Contacts of the helix formed by residues 340 - 359 (chain A) in PDB entry 3KXK
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 ASN 340 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ILE* 3.8 14.5 - - - +
331A ILE* 4.6 1.5 - - + +
332A PRO* 3.3 28.6 + - - +
333A ILE* 4.4 4.8 - - + +
338A ARG 3.9 1.0 + - - -
339A THR* 1.3 91.6 - - - +
341A LEU* 1.3 57.9 + - - +
342A GLU* 3.3 3.4 - - - +
343A LEU* 3.6 21.8 + - + +
344A LEU* 3.1 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU* 4.2 12.6 - - + -
198A SER* 3.6 31.2 - - - +
199A LEU* 4.8 6.7 - - + +
333A ILE* 4.7 7.9 - - + -
335A ALA* 4.7 7.0 - - - +
338A ARG* 3.5 49.0 + - + +
339A THR 3.1 10.1 - - - +
340A ASN* 1.3 76.9 - - - +
342A GLU* 1.3 61.1 + - - +
344A LEU* 3.2 23.6 + - + +
345A ARG* 2.8 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A ASN* 3.3 1.5 - - - +
341A LEU* 1.3 78.7 - - - +
343A LEU* 1.3 61.9 + - - +
345A ARG* 3.1 22.5 + - - +
346A ASP* 2.9 41.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ILE* 4.8 20.9 - - + -
332A PRO* 6.2 1.6 - - + -
340A ASN* 3.6 24.3 + - + +
341A LEU 3.3 0.2 - - - -
342A GLU* 1.3 77.9 - - - +
344A LEU* 1.3 57.9 + - - +
346A ASP* 3.1 18.0 + - + +
347A LYS* 2.9 51.4 + - + +
350A GLN* 6.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU* 3.6 33.2 - - + -
199A LEU* 3.9 20.9 - - + -
262A ILE* 5.1 1.8 - - + -
296A LEU* 4.0 21.3 - - + -
298A THR* 4.1 9.4 - - + -
331A ILE* 3.6 25.3 - - + +
333A ILE* 4.4 10.3 - - + -
340A ASN 3.1 15.2 + - - +
341A LEU* 3.2 17.9 - - + +
342A GLU 3.1 0.2 - - - -
343A LEU* 1.3 76.7 - - - +
345A ARG* 1.3 57.0 + - - +
347A LYS* 3.1 3.1 + - + +
348A ILE* 2.8 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A SER 5.5 0.8 + - - -
199A LEU* 3.8 39.5 + - + +
221A ILE* 4.2 10.3 - - - +
222A PRO* 2.9 27.5 + - - +
223A ILE* 3.6 29.2 - - + +
341A LEU* 2.8 25.0 + - - +
342A GLU* 3.1 27.2 + - - +
344A LEU* 1.3 71.6 - - - +
346A ASP* 1.3 59.3 + - - +
348A ILE* 3.2 10.9 + - - +
349A TYR* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ILE* 5.7 0.6 - - - +
342A GLU* 2.9 34.9 + - - +
343A LEU* 3.2 22.8 - - + +
345A ARG* 1.3 77.1 - - - +
347A LYS* 1.3 57.6 + - - +
349A TYR* 3.1 8.4 + - - +
350A GLN* 2.8 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LEU* 4.1 17.9 - - + -
328A PHE* 3.4 16.9 - - + -
329A ASP* 3.2 29.8 + - - +
331A ILE* 4.6 9.4 - - + -
343A LEU* 2.9 39.6 + - + +
344A LEU* 3.5 9.0 - - + +
346A ASP* 1.3 76.8 - - - +
348A ILE* 1.3 58.9 + - - +
350A GLN* 3.4 29.4 + - - +
351A LEU* 2.8 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ILE* 5.1 8.7 - - + -
199A LEU* 5.2 7.6 - - + -
221A ILE* 5.3 3.4 - - + -
223A ILE* 3.7 21.1 - - + -
228A ILE* 4.2 22.4 - - + -
230A LEU* 5.3 4.5 - - + -
262A ILE* 3.5 32.5 - - + -
296A LEU* 3.7 18.2 - - + -
344A LEU* 2.8 35.9 + - + +
345A ARG* 3.4 9.4 - - - +
347A LYS* 1.3 76.1 - - - +
349A TYR* 1.3 57.1 + - - +
351A LEU* 3.3 10.1 + - + +
352A ALA* 2.8 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ILE* 3.3 36.7 - - + +
224A ASN* 3.5 28.1 - - + +
225A ASN* 2.9 34.1 + - - -
226A ARG* 3.5 26.8 + - + -
