Contacts of the helix formed by residues 333 - 349 (chain A) in PDB entry 1LII
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 THR 333 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A GLY 5.4 0.7 - - - +
332A LYS 1.3 71.3 - - - -
334A VAL* 1.3 53.8 + - - +
335A LYS* 3.7 7.7 + - - +
336A GLN* 2.3 56.3 + - - +
337A CYS* 2.7 33.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LEU* 4.1 29.6 - - + -
286A ALA* 4.2 24.2 - - + -
288A GLU* 4.4 17.3 - - + +
298A HIS* 4.6 17.9 - - + +
324A PHE* 5.0 5.4 - - + -
328A LEU* 6.1 4.0 - - + -
332A LYS 4.1 0.2 + - - -
333A THR* 1.3 72.8 - - - +
335A LYS* 1.3 63.8 + - - +
337A CYS* 3.0 9.0 + - - +
338A ILE* 2.9 34.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A HIS* 4.5 24.3 - - + +
300A VAL* 4.2 26.9 - - + +
333A THR* 3.3 7.4 + - - +
334A VAL* 1.3 78.4 - - - +
336A GLN* 1.3 65.4 + - + +
338A ILE* 3.3 10.2 + - - +
339A MET* 3.0 47.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A GLY 4.7 0.2 + - - -
332A LYS* 3.1 32.3 - - + +
333A THR* 2.3 61.9 + - - +
335A LYS* 1.3 80.5 - - + +
337A CYS* 1.3 68.5 + - - +
339A MET* 3.2 10.3 + - - +
340A CYS* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A PHE* 3.6 39.9 - - + +
327A GLY* 3.9 4.9 - - - -
328A LEU* 3.6 45.3 - - - -
332A LYS* 3.8 13.2 - - - -
333A THR 2.7 21.2 + - - -
334A VAL* 3.0 8.5 + - - +
336A GLN* 1.3 74.2 - - - +
338A ILE* 1.3 63.7 + - - +
340A CYS* 3.2 7.0 + - - +
341A GLY* 2.9 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A VAL* 4.8 1.3 - - + -
284A VAL* 4.0 25.8 - - + +
286A ALA* 3.8 29.2 - - + +
298A HIS* 5.2 1.1 - - + -
300A VAL* 4.0 37.2 - - + -
320A PHE* 3.7 11.0 - - + -
324A PHE* 3.8 19.7 - - + -
334A VAL* 2.9 18.3 + - + +
335A LYS* 3.5 9.2 - - - +
337A CYS* 1.3 78.2 - - - +
339A MET* 1.3 58.0 + - - +
341A GLY* 3.2 1.2 + - - -
342A ASN* 2.9 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A VAL* 4.4 12.3 - - + -
301A GLY 5.9 0.2 - - - +
335A LYS* 3.0 49.7 + - - +
336A GLN* 3.2 9.8 + - - +
338A ILE* 1.3 75.0 - - - +
340A CYS* 1.3 57.0 + - - +
342A ASN* 3.4 8.6 + - - +
343A ALA* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 5.0 2.0 - - - -
323A GLY* 3.3 27.6 - - - +
326A TYR* 4.0 21.5 - - - -
327A GLY* 4.8 4.3 - - - -
336A GLN 3.1 12.0 + - - +
337A CYS* 3.6 9.6 - - - +
339A MET* 1.3 74.1 - - - +
341A GLY* 1.3 65.7 + - - +
343A ALA* 3.3 6.5 + - - +
344A CYS* 3.0 34.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A PHE* 3.3 45.4 - - - -
323A GLY* 4.1 2.2 - - - -
324A PHE* 3.9 5.3 - - - +
337A CYS 2.9 14.0 + - - -
338A ILE 3.2 3.1 + - - -
340A CYS* 1.3 77.2 - - - +
342A ASN* 1.3 61.1 + - - +
344A CYS* 3.2 2.3 + - - +
345A ALA* 2.9 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A VAL* 3.7 7.2 - - - +
