Contacts of the helix formed by residues 308 - 321 (chain H) in PDB entry 3LUE
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 GLY 308 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219H VAL* 3.8 16.2 - - - -
221H LEU* 6.1 0.2 - - - +
306H TYR 3.5 0.2 + - - -
307H PRO* 1.4 71.8 - - - +
309H ILE* 1.4 62.6 + - - +
310H ALA 3.4 2.9 + - - -
311H ASP* 3.5 17.5 + - - +
312H ARG* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 309 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153H MET* 5.3 9.2 - - + -
219H VAL* 4.0 15.9 - - + +
261H LEU* 4.4 17.0 - - + -
262H PHE* 4.3 18.2 - - + -
274H ILE* 5.5 1.8 - - + -
299H LEU* 3.8 17.3 - - + -
303H THR 4.1 19.5 - - - +
304H THR* 3.2 29.6 - - + +
306H TYR* 3.1 23.5 + - + +
307H PRO 3.5 1.0 + - - -
308H GLY* 1.4 76.2 - - - +
310H ALA* 1.3 61.3 + - - +
312H ARG 4.5 0.2 - - - +
313H MET* 2.8 39.3 + - + +
335H ARG* 4.3 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 310 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299H LEU* 4.4 3.4 - - - -
308H GLY 3.4 0.2 - - - -
309H ILE* 1.3 82.6 - - + +
311H ASP* 1.3 60.7 + - - +
313H MET* 3.6 1.9 - - - +
314H GLN* 2.9 29.9 + - - +
329H ILE* 3.6 23.1 - - + +
331H ALA* 4.3 19.1 - - + -
335H ARG* 6.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 311 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221H LEU* 4.0 19.4 - - + +
308H GLY* 3.5 17.8 + - - +
310H ALA* 1.3 79.9 - - - +
312H ARG* 1.3 57.8 + - - +
314H GLN* 3.5 8.5 + - - +
315H LYS* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 312 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219H VAL* 3.9 14.8 - - + +
220H ALA 2.6 36.7 + - - +
221H LEU* 3.7 26.0 + - + +
223H PHE* 4.7 5.2 - - - +
259H GLU* 2.8 28.7 + - - -
262H PHE* 3.5 40.7 - - + +
263H GLN* 4.8 4.9 - - - +
275H HIS* 5.6 0.4 - - - -
308H GLY 2.9 17.9 + - - +
309H ILE* 4.1 1.3 - - - +
311H ASP* 1.3 73.6 - - - +
313H MET* 1.3 64.2 + - - +
315H LYS* 4.0 6.2 - - - +
316H GLU* 2.7 65.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 313 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153H MET* 3.8 39.9 - - + -
262H PHE* 4.0 14.4 - - + -
274H ILE* 4.0 17.7 - - + +
275H HIS* 4.1 12.6 - - - -
278H THR* 3.9 12.1 - - + +
297H THR* 5.2 1.1 - - + -
299H LEU* 3.9 17.3 - - + -
309H ILE* 2.8 27.6 + - + +
310H ALA* 3.6 5.6 - - - +
312H ARG* 1.3 74.4 - - - +
314H GLN* 1.3 61.1 + - - +
316H GLU* 3.0 4.3 + - - +
317H ILE* 2.9 44.9 + - + +
329H ILE* 4.3 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 314 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310H ALA 2.9 17.9 + - - +
311H ASP* 3.5 9.4 - - - +
313H MET* 1.3 73.9 - - - +
315H LYS* 1.3 62.4 + - - +
317H ILE* 3.0 0.5 + - - +
318H THR* 2.7 52.4 + - - +
327H ILE* 3.0 33.7 + - - +
328H LYS* 4.6 0.2 - - - +
329H ILE* 3.9 25.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 315 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221H LEU* 2.9 44.8 + - + +
222H ASP* 4.6 14.5 + - - +
311H ASP 2.9 20.4 + - - +
312H ARG* 3.8 6.5 - - - +
314H GLN* 1.3 72.5 - - - +
316H GLU* 1.3 91.2 + - + +
318H THR* 3.7 7.5 - - - -
319H ALA* 3.3 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 316 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262H PHE* 4.7 1.7 - - + -
275H HIS* 3.7 37.8 + - + -
312H ARG* 2.7 59.6 + - + +
313H MET 3.0 5.1 + - - +
315H LYS* 1.3 98.0 + - - +
317H ILE* 1.3 64.0 + - - +
319H ALA* 3.4 16.8 + - - +
320H LEU* 3.2 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 317 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275H HIS* 4.1 16.4 - - - +
278H THR* 3.6 30.3 - - + -
279H PHE* 5.4 6.7 - - + +
282H ILE* 5.8 0.7 - - + -
294H TYR* 4.0 19.1 - - + -
297H THR* 4.2 6.1 - - + +
313H MET* 2.9 37.7 + - - +
314H GLN 3.9 1.6 - - - +
316H GLU* 1.3 76.6 - - - +
318H THR* 1.3 59.1 + - - +
319H ALA 3.2 0.3 + - - -
320H LEU* 3.3 6.4 + - + +
321H ALA* 2.9 28.9 + - - +
327H ILE* 3.6 28.7 - - + -
329H ILE* 4.1 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 318 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314H GLN* 2.7 41.1 + - - +
315H LYS* 3.7 8.7 - - - -
317H ILE* 1.3 76.3 - - - +
319H ALA* 1.3 59.5 + - - +
321H ALA* 3.9 10.7 - - - +
327H ILE* 3.6 19.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 319 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315H LYS 3.3 14.1 + - - +
316H GLU* 3.4 15.2 + - - +
317H ILE 3.2 1.2 - - - -
318H THR* 1.3 78.3 - - - +
320H LEU* 1.3 62.4 + - + +
321H ALA 4.2 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 320 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246F GLN* 6.0 0.2 - - - +
275H HIS* 3.9 38.8 - - + +
276H GLU* 3.5 22.9 - - - +
279H PHE* 3.4 47.8 - - + -
316H GLU 3.2 21.0 + - - +
317H ILE* 3.3 5.4 + - - +
319H ALA* 1.3 78.0 - - + +
321H ALA* 1.3 64.1 + - - +
322H PRO* 3.8 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 321 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244F ASP 3.8 5.6 - - - +
294H TYR* 3.7 19.7 - - + -
317H ILE 2.9 17.2 + - - +
318H THR 3.9 10.3 - - - +
319H ALA 3.4 3.2 - - - +
320H LEU* 1.3 80.6 - - - +
322H PRO* 1.4 75.1 - - + +
323H SER* 3.5 3.5 + - - -
325H MET* 4.2 0.7 - - + -
327H ILE* 3.4 23.8 - - + -
----------------------------------------------------------
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