228A ILE* 5.2 0.7 - - - -
345A ARG 2.9 7.5 + - - +
346A ASP* 3.4 11.2 - - - +
348A ILE* 1.3 74.1 - - - +
350A GLN* 1.3 67.7 + - + +
352A ALA* 3.1 7.3 + - - +
353A THR* 2.8 42.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A PHE* 3.9 12.8 - - + -
343A LEU* 6.2 0.2 - - - +
346A ASP* 2.8 33.2 + - - +
347A LYS* 3.7 36.1 + - - +
349A TYR* 1.3 80.9 - - + +
351A LEU* 1.3 57.3 + - - +
353A THR* 3.2 9.2 + - - -
354A GLN* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ILE* 4.2 15.7 - - + -
260A ALA* 3.7 20.4 - - + -
261A LEU 5.3 1.6 - - - +
262A ILE* 5.8 0.4 - - + -
294A PRO* 3.9 24.5 - - + +
296A LEU* 4.7 22.9 - - + -
328A PHE* 3.5 32.7 - - + -
347A LYS 2.8 18.2 + - - +
348A ILE* 3.4 10.1 - - + +
350A GLN* 1.3 77.2 - - - +
352A ALA* 1.3 57.6 + - - +
354A GLN* 3.2 6.5 + - - +
355A LEU* 2.8 47.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A PRO* 4.7 12.6 - - + +
182A ILE* 6.1 1.1 - - + +
226A ARG* 3.9 19.0 + - + +
228A ILE* 4.0 25.4 - - + -
348A ILE 2.8 14.8 + - - +
349A TYR* 3.3 9.0 - - - +
351A LEU* 1.3 75.8 - - - +
353A THR* 1.3 57.1 + - - +
355A LEU* 3.4 11.9 + - - +
356A SER* 3.0 30.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ARG* 3.3 25.6 + - - +
349A TYR* 2.8 31.8 + - - -
350A GLN* 3.4 11.4 - - - -
352A ALA* 1.3 74.1 - - - +
354A GLN* 1.3 64.6 + - - +
356A SER* 2.7 21.0 + - - -
357A LEU* 3.0 36.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A PRO* 3.9 29.3 - - - +
326A PRO* 6.1 2.4 - - - +
328A PHE* 3.3 27.4 - - + -
350A GLN 2.9 13.8 + - - +
351A LEU* 3.2 10.5 + - + +
353A THR* 1.3 77.4 - - - +
355A LEU* 1.3 57.5 + - - +
357A LEU* 3.0 8.6 + - - +
358A GLU* 2.9 42.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A PRO* 4.1 16.4 - - + -
182A ILE* 3.8 28.5 - - + -
259A ASP* 3.6 38.4 - - + +
260A ALA* 4.0 5.6 - - + -
294A PRO* 4.2 11.9 - - + -
351A LEU* 2.8 27.8 + - + +
352A ALA* 3.7 6.3 - - - +
353A THR 3.3 0.2 - - - -
354A GLN* 1.3 77.7 - - - +
356A SER* 1.3 60.7 + - - +
357A LEU 3.4 0.5 + - - -
358A GLU* 3.4 39.9 + - - +
359A HIS* 4.8 4.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
178A ASN* 5.7 9.6 - - - -
180A PRO* 5.9 3.8 - - - +
226A ARG* 3.0 38.3 + - - -
352A ALA 3.0 7.6 + - - -
353A THR 2.7 19.1 + - - -
355A LEU* 1.3 75.7 - - - +
357A LEU* 1.3 64.8 + - - +
358A GLU 3.4 0.2 - - - -
359A HIS 4.9 2.3 + - - +
360A HIS* 4.4 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ARG* 5.5 2.7 - - - +
353A THR* 3.0 42.5 + - + +
354A GLN* 3.0 7.4 + - - +
356A SER* 1.3 86.3 - - - +
358A GLU* 1.3 66.0 + - - +
359A HIS 3.5 1.7 + - - -
360A HIS* 3.5 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A PRO* 4.0 14.7 - - - +
354A GLN* 2.9 35.8 + - + +
355A LEU* 3.4 37.2 - - - +
356A SER 3.4 1.0 - - - -
357A LEU* 1.3 81.3 - - - +
359A HIS* 1.3 85.3 + - + +
360A HIS 3.4 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A LEU 4.8 4.8 + - - -
356A SER 4.9 2.9 + - - +
357A LEU 3.5 0.4 - - - -
358A GLU* 1.3 100.4 + - + +
360A HIS* 1.3 58.5 + - - +
----------------------------------------------------------
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