Contacts of the helix formed by residues 315 - 326 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290E TYR 3.7 1.8 - - - -
291E LYS 3.3 13.2 - - - -
292E ALA 3.6 2.2 + - - -
293E GLU* 2.8 32.0 - - - +
314E LEU* 1.3 73.3 - - - +
316E THR* 1.3 67.6 + - - -
317E LYS 3.2 2.7 - - - -
318E THR* 2.9 19.7 + - - -
319E VAL* 2.9 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 316 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290E TYR* 2.8 20.7 + - - +
291E LYS* 3.4 6.0 + - - -
313E TRP* 3.0 27.7 + - + +
315E GLY* 1.3 70.2 - - - -
317E LYS* 1.3 52.2 + - - +
319E VAL* 3.0 12.8 + - + +
320E HIS* 2.7 34.2 + - + +
351E PRO* 5.7 2.7 - - + -
358E TYR* 3.3 43.5 - - + -
395E PHE* 4.3 16.2 - - + -
423E TRP* 5.0 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 317 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291E LYS* 3.3 31.1 + - + +
315E GLY 3.2 0.4 - - - -
316E THR* 1.3 79.6 - - - +
318E THR* 1.3 58.2 + - - +
320E HIS* 3.4 8.1 + - - +
321E GLN* 2.6 68.5 + - - +
353E ASN* 6.3 0.7 - - - -
354E GLU* 5.3 4.7 - - + +
358E TYR* 3.0 36.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 318 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250E PRO* 5.6 0.4 - - + -
257E TYR* 2.9 45.7 - - + +
291E LYS 4.5 0.5 + - - -
292E ALA 5.1 3.6 + - - -
314E LEU* 3.8 20.0 - - + +
315E GLY* 2.9 15.6 + - - -
317E LYS* 1.3 75.9 - - - +
319E VAL* 1.3 57.6 + - - +
321E GLN* 3.2 8.4 + - + +
322E LEU* 2.8 34.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 319 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273E VAL* 3.1 33.7 - - + -
313E TRP* 5.3 3.1 - - + -
314E LEU* 3.8 10.1 - - + +
315E GLY 3.1 16.4 - - - +
316E THR* 3.2 11.2 - - + +
318E THR* 1.3 77.1 - - - +
320E HIS* 1.3 61.9 + - - +
322E LEU* 3.0 24.0 + - - +
323E THR* 3.1 10.0 + - + +
349E PHE* 3.8 19.5 - - + -
351E PRO* 5.0 4.9 - - + -
423E TRP* 5.9 4.7 - - + -
472E MET* 6.0 0.2 - - + -
474E LEU* 3.7 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 320 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316E THR 2.7 18.3 + - - +
317E LYS* 3.6 10.5 + - - +
319E VAL* 1.3 72.9 - - - +
321E GLN* 1.3 76.8 + - - +
323E THR* 2.9 5.9 + - - -
324E LYS* 2.8 55.0 + - + +
351E PRO* 3.0 29.1 + - + +
352E GLU* 2.8 30.0 + - - -
353E ASN* 3.0 31.0 + - + +
358E TYR* 3.9 18.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 321 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251E ASP* 4.3 27.4 + - - +
253E PHE* 5.5 8.0 - - + -
317E LYS* 2.6 51.6 + - + +
318E THR* 3.6 7.2 - - - +
320E HIS* 1.3 80.1 + - - +
322E LEU* 1.3 63.7 + - - +
324E LYS* 3.1 37.6 + - - +
325E GLN* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 322 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E HIS* 4.2 15.5 - - + +
248E ILE* 5.9 1.8 - - + -
250E PRO* 5.0 17.3 - - + -
251E ASP* 5.7 0.4 - - - -
257E TYR* 4.7 13.9 - - - +
271E THR* 4.9 13.2 - - + -
273E VAL* 5.0 2.7 - - + -
314E LEU* 5.3 3.6 - - + -
318E THR 2.8 13.8 + - - +
319E VAL* 3.0 17.0 - - - +
321E GLN* 1.3 79.7 - - - +
323E THR* 1.3 58.9 + - + +
325E GLN* 3.8 11.0 + - - +
326E HIS 3.7 8.7 + - - +
328E GLN* 3.6 32.6 + - - +
474E LEU* 3.7 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 323 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319E VAL 3.1 9.5 + - - +
320E HIS 2.9 9.6 + - - -
322E LEU* 1.3 73.5 - - - +
324E LYS* 1.3 63.5 + - - +
325E GLN 3.3 0.7 - - - -
326E HIS 3.7 2.2 - - - -
327E THR 3.1 18.5 + - - -
328E GLN* 3.5 27.4 - - + -
349E PHE* 3.6 32.3 - - + +
350E ARG* 3.3 17.3 + - - +
351E PRO* 2.8 36.9 + - + +
474E LEU* 4.7 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 324 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320E HIS* 2.8 37.8 + - + +
321E GLN* 3.1 35.5 + - - +
323E THR* 1.3 75.9 + - - +
325E GLN* 1.3 70.5 + - - +
326E HIS* 3.2 1.2 + - - -
350E ARG* 4.2 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 325 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230E MET* 3.0 29.2 - - - +
250E PRO* 3.4 36.3 + - - +
251E ASP* 3.9 11.5 + - - +
321E GLN 3.0 13.6 + - - +
322E LEU* 3.9 10.9 + - - +
324E LYS* 1.3 81.0 - - - +
326E HIS* 1.3 79.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 326 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322E LEU 3.7 1.9 + - - +
323E THR 3.3 5.3 + - - -
324E LYS 3.1 2.9 - - - -
325E GLN* 1.3 90.9 - - + +
327E THR* 1.3 76.3 + - - +
328E GLN* 2.8 22.1 + - - +
350E ARG* 5.1 1.1 - - - +
476E PRO* 5.5 0.3 - - - +
----------------------------------------------------------
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