Contacts of the helix formed by residues 323 - 342 (chain I) in PDB entry 6MZL
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 VAL 323 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316I GLN 4.4 2.0 - - - +
317I LEU* 3.9 28.3 - - + -
319I LEU 3.3 11.2 - - - +
320I ARG* 3.3 27.1 - - + +
321I PRO 3.5 1.8 - - - -
322I ASP* 1.3 73.6 - - - +
324I ASP* 1.3 62.7 + - - +
325I ASN 3.4 0.7 - - - -
326I HIS* 3.0 26.5 + - + +
327I TRP* 2.9 47.8 + - + +
330I ARG* 4.8 3.8 - - - +
371I THR* 6.2 0.4 - - - -
415I ILE* 5.7 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 324 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321I PRO 3.3 22.1 - - - +
322I ASP* 3.1 4.2 - - - +
323I VAL* 1.3 80.1 + - - +
325I ASN* 1.3 69.0 + - - +
327I TRP* 3.1 29.3 + - - +
328I ALA* 3.9 4.2 + - - +
422I HIS* 5.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 325 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276I LEU* 4.4 30.1 - - + +
322I ASP* 4.2 9.9 + - - +
323I VAL 3.4 0.6 - - - -
324I ASP* 1.3 82.9 - - - +
326I HIS* 1.3 56.9 + - - +
328I ALA* 3.2 10.7 + - - +
329I LEU* 2.9 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 326 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274I ASN* 4.8 0.7 - - - -
276I LEU* 3.5 35.2 - - + +
279I LEU* 4.8 1.7 - - + +
316I GLN* 3.1 49.1 + - + +
317I LEU* 5.0 0.2 - - - -
318I CYS* 3.6 22.2 + - - -
322I ASP 3.1 28.0 + - - -
323I VAL* 3.0 18.5 + - + +
325I ASN* 1.3 76.2 - - - +
327I TRP* 1.3 59.5 + - - +
329I LEU* 3.3 14.7 - - - +
330I ARG* 2.9 48.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 327 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323I VAL* 2.9 50.3 + - + +
324I ASP* 3.1 22.2 + - - +
325I ASN 3.2 0.6 - - - -
326I HIS* 1.3 78.6 - - - +
328I ALA* 1.3 57.4 + - - +
330I ARG* 3.1 25.4 + - - +
331I ASP* 2.9 34.3 + - - +
370I TRP* 4.9 1.8 - - + -
371I THR* 4.0 22.2 - - - -
374I TYR* 3.4 42.9 - + + +
419I GLY* 4.5 11.0 - - - -
422I HIS* 3.2 37.9 + + - +
423I VAL* 3.6 21.1 - - + -
426I LEU* 4.9 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 328 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324I ASP 3.9 3.5 + - - +
325I ASN* 3.2 14.8 + - - +
327I TRP* 1.3 75.5 - - - +
329I LEU* 1.3 60.2 + - - +
331I ASP* 3.2 14.7 + - - +
332I PHE* 2.9 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 329 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276I LEU* 3.9 21.3 - - + +
279I LEU* 4.4 12.6 - - + -
280I ILE* 3.7 43.1 - - + +
283I MET* 5.6 8.2 - - + +
311I CYS 5.7 0.9 - - - -
316I GLN* 4.1 11.2 - - - +
325I ASN* 2.9 16.9 + - + +
326I HIS* 3.3 37.7 - - - +
327I TRP 3.2 0.2 - - - -
328I ALA* 1.3 76.3 - - - +
330I ARG* 1.3 55.6 + - - +
332I PHE* 3.4 9.9 + - + +
333I ALA* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 330 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311I CYS 4.3 9.0 - - - +
312I ILE* 3.7 27.0 + - + +
313I VAL 4.9 0.4 - - - -
314I SER 4.7 0.2 - - - -
315I ARG 4.5 0.4 - - - +
316I GLN* 3.9 35.1 + - - +
317I LEU* 5.7 1.4 - - - +
323I VAL* 4.8 4.8 - - - +
326I HIS* 2.9 47.9 + - - +
327I TRP* 3.1 28.4 + - - +
329I LEU* 1.3 73.6 - - - +
331I ASP* 1.3 61.3 + - - +
333I ALA* 3.6 6.5 - - - +
334I ALA* 2.9 32.2 + - - +
371I THR* 2.7 40.8 + - - -
374I TYR* 3.5 26.0 - - + -
375I GLY* 4.4 7.4 - - - +
378I ALA* 5.0 2.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 331 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327I TRP* 2.9 18.1 + - - +
328I ALA* 3.2 16.7 + - - +
330I ARG* 1.3 77.8 - - - +
332I PHE* 1.3 56.3 + - - +
334I ALA* 3.4 4.1 + - - +
335I ARG* 2.9 31.1 + - - +
374I TYR* 2.3 30.8 + - - -
378I ALA* 4.8 6.7 - - - +
382I GLU* 4.6 3.8 - - - +
426I LEU* 5.4 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 332 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280I ILE* 5.9 2.5 - - + -
283I MET* 3.5 42.0 - - + -
284I ARG* 3.6 38.1 - - + -
287I LYS* 4.0 23.3 - - + -
328I ALA 2.9 16.8 + - - +
329I LEU* 3.7 11.0 - - + +
331I ASP* 1.3 74.7 - - - +
333I ALA* 1.3 57.2 + - - +