300A VAL* 4.7 1.4 - - - +
301A GLY 3.7 19.1 - - - +
302A VAL* 3.8 11.5 - - - +
303A PRO* 4.4 12.0 - - + +
320A PHE* 3.4 18.4 - - - -
338A ILE* 2.9 27.4 + - - +
339A MET* 3.6 9.5 - - - +
341A GLY* 1.3 76.6 - - - +
343A ALA* 1.3 60.7 + - - +
345A ALA* 3.3 0.9 + - - +
346A GLN* 2.8 34.6 + - + +
799A ACP 2.8 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A MET 3.0 18.1 + - - +
340A CYS* 3.8 6.7 - - - +
341A GLY 3.2 0.4 - - - -
342A ASN* 1.3 77.0 - - - +
344A CYS* 1.3 63.1 + - - +
346A GLN* 3.3 7.7 + - - +
347A ASP* 3.2 20.1 + - - +
358A PHE* 5.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL* 4.2 14.8 - - + -
81A LEU* 4.4 11.2 - - - -
319A ALA* 3.5 22.2 - - + +
323A GLY* 3.7 18.8 - - - -
340A CYS* 3.0 22.7 + - - +
341A GLY 3.6 2.7 - - - +
343A ALA* 1.3 77.2 - - - +
345A ALA* 1.3 63.7 + - - +
347A ASP* 3.3 5.4 + - - +
348A VAL* 3.2 24.8 + - - +
358A PHE* 3.9 24.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ALA* 3.5 17.5 - - - +
319A ALA* 3.8 10.7 - - - +
320A PHE* 4.2 2.2 - - + +
341A GLY 2.9 16.9 + - - +
342A ASN 3.7 2.7 - - - +
344A CYS* 1.3 74.2 - - - +
346A GLN* 1.3 65.0 + - - +
348A VAL* 3.3 2.0 + - - +
349A ILE* 3.0 29.1 + - - +
799A ACP 3.4 35.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A VAL* 3.2 12.1 - - - +
303A PRO* 3.0 41.7 + - - +
304A VAL 4.8 0.3 - - - +
305A VAL* 3.2 22.2 - - + +
342A ASN 2.8 20.5 + - - +
343A ALA* 3.7 6.7 - - - +
345A ALA* 1.3 77.6 - - - +
347A ASP* 1.3 63.3 + - - +
349A ILE* 3.5 11.2 - - - +
350A GLN* 3.0 29.9 + - - +
799A ACP 2.8 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ALA 3.2 11.8 + - - +
344A CYS 3.4 8.7 - - - +
345A ALA 3.2 0.6 - - - -
346A GLN* 1.3 77.4 - - - +
348A VAL* 1.3 59.6 + - - +
350A GLN* 3.0 27.4 + - - +
351A HIS* 3.6 18.9 + - - -
355A SER* 4.8 1.4 + - - -
357A SER* 3.3 15.4 + - - -
358A PHE* 3.2 50.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ASP 4.1 1.4 - - - +
314A ASN 3.6 22.0 - - - +
315A GLY 3.9 15.9 - - - -
316A ALA* 4.2 3.1 - - - +
319A ALA* 3.5 24.0 - - + -
344A CYS 3.2 6.3 + - - +
345A ALA 3.3 6.5 + - - +
347A ASP* 1.3 81.5 - - - +
349A ILE* 1.3 60.9 + - - +
350A GLN 3.0 1.3 + - - -
351A HIS* 3.2 20.4 + - - +
353A GLY 3.9 10.2 - - - +
354A PHE* 4.1 12.1 - - + -
355A SER* 3.7 29.8 - - - +
358A PHE* 4.7 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A VAL* 4.5 8.5 - - + -
310A ILE* 3.6 31.7 - - + -
311A VAL 3.0 22.9 + - - -
312A ASP 3.4 16.2 - - - +
313A THR* 4.1 17.7 - - + -
316A ALA* 3.7 27.1 - - + -
345A ALA 3.0 20.2 + - - +
346A GLN* 3.5 16.4 - - - +
348A VAL* 1.3 75.5 - - - +
350A GLN* 1.3 62.0 + - + +
351A HIS 3.2 2.4 + - - -
799A ACP 4.0 34.5 - - + +
----------------------------------------------------------
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