Contacts of the helix formed by residues 315 - 326 (chain H) in PDB entry 1LWU
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 315 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290H TYR 3.7 1.3 - - - -
291H LYS 3.3 13.7 - - - -
292H ALA 3.6 2.2 + - - -
293H GLU* 2.9 31.4 - - - +
314H LEU* 1.3 73.9 - - - +
316H THR* 1.3 69.5 + - - -
317H LYS 3.2 2.7 - - - -
318H THR* 2.9 18.9 + - - -
319H VAL* 2.9 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 316 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290H TYR* 2.8 20.0 + - - +
291H LYS* 3.3 6.0 + - - -
313H TRP* 3.0 28.2 + - + +
315H GLY* 1.3 70.7 - - - -
317H LYS* 1.3 52.2 + - - +
319H VAL* 3.0 12.2 + - + +
320H HIS* 2.6 34.1 + - + +
351H PRO* 5.7 2.5 - - + -
358H TYR* 3.3 43.1 - - + -
395H PHE* 4.3 15.9 - - + -
423H TRP* 5.1 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 317 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291H LYS* 3.2 33.5 + - + +
315H GLY 3.2 0.6 - - - -
316H THR* 1.3 79.8 - - - +
318H THR* 1.3 57.3 + - - +
320H HIS* 3.3 8.5 + - - +
321H GLN* 2.6 69.7 + - + +
353H ASN* 6.3 0.9 - - - -
354H GLU* 5.7 4.3 - - - +
358H TYR* 3.0 35.4 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
250H PRO* 5.7 0.2 - - + -
257H TYR* 2.9 45.9 - - + +
291H LYS 4.5 0.4 + - - -
292H ALA 5.0 3.5 + - - -
314H LEU* 3.9 20.4 - - + +
315H GLY* 2.9 16.1 + - - -
317H LYS* 1.3 75.3 - - - +
319H VAL* 1.3 63.1 + - - +
321H GLN* 3.1 7.9 + - - +
322H LEU* 2.8 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 319 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273H VAL* 3.1 34.1 - - + -
313H TRP* 5.4 2.9 - - + -
314H LEU* 3.8 10.1 - - + +
315H GLY 2.9 17.5 + - - +
316H THR* 3.2 11.4 - - + +
318H THR* 1.3 76.9 - - - +
320H HIS* 1.3 62.1 + - - +
322H LEU* 3.0 24.0 + - - +
323H THR* 3.1 9.9 + - - +
349H PHE* 3.8 20.4 - - + -
351H PRO* 4.9 4.9 - - + -
423H TRP* 5.9 4.5 - - + -
472H MET* 5.9 0.4 - - + -
474H LEU* 3.7 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 320 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316H THR 2.6 17.1 + - - +
317H LYS* 3.5 12.9 + - - +
318H THR 3.1 0.2 - - - -
319H VAL* 1.3 73.5 - - - +
321H GLN* 1.3 77.8 + - - +
323H THR* 2.9 6.2 + - - -
324H LYS* 2.8 56.9 + - + +
351H PRO* 2.9 28.7 + - + +
352H GLU* 2.8 30.4 + - - -
353H ASN* 3.1 29.9 + - + +
358H TYR* 3.9 18.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 321 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251H ASP* 4.3 28.1 + - - +
253H PHE* 5.5 7.6 - - + -
317H LYS* 2.6 50.3 + - - +
318H THR* 3.6 9.2 - - + +
320H HIS* 1.3 80.6 + - - +
322H LEU* 1.3 62.7 + - - +
324H LYS* 3.1 38.3 + - - +
325H GLN* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 322 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231H HIS* 4.2 15.3 - - + +
248H ILE* 5.9 2.2 - - + -
250H PRO* 5.0 17.5 - - + -
257H TYR* 4.7 13.9 - - - +
271H THR* 4.9 12.6 - - + -
273H VAL* 5.0 2.9 - - + -
314H LEU* 5.3 4.5 - - + -
318H THR* 2.8 12.1 + - + +
319H VAL* 3.0 17.7 + - - +
321H GLN* 1.3 79.2 - - - +
323H THR* 1.3 59.2 + - + +
325H GLN* 3.9 11.2 + - - +
326H HIS 3.7 8.1 + - - +
328H GLN* 3.5 34.1 + - - +
474H LEU* 3.7 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 323 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319H VAL 3.1 9.3 + - - +
320H HIS 2.9 8.5 + - - -
322H LEU* 1.3 75.0 - - - +
324H LYS* 1.3 64.2 + - - +
325H GLN 3.4 0.4 - - - -
326H HIS 3.8 2.7 - - - -
327H THR 3.2 18.2 + - - -
328H GLN* 3.5 25.6 - - + -
349H PHE* 3.6 34.3 - - + +
350H ARG* 3.3 16.8 + - - +
351H PRO* 2.8 36.8 + - + +
474H LEU* 4.6 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 324 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320H HIS* 2.8 39.7 + - + +
321H GLN* 3.1 36.4 + - - +
323H THR* 1.3 75.7 + - - +
325H GLN* 1.3 69.0 + - - +
326H HIS* 3.1 2.0 + - - -
350H ARG* 4.2 16.5 + - - +
351H PRO 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 325 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230H MET* 3.0 28.7 - - - +
250H PRO* 3.4 32.5 + - - +
251H ASP* 3.9 15.3 + - - +
321H GLN* 3.0 14.4 + - - +
322H LEU* 4.0 10.9 + - - +
324H LYS* 1.3 80.8 - - - +
326H HIS* 1.3 79.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 326 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322H LEU 3.7 2.2 + - - +
323H THR 3.4 6.1 + - - -
324H LYS 3.1 2.9 - - - -
325H GLN* 1.3 90.3 - - + +
327H THR* 1.3 76.7 + - - +
328H GLN* 2.8 22.1 + - - +
350H ARG* 5.1 1.3 - - - +
476H PRO* 5.5 0.2 - - - +
----------------------------------------------------------
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