Contacts of the helix formed by residues 314 - 322 (chain B) in PDB entry 4LQL
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 LEU 314 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B LYS 3.1 23.6 - - - +
311B MET* 4.1 7.9 - - + -
312B ALA 2.8 2.8 + - - -
313B GLY* 1.3 69.9 - - - +
315B THR* 1.3 61.7 + - - +
316B ARG 3.5 0.8 - - - +
317B LEU* 3.3 18.1 - - + +
318B LEU* 2.6 46.7 + - + +
391B ILE* 5.1 7.2 - - + -
392B THR* 4.3 10.8 - - - +
393B LEU* 4.0 33.4 - - + +
402B PHE* 5.7 7.2 - - + -
449B VAL* 4.0 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B TYR 4.9 1.1 - - - -
302B GLY* 4.2 10.8 - - - -
303B PHE 4.0 5.3 + - - -
311B MET 3.2 19.8 + - - -
312B ALA 3.2 4.4 + - - -
314B LEU* 1.3 79.7 - - - +
316B ARG* 1.3 56.6 + - - -
318B LEU* 3.6 0.2 - - - -
319B LYS* 2.5 48.4 + - - +
328B ALA 4.3 2.3 + - - -
329B LEU* 3.8 24.4 - - - +
449B VAL* 3.9 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LYS* 5.8 6.1 - - - +
172B GLU* 4.8 15.7 + - - +
176B ILE* 4.2 25.0 - - + +
273B ASP* 3.9 37.6 - - - +
274B ALA* 4.4 4.7 - - + -
300B GLY 4.3 16.6 + - - -
302B GLY* 3.8 22.0 - - - +
312B ALA 3.5 6.3 + - - +
314B LEU 3.5 0.2 - - - -
315B THR* 1.3 78.9 - - - +
317B LEU* 1.3 64.5 + - - +
319B LYS* 3.9 8.0 - - - +
320B ILE* 3.0 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ALA* 4.5 21.0 - - + +
173B SER* 4.3 21.5 - - - +
176B ILE* 5.6 4.2 - - + +
202B LEU* 6.5 0.7 - - + -
204B TRP* 6.2 1.1 - - + -
313B GLY* 4.9 3.5 - - - +
314B LEU* 3.1 29.7 + - + +
315B THR 3.0 0.2 + - - -
316B ARG* 1.3 83.0 - - - +
318B LEU* 1.3 67.5 + - + +
320B ILE* 3.3 16.0 + - - +
321B ALA* 3.4 7.0 + - - +
462B LEU* 5.4 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B LEU* 2.6 31.9 + - + +
315B THR 4.1 0.4 - - - +
317B LEU* 1.3 75.9 - - + +
319B LYS* 1.3 58.9 + - - +
321B ALA* 2.8 26.9 + - + +
322B ALA* 3.3 6.4 + - - +
327B THR* 4.4 2.9 - - - +
391B ILE* 6.1 5.4 - - + -
449B VAL* 4.6 17.9 - - + -
451B THR* 5.8 0.9 - - - -
454B LEU* 3.5 29.2 - - + +
459B LEU* 5.5 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B MET* 3.8 25.1 + - - +
300B GLY* 3.7 15.5 - - - +
301B TYR 3.5 23.3 - - - +
315B THR* 2.5 45.9 + - - +
316B ARG* 3.8 5.2 - - - +
318B LEU* 1.3 66.6 - - - +
320B ILE* 1.3 63.5 + - - +
322B ALA* 3.0 22.2 + - - +
323B ASP* 3.8 4.2 + - - -
326B GLN 4.2 4.8 + - - -
327B THR* 3.4 42.2 + - + +
328B ALA* 5.1 7.0 - - - +
353B ASP* 4.4 14.0 - - - -
355B THR* 4.7 2.4 + - - -
449B VAL* 5.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LYS* 6.3 3.4 - - + -
4B MET* 5.9 2.8 - - - +
168B VAL* 4.4 22.6 - - + +
169B ALA* 4.8 10.1 - - + -
172B GLU* 4.8 15.3 - - + -
316B ARG* 3.0 34.9 + - - +
317B LEU* 3.4 6.7 - - - +
318B LEU 3.2 0.2 - - - -
319B LYS* 1.3 79.6 - - - +
321B ALA* 1.3 64.2 + - - +
322B ALA 3.2 0.5 + - - -
323B ASP* 3.8 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B HIS* 4.0 38.2 - - - +
166B VAL* 5.8 5.6 - - + -
168B VAL* 5.8 0.9 - - - -
169B ALA* 5.4 6.5 - - + -
317B LEU 3.4 5.7 + - - +
318B LEU* 2.8 18.0 + - + +
320B ILE* 1.3 84.3 - - + +
322B ALA* 1.3 56.8 + - - +
323B ASP 3.5 3.3 + - - +
325B LYS* 5.0 1.9 - - - +
454B LEU* 3.9 23.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B LEU 3.3 7.6 + - - +
319B LYS 3.0 13.9 + - - +
321B ALA* 1.3 77.9 - - - +
323B ASP* 1.3 59.6 + - - +
325B LYS* 3.1 42.9 + - + +
326B GLN 3.8 3.9 + - - +
327B THR* 4.1 15.3 - - + -
453B ALA* 3.8 16.6 - - + -
454B LEU* 4.2 8.5 - - + -
----------------------------------------------------------
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