Contacts of the helix formed by residues 338 - 356 (chain A) in PDB entry 1KYO
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 MET 338 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A TYR* 3.9 34.1 - - + -
310A LEU* 4.0 17.0 - - + +
335A ASN* 3.2 38.4 + - - +
337A THR* 1.3 89.8 + - - +
339A ILE* 1.3 63.1 + - - +
340A ASP* 3.2 6.5 - - - +
341A ASP* 3.1 24.8 + - - +
342A LEU* 3.4 8.7 + - - +
1C MET* 3.6 35.7 - - + -
5C LYS* 5.0 0.9 - - - +
4S PRO* 4.8 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ALA* 4.0 13.7 - - + -
260A ILE* 5.0 9.0 - - + -
310A LEU 5.8 0.4 - - - -
333A THR* 4.3 12.6 - - + -
335A ASN 3.5 15.5 - - - +
336A VAL* 3.5 20.2 + - - +
337A THR 3.6 2.0 - - - -
338A MET* 1.3 77.2 - - - +
340A ASP* 1.3 61.7 + - - +
342A LEU* 3.3 11.3 + - + +
343A ILE* 3.2 24.4 + - + +
437A GLN 3.4 26.0 - - - +
438A ILE* 4.5 8.7 - - + -
440A GLY* 4.2 8.9 + - - +
441A LEU* 3.7 34.1 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
337A THR 4.2 11.8 - - - +
338A MET 4.4 1.0 - - - -
339A ILE* 1.3 78.3 - - - +
341A ASP* 1.3 61.0 + - - +
343A ILE* 3.9 6.8 - - - +
344A HIS* 3.0 28.8 + - - +
440A GLY* 4.2 6.0 + - - +
441A LEU* 6.0 0.4 - - - +
442A LEU* 4.0 36.1 - - + +
446A ARG* 5.6 0.2 - - - +
4C ARG* 3.8 13.1 + - - -
5C LYS* 3.3 34.9 + - - -
19C ASP* 4.2 5.9 - - - +
13H TRP* 5.3 8.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A LEU* 3.9 16.6 - - + -
338A MET* 3.1 19.0 + - + +
340A ASP* 1.3 77.7 - - - +
342A LEU* 1.3 67.8 + - - +
344A HIS* 3.8 5.1 - - - +
345A PHE* 2.9 31.8 + - + -
1C MET* 3.6 18.2 - - - +
2C ALA* 3.1 32.5 + - - +
4C ARG* 4.9 0.3 + - - -
5C LYS* 2.9 36.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ILE* 5.9 0.4 - - + -
305A ILE* 4.5 13.0 - - + -
310A LEU* 3.3 43.6 - - + +
311A CYS* 3.9 15.7 - - + -
314A PHE* 5.5 2.5 - - + -
329A PHE* 4.8 7.6 - - + -
331A THR* 3.7 35.7 - - + +
333A THR* 4.7 9.4 - - + -
338A MET 3.4 6.5 + - - +
339A ILE* 3.3 15.1 + - + +
341A ASP* 1.3 79.8 - - - +
343A ILE* 1.3 65.9 + - + +
345A PHE* 4.1 0.9 - - - +
346A THR* 2.8 40.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ILE* 3.9 31.0 - - + -
262A LEU* 4.2 10.5 - - + -
329A PHE* 4.5 12.6 - - + -
339A ILE* 3.2 16.9 + - + +
340A ASP* 3.9 6.7 - - - +
342A LEU* 1.3 82.7 - - + +
344A HIS* 1.3 56.3 + - - +
346A THR* 3.1 7.5 + - - -
347A LEU* 2.8 44.1 + - + +
441A LEU* 3.9 20.2 - - + -
447A ILE* 3.7 35.9 - - + -
450A ASP* 5.1 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A ASP* 3.0 19.8 + - - +
341A ASP* 3.8 6.3 - - - +
343A ILE* 1.3 76.7 - - - +
345A PHE* 1.3 79.7 + + - +
347A LEU* 3.5 0.9 + - - +
348A LYS* 2.9 62.4 + - + +
450A ASP* 3.3 29.8 + - - +
2C ALA* 4.1 26.4 - - + +
4C ARG* 5.1 8.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A LEU* 3.7 14.6 - - + -
304A ASN* 3.6 40.6 - - + +
305A ILE* 5.2 1.8 - - + -
310A LEU* 3.6 20.0 - - + -
341A ASP* 2.9 27.1 + - + +
342A LEU 4.1 2.0 - - - +
344A HIS* 1.3 89.3 - + - +
346A THR* 1.3 63.6 - - - +
348A LYS* 3.3 6.1 + - + +
349A GLN* 3.0 26.2 + - - +
1C MET* 3.4 48.5 - - - -
2C ALA* 3.8 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A LEU* 3.7 23.4 - - + +
316A HIS* 4.3 6.1 - - + -
329A PHE* 3.6 35.9 - - + -
342A LEU* 2.8 34.8 + - - +
343A ILE 3.1 3.9 + - - -
345A PHE* 1.3 77.5 - - - +
347A LEU* 1.3 61.0 + - + +
349A GLN* 2.8 22.6 + - - +
350A TRP* 3.1 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LEU* 4.1 17.9 - - + -
329A PHE* 4.5 2.9 - - + -
343A ILE* 2.8 29.0 + - + +
344A HIS 4.2 0.4 - - - +
