3.0 31.3 + - - +
322G THR* 1.3 79.2 - - - +
324G THR* 1.3 69.7 + - + +
326G LEU* 3.1 3.6 + - - +
327G ARG* 2.7 78.9 + - - +
361G VAL* 4.2 21.8 - - + +
364G LEU* 3.7 29.0 - - + +
365G ASP* 3.8 30.4 + - + -
368G GLU* 3.0 41.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 324 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312G LYS* 5.0 16.6 - - + +
313G SER 6.0 1.1 - - - -
319G TRP 5.2 0.9 + - - -
320G ASN 3.4 8.0 + - - -
321G SER* 2.9 17.3 + - - -
323G TYR* 1.3 89.4 - - + +
325G MET* 1.3 56.7 + - - +
327G ARG* 3.1 7.0 + - + +
328G SER* 2.9 32.3 + - - -
368G GLU* 5.4 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 325 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288G ILE* 4.9 1.6 - - - +
291G CYS* 3.7 20.0 - - + +
292G LYS* 4.0 18.4 - - - -
295G VAL* 4.8 3.5 - - + +
312G LYS* 3.0 27.8 - - - +
313G SER* 4.2 6.3 - - - -
314G GLU* 4.0 30.3 - - + +
321G SER 3.3 8.4 + - - +
322G THR* 3.0 11.6 + - - +
324G THR* 1.3 80.5 - - - +
326G LEU* 1.3 77.6 + - + +
328G SER* 2.5 22.4 + - - -
329G ILE* 3.3 29.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 326 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288G ILE* 5.0 10.3 - - + -
291G CYS* 5.3 5.2 - - + -
314G GLU* 5.4 0.2 - - - +
322G THR* 2.9 50.8 + - + +
323G TYR* 4.1 3.4 - - - +
325G MET* 1.3 101.1 - - + +
327G ARG* 1.3 62.4 + - - +
329G ILE* 3.5 7.1 + - + +
330G LEU* 2.9 31.5 + - - +
357G ILE* 4.2 18.4 - - + -
360G MET* 4.1 38.6 - - + -
361G VAL* 4.6 7.6 - - + -
364G LEU* 5.1 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 327 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B SER* 3.0 38.0 + - - +
323G TYR* 2.7 58.7 + - + +
324G THR* 3.4 8.3 - - - +
326G LEU* 1.3 75.9 - - - +
328G SER* 1.3 57.8 + - - +
330G LEU* 2.8 23.7 + - + +
331G ASP* 2.9 48.6 + - - +
361G VAL* 4.4 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 328 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309G SER* 5.8 0.7 - - - -
310G SER 3.8 7.4 - - - -
311G LEU* 3.3 15.6 - - - +
312G LYS* 3.4 34.3 + - - -
324G THR 2.9 10.9 + - - -
325G MET 2.5 29.3 + - - -
327G ARG* 1.3 76.5 - - - +
329G ILE* 1.3 59.2 + - - +
331G ASP* 4.7 5.4 - - - +
332G ASN* 3.1 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 329 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291G CYS* 3.4 42.0 - - + +
294G ILE* 4.7 13.7 - - + -
295G VAL* 5.0 4.0 - - + -
311G LEU* 4.1 18.4 - - + -
325G MET* 3.3 33.2 - - + +
326G LEU* 3.6 8.1 - - - +
327G ARG 3.1 0.4 - - - -
328G SER* 1.3 78.1 - - - +
330G LEU* 1.3 56.3 + - + +
332G ASN 3.1 5.2 - - - +
333G TRP* 2.8 60.8 + - + -
336G VAL* 4.4 8.3 - - + +
349G ILE* 6.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 330 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326G LEU 2.9 22.0 - - - +
327G ARG* 2.8 10.0 + - + +
329G ILE* 1.3 84.2 - - + +
331G ASP* 1.3 65.4 + - - +
332G ASN 2.9 6.8 + - - -
333G TRP* 3.1 27.3 + - + +
334G GLU* 5.4 0.9 - - - +
354G LYS* 5.7 5.6 - - + -
357G ILE* 3.3 25.8 - - + -
358G GLN* 3.1 46.0 - - + +
361G VAL* 3.5 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 331 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308G ARG* 2.9 27.6 + - - +
309G SER* 5.0 4.9 - - - +
327G ARG* 2.9 66.9 + - - +
328G SER* 4.3 5.7 - - - +
330G LEU* 1.3 74.8 - - - +
332G ASN* 1.3 62.5 - - - +
333G TRP 3.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 332 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307G LEU* 3.7 24.4 - - + +
308G ARG* 3.6 22.3 + - - +
309G SER* 2.7 41.6 + - - +
310G SER 4.1 1.4 + - - -
311G LEU* 3.9 13.6 - - + +
328G SER* 3.1 22.6 + - - +
329G ILE 3.1 5.0 + - - +
330G LEU 2.9 0.4 - - - -
331G ASP* 1.3 80.2 - - - +
333G TRP* 1.3 57.0 + - - +
334G GLU 3.3 3.4 - - - -
335G SER* 3.2 9.9 + - - -
336G VAL* 3.0 28.0 + - + +
----------------------------------------------------------
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