335I ARG* 3.3 28.0 - - - +
336I LEU* 2.9 41.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 333 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283I MET* 5.3 6.5 - - + -
308I VAL* 4.2 10.5 - - + +
311I CYS* 4.9 10.1 - - + -
312I ILE* 3.9 21.8 - - + -
329I LEU 2.9 18.6 + - - +
330I ARG* 3.6 7.9 - - - +
331I ASP 3.2 0.2 - - - -
332I PHE* 1.3 78.3 - - - +
334I ALA* 1.3 57.5 + - - +
336I LEU* 3.0 15.2 + - - +
337I VAL* 2.9 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 334 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312I ILE* 4.7 6.9 - - + +
330I ARG 2.9 17.4 + - - +
331I ASP* 3.9 2.2 - - - +
333I ALA* 1.3 75.1 - - - +
335I ARG* 1.3 57.7 + - - +
337I VAL* 3.2 11.1 + - - +
338I ALA 2.9 24.1 + - - -
375I GLY 5.1 1.6 - - - +
378I ALA* 3.7 18.4 - - + +
379I GLY* 3.7 15.9 - - - +
382I GLU* 3.3 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 335 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331I ASP 2.9 19.4 + - - +
332I PHE* 3.3 27.8 - - + +
334I ALA* 1.3 76.6 - - - +
336I LEU* 1.3 58.5 + - + +
338I ALA* 3.2 4.7 + - - +
339I GLN* 3.0 46.2 + - + +
382I GLU* 3.4 23.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 336 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283I MET* 3.4 37.5 - - + +
286I VAL* 4.8 9.4 - - + -
287I LYS* 3.6 37.7 - - + +
290I MET* 5.3 4.7 - - + +
308I VAL* 4.9 7.2 - - + -
332I PHE* 2.9 38.1 + - + +
333I ALA* 3.0 11.6 + - - +
335I ARG* 1.3 77.2 - - + +
337I VAL* 1.3 56.4 + - - +
339I GLN* 3.0 20.2 + - + +
340I ILE* 2.9 34.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 337 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305I ILE* 6.0 2.2 - - + -
308I VAL* 3.7 22.2 - - + -
309I MET* 5.3 5.2 - - + -
312I ILE* 3.7 19.5 - - + -
333I ALA 2.9 18.5 + - - +
334I ALA* 3.5 9.4 - - - +
336I LEU* 1.3 76.0 - - - +
338I ALA* 1.3 58.9 + - - +
340I ILE* 2.9 14.5 + - + +
341I CYS* 2.9 48.9 + - - -
355I ILE* 4.7 24.0 - - + -
359I PHE* 5.5 4.5 - - + -
379I GLY* 5.6 5.4 - - - +
382I GLU* 6.3 0.2 - - + -
383I LEU* 5.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 338 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334I ALA 2.9 8.3 + - - +
335I ARG 3.3 6.1 - - - +
337I VAL* 1.3 79.5 - - - +
339I GLN* 1.3 60.2 + - + +
340I ILE 3.4 0.2 + - - -
341I CYS* 3.5 13.2 + - - +
342I LYS* 3.8 25.4 - - - +
382I GLU* 3.3 49.6 - - + +
383I LEU* 5.5 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 339 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287I LYS* 3.5 30.2 + - - +
290I MET* 4.5 22.6 - - + +
291I ASP* 4.8 5.7 - - - +
335I ARG* 3.0 34.1 + - + +
336I LEU* 3.0 24.9 + - - +
338I ALA* 1.3 77.0 - - + +
340I ILE* 1.3 59.7 + - - +
342I LYS* 4.2 3.8 + - - +
343I HIS* 3.1 29.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 340 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286I VAL* 5.9 1.8 - - + -
290I MET* 3.7 27.1 - - + -
301I VAL* 6.4 0.2 - - + -
305I ILE* 3.7 37.9 - - + -
308I VAL* 4.8 12.3 - - + -
336I LEU* 2.9 23.7 + - + +
337I VAL* 2.9 23.1 + - + +
339I GLN* 1.3 78.5 - - - +
341I CYS* 1.3 63.0 + - - +
342I LYS 2.9 8.5 + - - -
343I HIS* 3.2 4.5 + - - -
344I PHE* 3.1 45.5 - - + -
351I ILE* 4.8 12.3 - - + -
355I ILE* 6.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 341 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337I VAL* 2.9 36.0 + - - +
338I ALA* 3.5 5.6 + - - +
339I GLN 3.5 0.8 - - - -
340I ILE* 1.3 75.9 - - - +
342I LYS* 1.3 58.0 + - + +
343I HIS 3.2 4.9 + - - -
344I PHE 4.3 1.8 + - - -
345I SER* 3.8 18.2 + - - -
351I ILE* 3.7 31.4 - - + +
352I GLN* 4.9 10.6 + - + +
355I ILE* 4.8 7.4 - - - -
383I LEU* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 342 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338I ALA* 3.8 20.2 - - - +
339I GLN* 4.7 2.5 - - - +
340I ILE 2.9 2.2 + - - -
341I CYS* 1.3 77.3 - - + +
343I HIS* 1.3 78.6 + - + +
382I GLU 6.1 0.7 - - - -
383I LEU 6.2 0.2 - - - -
----------------------------------------------------------
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