Contacts of the helix formed by residues 320 - 332 (chain H) 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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271H SER* 5.8 1.2 - - - +
274H LEU* 3.8 19.5 - - - +
318H ARG 3.4 0.8 + - - -
319H TRP* 1.3 76.5 - - - +
321H SER* 1.3 67.7 + - - +
322H THR 3.5 1.8 - - - -
323H TYR* 3.4 20.6 + - - +
324H THR* 3.4 21.1 + - - +
364H LEU* 3.3 24.6 + - - +
367H PHE* 4.3 1.5 - - - +
368H GLU* 3.0 49.4 + - - +
371H PHE* 3.9 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 321 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313H SER 5.0 0.9 - - - +
314H GLU* 3.2 23.7 - - - +
315H CYS 3.7 17.5 - - - -
316H PRO* 3.3 13.3 + - - +
318H ARG* 2.8 23.1 + - - -
319H TRP 3.3 1.0 - - - -
320H ASN* 1.3 72.6 + - - +
322H THR* 1.3 68.0 + - - +
324H THR* 2.5 26.9 + - - -
325H MET* 3.2 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 322 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278H PHE* 4.7 17.6 - - + -
288H ILE* 4.1 27.2 - - + +
314H GLU* 3.6 13.9 + - - +
320H ASN 3.5 0.2 - - - -
321H SER* 1.3 77.2 - - - +
323H TYR* 1.3 68.0 + - - +
325H MET* 2.8 19.0 + - + +
326H LEU* 3.0 37.7 + - + +
360H MET* 5.2 0.4 - - + -
364H LEU* 4.8 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 323 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320H ASN* 3.4 30.0 + - - +
321H SER 3.3 0.4 - - - -
322H THR* 1.3 79.1 - - - +
324H THR* 1.3 86.7 + - + +
326H LEU* 2.9 4.5 + - - +
327H ARG* 2.9 68.9 + - + +
361H VAL* 4.0 14.5 - - + +
364H LEU* 3.6 34.1 - - + +
365H ASP* 3.5 32.9 + - + +
368H GLU* 3.1 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 324 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312H LYS* 4.8 11.3 - - - +
313H SER 4.9 3.1 + - - -
314H GLU 5.1 3.1 + - - -
319H TRP 5.1 3.4 - - - +
320H ASN 3.4 11.1 + - - +
321H SER* 2.5 24.1 + - - -
323H TYR* 1.3 97.3 - - + +
325H MET* 1.3 62.8 + - - +
327H ARG* 3.3 13.4 + - - +
328H SER* 3.3 13.3 + - - -
368H GLU* 4.9 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 325 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288H ILE* 4.7 0.9 - - - +
291H CYS* 3.4 35.4 - - + +
292H LYS* 3.5 28.9 - - - -
295H VAL* 5.0 3.4 - - + -
312H LYS 3.2 17.3 - - - +
313H SER* 3.1 29.4 - - - +
314H GLU* 4.2 9.6 - - - +
321H SER 3.7 7.6 - - - +
322H THR* 2.8 14.0 + - - +
324H THR* 1.3 76.8 + - - +
326H LEU* 1.3 77.9 + - + -
328H SER* 2.6 19.7 + - - -
329H ILE* 3.5 10.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 326 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288H ILE* 5.1 7.0 - - + -
291H CYS* 4.2 10.8 - - + -
322H THR* 3.0 36.0 + - + +
323H TYR* 2.9 6.2 + - - +
325H MET* 1.3 106.1 - - + +
327H ARG* 1.3 61.2 + - - +
328H SER 3.0 2.5 - - - -
329H ILE* 3.1 8.0 + - - +
330H LEU* 2.8 32.1 + - - +
357H ILE* 4.1 31.6 - - + +
360H MET* 4.3 25.8 - - + -
361H VAL* 4.1 13.5 - - + -
364H LEU* 5.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 327 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323H TYR* 2.9 61.0 + - + +
324H THR* 3.5 7.9 - - - +
326H LEU* 1.3 78.6 - - - +
328H SER* 1.3 51.8 + - - +
330H LEU* 3.7 6.0 - - - +
331H ASP* 2.8 69.6 + - - +
361H VAL* 4.4 19.1 - - + +
365H ASP* 5.3 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 328 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309H SER* 5.7 2.0 - - - -
310H SER 4.0 4.9 - - - -
311H LEU* 3.8 10.9 - - - -
312H LYS* 3.5 34.3 + - - +
324H THR 3.3 7.5 + - - -
325H MET* 2.6 30.0 + - - -
327H ARG* 1.3 70.9 - - - +
329H ILE* 1.3 66.9 + - - +
330H LEU 3.0 1.8 + - - -
331H ASP* 3.1 4.5 + - - -
332H ASN* 3.0 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 329 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291H CYS* 3.4 56.1 - - + +
294H ILE* 4.4 17.3 - - + -
295H VAL* 5.2 2.9 - - + -
311H LEU* 4.2 20.9 - - + -
325H MET* 3.5 19.5 - - + +
326H LEU* 3.1 7.1 + - - +
328H SER* 1.3 76.5 + - - +
330H LEU* 1.3 64.1 + - + +
332H ASN 3.4 4.8 - - - +
333H TRP* 3.4 44.7 + - + -
336H VAL* 4.4 7.4 - - + +
352H ILE* 6.1 0.4 - - + -
357H ILE* 5.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 330 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326H LEU 2.8 13.1 + - - +
327H ARG* 3.7 9.9 - - - +
329H ILE* 1.3 78.4 - - + +
331H ASP* 1.3 68.6 + - - +
332H ASN 3.1 1.0 + - - -
333H TRP* 3.3 21.2 + - + +
354H LYS* 4.2 24.7 - - + +
357H ILE* 3.2 36.3 - - + -
358H GLN* 3.8 32.1 - - + +
361H VAL* 4.1 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 331 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309H SER* 5.7 4.9 + - - -
327H ARG* 2.8 64.2 + - - +
328H SER* 3.1 5.1 + - - +
330H LEU* 1.3 74.6 - - - +
332H ASN* 1.3 66.1 - - - +
333H TRP 3.7 1.4 + - - -
334H GLU* 6.1 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 332 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307H LEU* 3.9 19.7 - - + +
308H ARG* 3.8 14.4 + - - +
309H SER* 2.7 50.5 + - - -
311H LEU* 4.0 0.8 - - + +
328H SER* 3.0 29.4 + - - +
329H ILE 3.4 3.8 - - - -
331H ASP* 1.3 83.2 - - - +
333H TRP* 1.3 59.3 + - - +
334H GLU* 3.6 1.3 - - - -
335H SER* 4.0 16.5 + - - +
336H VAL* 3.0 28.8 + - + +
----------------------------------------------------------
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