Contacts of the helix formed by residues 338 - 349 (chain A) in PDB entry 1SL2
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 SER 338 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A ASN* 2.9 21.1 + - - +
336A PRO 4.6 0.2 - - - -
337A SER* 1.3 77.2 - - - +
339A ARG* 1.3 61.9 + - - +
340A ASP 3.2 4.0 + - - -
341A HIS* 3.0 26.3 + - - -
342A ILE* 2.9 29.6 + - - +
12T T 3.4 16.1 + - - -
13T G 2.6 28.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A SER 3.6 7.7 + - - +
338A SER* 1.3 72.9 - - - +
340A ASP* 1.3 59.2 + - - +
342A ILE* 3.7 8.3 - - - +
343A GLN* 2.9 31.1 + - - +
364A VAL* 2.9 43.7 + - + +
365A ASP* 4.2 5.3 - - - +
366A ASP 4.7 1.4 - - - +
369A LEU* 4.7 1.6 - - - +
390A LEU* 3.4 41.0 - - - +
17P T 5.4 3.8 + - - +
18P G 3.2 49.1 + - - +
19P C 4.1 11.3 + - - -
12T T 5.2 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLN* 4.7 8.8 - - - +
338A SER* 3.1 8.2 + - - +
339A ARG* 1.3 80.0 - - - +
341A HIS* 1.3 67.1 + - - +
343A GLN* 3.0 26.3 + - - +
344A LYS* 2.9 31.0 + - - +
13T G 3.8 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A TRP* 3.7 18.7 - + + -
266A GLN* 4.9 4.9 + - - -
332A VAL* 3.4 33.2 - - + +
333A VAL 3.5 8.8 + - - -
334A PHE* 3.8 13.5 - - + -
335A ASN* 3.0 38.9 + - + +
338A SER* 3.0 22.6 + - - +
340A ASP* 1.3 81.2 - - - +
342A ILE* 1.3 67.2 + - - +
344A LYS* 3.2 6.1 + - - +
345A LYS* 3.1 28.6 + - - +
13T G 3.4 20.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A PHE* 4.2 16.8 - - + -
336A PRO 3.9 16.4 - - - +
338A SER 2.9 24.6 + - - +
339A ARG* 3.7 9.2 - - - +
341A HIS* 1.3 76.0 - - - +
343A GLN* 1.3 63.2 + - - +
345A LYS* 3.4 1.4 + - - +
346A LEU* 3.1 47.0 + - + +
364A VAL* 3.9 19.5 - - + -
369A LEU* 4.1 7.9 - - + -
386A ILE* 4.3 22.9 - - + -
390A LEU* 5.8 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ARG 2.9 16.8 + - - +
340A ASP* 3.0 36.1 + - - +
342A ILE* 1.3 78.1 - - - +
344A LYS* 1.3 67.1 + - - +
346A LEU* 4.2 0.3 - - - +
347A GLN* 2.7 50.4 + - - +
351A TRP* 4.3 13.9 - - + -
362A PRO* 3.2 33.5 - - + +
364A VAL* 3.9 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A TRP* 3.4 58.5 - - + +
266A GLN* 5.0 3.6 - - - +
340A ASP* 2.9 21.4 + - - +
341A HIS* 3.2 6.7 + - - +
343A GLN* 1.3 86.5 - - - +
345A LYS* 1.3 67.5 + - + +
347A GLN* 4.3 1.9 - - - +
348A GLU* 2.6 53.6 + - - +
61B ASP* 6.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A PHE* 3.7 39.6 - - + +
262A GLY 3.1 23.8 + - - +
263A SER 5.0 0.6 + - - -
264A TRP* 3.4 38.7 - - + +
334A PHE* 3.7 17.7 - - + -
341A HIS 3.1 16.5 + - - +
342A ILE 4.1 2.5 - - - +
344A LYS* 1.3 81.0 - - + +
346A LEU* 1.3 61.4 + - + +
348A GLU* 3.5 23.4 + - - +
349A ALA* 3.1 26.0 + - - +
379A LYS* 5.5 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A PHE* 4.7 17.0 - - + -
342A ILE* 3.1 37.6 + - + +
343A GLN 4.3 0.2 - - - +
345A LYS* 1.3 76.9 - - + +
347A GLN* 1.3 61.5 + - - +
349A ALA* 3.1 14.4 + - + +
350A GLY 3.3 0.5 + - - -
351A TRP* 2.8 47.6 + - + +
369A LEU* 4.0 18.2 - - + -
372A VAL* 4.4 17.3 - - + -
374A VAL* 4.1 9.4 - - + +
379A LYS* 4.9 3.1 - - + +
383A ILE* 4.1 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A GLN* 2.7 44.8 + - - +
344A LYS* 4.3 2.9 - - - +
346A LEU* 1.3 74.3 - - - +
348A GLU* 1.3 59.9 + - - +
350A GLY* 2.7 24.8 + - - -
351A TRP* 3.2 31.5 + - + +
352A VAL* 4.9 0.5 - - - +
353A PRO* 3.2 26.0 - - - +
356A TYR* 4.8 3.7 + - - -
362A PRO* 4.6 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LYS* 2.6 54.1 + - - +
345A LYS* 3.5 28.9 + - + +
347A GLN* 1.3 80.3 - - - +
349A ALA* 1.3 55.8 + - - +
350A GLY* 3.0 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A PHE* 5.8 0.4 - - + -
345A LYS 3.1 17.3 + - - +
346A LEU* 3.5 11.4 - - + +
347A GLN 3.0 0.8 - - - -
348A GLU* 1.3 74.3 - - - +
350A GLY* 1.3 56.9 + - - +
374A VAL* 3.5 30.8 - - + +
375A ASP* 4.4 7.1 + - - +
376A ASP* 5.5 1.0 + - + -
379A LYS* 3.9 32.8 - - + +
----------------------------------------------------------
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