Contacts of the helix formed by residues 349 - 365 (chain D) in PDB entry 5I94
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 349 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348D VAL* 1.3 78.5 - - - +
350D ASN* 1.3 62.2 - - - +
351D ALA* 3.6 11.5 + - - +
352D GLU* 2.8 40.8 + - - +
353D LYS* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 350 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348D VAL 5.1 0.2 - - - +
349D ASN* 1.3 73.9 - - - +
351D ALA* 1.3 58.5 + - - +
353D LYS* 4.1 19.9 + - - +
354D PHE* 2.7 38.7 + - - +
408D GLY* 3.1 32.3 + - - +
411D ASP* 4.2 8.9 - - - +
412D PHE* 4.0 23.6 - - + +
415D GLN* 4.3 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 351 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349D ASN* 3.3 14.4 - - - +
350D ASN* 1.3 77.0 - - - +
352D GLU* 1.3 59.6 + - + +
354D PHE* 3.6 3.7 + - - +
355D ASP* 3.1 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 352 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345D LYS* 5.8 1.1 - - - -
348D VAL* 3.3 31.0 - - + +
349D ASN* 2.8 28.7 + - - +
351D ALA* 1.3 74.4 - - + +
353D LYS* 1.3 66.8 + - - +
355D ASP* 3.1 11.2 + - - +
356D TYR* 2.9 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 353 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341D THR 5.3 0.6 + - - -
342D SER 5.6 1.6 + - - -
344D ILE* 3.6 10.0 + - + +
345D LYS* 3.3 40.4 - - + +
346D GLN* 4.6 5.5 - - - +
347D GLY 4.8 0.8 - - - +
348D VAL* 3.4 22.1 + - + +
349D ASN 3.0 14.8 + - - +
350D ASN* 3.7 18.9 + - - +
352D GLU* 1.3 74.9 - - - +
354D PHE* 1.3 64.2 + - - +
356D TYR* 3.0 10.0 + - - +
357D VAL* 2.9 24.1 + - - +
409D ILE* 3.8 27.7 - - - +
412D PHE* 3.6 32.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 354 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350D ASN 2.7 22.5 + - - +
351D ALA* 3.8 4.5 - - - +
353D LYS* 1.3 72.5 - - - +
355D ASP* 1.3 70.8 + - - +
357D VAL* 3.4 2.1 + - - +
358D MET* 2.9 54.0 + - + +
372D PHE* 3.6 31.2 - + + -
412D PHE* 3.9 17.4 - + + -
415D GLN* 3.6 42.2 - - + +
416D LEU* 4.7 3.6 - - + -
419D ILE* 4.0 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 355 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351D ALA* 3.1 22.3 + - - +
352D GLU* 3.1 12.8 + - - +
354D PHE* 1.3 81.8 - - - +
356D TYR* 1.3 55.3 + - - +
358D MET* 2.9 8.8 + - - +
359D GLN* 2.7 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 356 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294D ILE* 4.1 15.5 - - + -
298D ASP* 2.4 37.4 + - - -
344D ILE* 4.4 12.6 - - + -
345D LYS* 3.5 40.8 - - + -
352D GLU 2.9 13.2 + - - +
353D LYS* 3.3 10.1 - - - +
355D ASP* 1.3 76.4 - - - +
357D VAL* 1.3 65.1 + - + +
359D GLN* 3.5 27.5 + - - +
360D PHE* 3.0 40.8 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 357 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D VAL* 5.7 1.8 - - + -
291D LYS* 5.7 3.6 - - + -
294D ILE* 4.1 20.0 - - + -
344D ILE* 4.3 23.1 - - + -
353D LYS 2.9 15.1 + - - +
354D PHE 3.9 5.8 - - - +
356D TYR* 1.3 77.8 - - + +
358D MET* 1.3 58.8 + - - +
360D PHE* 2.9 8.7 + - - +
361D LEU* 2.8 46.5 + - + +
412D PHE* 4.1 17.0 - - + -
416D LEU* 3.5 26.7 - - + -