346A THR* 1.3 86.2 - - + +
348A LYS* 1.3 55.7 + - - +
349A GLN 3.2 0.2 - - - -
350A TRP* 3.4 26.5 + - + +
351A ASN* 2.9 30.5 + - - -
430A ILE* 5.2 0.2 - - + -
447A ILE* 3.5 44.0 - - + +
450A ASP* 3.7 21.8 - - + +
451A MET* 3.9 22.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A HIS* 2.9 44.2 + - + +
345A PHE* 3.8 7.2 - - + +
346A THR 3.1 0.2 - - - -
347A LEU* 1.3 74.7 - - - +
349A GLN* 1.3 64.8 + - - +
351A ASN* 2.9 39.7 - - - +
352A ARG* 3.6 10.4 - - - +
449A SER 5.5 0.6 + - - -
450A ASP* 3.3 25.8 + - - +
452A SER 3.5 17.8 + - - -
453A MET* 3.8 22.5 - - + +
454A MET* 5.3 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A PHE* 3.6 35.1 - - + -
299A ILE* 5.7 0.2 - - - +
300A LYS* 3.5 13.2 - - - +
301A LEU* 3.5 44.9 - - + +
304A ASN* 4.9 6.8 - - - +
345A PHE 3.0 13.4 + - - +
346A THR* 2.8 11.5 + - - +
348A LYS* 1.3 76.2 - - - +
350A TRP* 1.3 60.3 + - - +
352A ARG* 2.9 70.0 + - - +
353A LEU 4.0 0.2 + - - -
361A GLU* 4.8 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LEU* 3.6 33.0 - - + -
264A VAL* 5.2 3.4 - - + -
284A PHE* 3.6 30.2 - + - -
316A HIS* 3.0 30.5 + + - -
327A TRP* 3.7 26.5 - + - -
328A GLY* 3.7 16.8 - - - -
329A PHE* 3.4 29.4 - + - -
346A THR* 3.1 25.1 + - + +
347A LEU* 3.5 23.3 - - + +
349A GLN* 1.3 77.9 - - + +
351A ASN* 1.3 63.2 + - - +
353A LEU* 3.0 21.2 + - - +
354A THR* 4.3 2.9 + - - -
425A LEU* 4.7 17.3 - - + +
451A MET* 4.2 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LEU 2.9 18.0 + - - +
348A LYS* 2.9 40.9 - - - +
349A GLN 3.1 0.6 - - - -
350A TRP* 1.3 77.9 - - - +
352A ARG* 1.3 63.4 + - + +
354A THR* 3.2 16.8 + - - -
355A ILE* 3.5 13.6 + - - +
426A TRP* 4.1 10.1 - - + -
450A ASP 3.2 13.5 + - - +
451A MET* 3.5 20.2 + - - +
452A SER* 3.4 6.6 - - - +
453A MET* 3.3 29.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ILE* 5.9 0.2 - - - +
284A PHE* 5.0 3.4 - - + -
300A LYS* 3.8 20.0 - - - +
348A LYS 3.6 9.2 - - - +
349A GLN* 2.9 54.3 + - - +
351A ASN* 1.3 77.4 - - + +
353A LEU* 1.3 57.8 + - + +
354A THR 2.9 4.5 + - - -
355A ILE* 4.2 5.4 - - + -
356A SER* 2.7 60.0 + - - +
357A VAL* 2.9 10.7 + - + +
358A THR* 4.6 4.2 - - - +
361A GLU* 3.0 41.9 + - - -
453A MET* 6.3 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ALA* 3.9 25.6 - - + -
283A ILE* 3.6 17.7 - - + -
284A PHE* 3.4 38.1 - - + -
327A TRP* 4.3 1.1 - - + -
350A TRP 3.0 10.6 + - - +
352A ARG* 1.3 77.3 - - + +
354A THR* 1.3 56.9 + - - +
357A VAL* 3.6 34.1 - - + +
417A VAL* 3.6 10.1 - - + +
418A LYS* 3.4 19.8 - - - +
420A TRP* 4.4 2.2 - - + -
421A ALA* 3.2 21.0 - - + +
425A LEU* 4.2 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A TRP 4.7 2.8 + - - -
351A ASN* 3.2 9.3 + - - -
352A ARG 3.0 0.6 - - - -
353A LEU* 1.3 78.7 - - - +
355A ILE* 1.3 66.6 + - + +
418A LYS* 3.8 25.4 - - - +
421A ALA* 3.1 24.0 + - - +
422A GLY* 3.9 22.7 - - - +
425A LEU* 4.9 0.9 - - - +
426A TRP* 3.8 31.3 + - + +
455A ARG* 6.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ASN 3.6 12.6 - - - +
352A ARG* 3.0 6.0 + - + +
354A THR* 1.3 88.7 - - + +
356A SER* 1.3 67.1 + - - +
357A VAL 4.0 0.4 - - - -
418A LYS* 3.6 16.0 + - - -
426A TRP* 4.2 22.4 - - + -
453A MET* 3.7 35.4 - - + -
455A ARG* 5.1 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ARG* 2.7 44.1 + - - +
355A ILE* 1.3 83.9 - - - +
357A VAL* 1.3 66.6 + - - +
358A THR* 3.3 13.9 + - - +
418A LYS* 4.6 3.1 - - - +
----------------------------------------------------------
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