419D ILE* 4.3 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 358 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354D PHE* 2.9 53.2 + - + +
355D ASP* 2.9 15.8 + - - +
357D VAL* 1.3 71.7 - - - +
359D GLN* 1.3 57.1 + - - +
361D LEU* 3.3 5.3 + - - +
362D ASN* 3.0 41.4 + - - +
370D VAL* 3.3 44.1 - - + +
371D GLY 4.2 7.9 - - - +
372D PHE* 5.3 2.2 - - + -
419D ILE* 4.1 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 359 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355D ASP* 2.7 18.6 + - + +
356D TYR* 3.8 30.8 - - - +
358D MET* 1.3 72.9 - - - +
360D PHE* 1.3 64.0 + - - +
362D ASN* 3.5 10.8 + - - +
363D LYS* 3.3 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 360 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294D ILE* 3.8 31.2 - - + -
297D ASN* 3.5 24.0 - - + -
356D TYR* 3.0 44.1 + + - +
357D VAL 2.9 9.7 + - - +
359D GLN* 1.3 81.4 - - - +
361D LEU* 1.3 61.6 + - - +
363D LYS* 3.1 18.6 + - + +
364D MET* 3.3 24.7 + - + +
446D VAL* 3.3 36.3 - - + -
447D LEU* 3.4 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 361 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283D LEU* 4.7 10.1 - - + -
287D VAL* 4.8 3.8 - - + -
290D LEU* 4.2 24.9 - - + -
294D ILE* 4.8 2.5 - - + -
357D VAL* 2.8 32.4 + - + +
358D MET* 3.7 6.1 - - - +
360D PHE* 1.3 72.5 - - - +
362D ASN* 1.3 63.1 + - - +
364D MET* 3.3 28.0 + - + +
365D ALA* 3.2 23.2 + - - +
370D VAL* 3.9 16.3 - - + +
419D ILE* 3.6 43.3 - - + -
429D MET* 3.9 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 362 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358D MET* 3.0 33.5 + - - +
359D GLN* 3.7 9.9 - - - +
360D PHE 3.2 0.2 - - - -
361D LEU* 1.3 77.5 - - - +
363D LYS* 1.3 60.9 + - + +
365D ALA 3.3 4.2 + - - -
367D ASN* 2.9 45.5 + - - +
368D GLU 3.9 7.8 - - - +
370D VAL* 3.3 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 363 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359D GLN* 3.3 39.4 + - + +
360D PHE* 3.1 12.8 + - + +
362D ASN* 1.3 77.5 - - + +
364D MET* 1.3 62.7 + - - +
366D GLY* 3.2 11.5 + - - -
367D ASN* 5.1 5.4 - - - +
439D CYS* 3.6 12.0 - - - +
442D THR* 4.9 1.4 + - - +
444D GLU* 3.0 31.3 - - - +
446D VAL* 3.7 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 364 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D LEU* 4.2 28.9 - - + +
294D ILE* 4.0 15.3 - - + -
360D PHE* 3.3 33.6 + - + +
361D LEU* 3.7 32.5 - - + +
362D ASN 3.3 0.6 - - - -
363D LYS* 1.3 77.1 - - - +
365D ALA* 1.3 59.0 + - - +
366D GLY 3.3 1.2 + - - -
428D VAL* 3.2 12.8 - - - +
429D MET* 3.3 17.1 - - + +
432D THR* 2.7 31.7 + - + +
433D LEU* 5.8 1.3 - - - -
439D CYS* 3.9 0.5 - - - -
446D VAL* 3.4 19.1 - - + -
447D LEU* 4.2 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 365 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361D LEU 3.2 15.5 + - - +
362D ASN 3.3 3.6 + - - +
363D LYS 3.2 0.6 - - - -
364D MET* 1.3 74.9 - - - +
366D GLY* 1.3 64.1 + - - +
367D ASN 3.1 0.2 - - - -
368D GLU* 3.1 31.1 - - - +
370D VAL* 4.2 8.1 - - + -
425D SER* 3.5 22.2 - - - +
428D VAL* 3.3 18.1 - - - +
429D MET* 3.7 15.9 - - + -
----------------------------------------------------------
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