Contacts of the helix formed by residues 349 - 367 (chain A) in PDB entry 2PME
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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A LYS* 3.4 32.4 - - + +
342A VAL* 4.2 8.3 - - - +
347A ILE* 3.5 9.5 - - - +
348A ASN* 1.3 96.9 + - - +
350A THR* 1.3 59.5 + - - +
351A VAL* 3.2 10.5 + - - +
352A LEU* 2.6 34.5 + - - +
353A GLY* 3.0 20.8 + - - -
409A ASP* 2.8 26.0 + - - +
521A ILE* 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A LYS 4.4 0.6 + - - -
307A ASP* 2.4 33.6 + - - +
308A HIS* 3.0 12.6 + - - -
311A PHE* 3.3 39.5 - - + -
342A VAL* 4.0 19.3 - - + -
349A ASN* 1.3 73.5 - - - +
351A VAL* 1.3 57.4 + - - +
354A TYR* 2.6 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A HIS* 4.2 21.8 - - + +
301A VAL* 4.2 9.4 - - + -
306A LYS* 3.7 16.8 - - + -
307A ASP 3.6 16.4 - - - +
308A HIS* 3.5 34.3 - - + +
349A ASN* 3.2 7.5 + - - +
350A THR* 1.3 78.4 + - - +
352A LEU* 1.3 62.4 + - - +
354A TYR* 3.5 5.0 + - - +
355A PHE* 3.2 32.0 + - + -
521A ILE* 3.8 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A ILE* 4.5 8.3 - - + -
348A ASN* 4.8 1.8 - - + -
349A ASN* 2.6 27.8 + - - +
351A VAL* 1.3 74.2 - - - +
353A GLY* 1.3 64.1 + - - +
354A TYR 3.3 0.5 + - - -
355A PHE* 3.4 2.9 + - - +
356A ILE* 3.1 46.1 + - + +
389A ASP* 3.6 27.6 - - - +
391A TRP* 3.9 20.2 - - + +
407A CYS* 3.9 19.5 - - - +
409A ASP* 3.8 31.6 - - + +
521A ILE* 4.4 10.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A PHE* 3.7 15.7 - - - -
338A LEU* 3.5 14.6 - - - +
342A VAL* 4.9 0.4 - - - -
347A ILE* 4.0 13.8 - - - +
349A ASN 3.0 15.2 + - - -
350A THR 3.2 3.3 + - - -
352A LEU* 1.3 78.0 - - - +
354A TYR* 1.3 61.6 + - - +
356A ILE* 3.3 9.0 + - - +
357A GLY 3.0 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLU* 4.6 1.6 - - - +
119A GLU* 2.9 38.2 + - + -
308A HIS* 3.4 42.4 - + + -
310A LYS* 3.3 46.4 + - + -
311A PHE* 3.6 9.6 - - + -
313A ASN* 5.2 2.0 - - + -
314A VAL* 3.8 24.0 - - + +
350A THR 2.6 22.3 + - - +
351A VAL 3.6 4.7 - - - +
352A LEU 3.2 0.2 - - - -
353A GLY* 1.3 72.3 - - - +
355A PHE* 1.3 72.4 + + - +
357A GLY* 3.1 4.2 + - - -
358A ARG* 2.8 47.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A PHE* 4.9 16.6 - + - -
119A GLU* 5.0 11.2 - - + -
121A ILE* 5.6 3.1 - - + -
268A ALA* 5.5 0.7 - - + -
297A ILE* 4.7 18.4 - - + -
299A HIS* 3.3 51.6 - + + -
308A HIS* 4.6 2.5 - + - -
351A VAL* 3.2 27.1 + - + -
352A LEU 3.4 6.3 + - - +
354A TYR* 1.3 96.9 - + - +
356A ILE* 1.3 56.0 + - - +
358A ARG* 3.5 4.8 - - + +
359A ILE* 2.6 43.2 + - + +
407A CYS* 4.4 7.9 - - - -
521A ILE* 3.8 13.2 - - + -
523A PRO* 4.1 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 4.3 14.1 - - + -
321A LEU* 5.1 0.7 - - + -
338A LEU* 4.6 4.7 - - + -
347A ILE* 4.0 23.1 - - + -
352A LEU* 3.1 37.9 + - + +
353A GLY* 3.4 7.9 - - - +
355A PHE* 1.3 76.5 - - - +
357A GLY* 1.3 57.8 + - - +
359A ILE* 3.3 7.7 + - - +
360A TYR* 2.9 24.3 + - - +
375A PHE* 3.5 37.9 - - + -
391A TRP* 4.0 29.2 - - + -
407A CYS* 4.7 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A VAL* 3.2 29.6 - - - -
317A LEU* 3.7 6.7 - - - +
319A LEU* 4.7 2.7 - - - -
338A LEU* 4.2 5.6 - - - +
353A GLY 3.0 12.0 + - - -
354A TYR 3.5 0.2 - - - -
356A ILE* 1.3 74.2 - - - +
358A ARG* 1.3 61.0 + - - +
360A TYR* 3.4 5.6 + - - +
361A LEU* 2.9 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A HIS* 3.0 68.3 + - - +
115A PHE* 3.8 16.8 - - + -
118A GLU* 3.3 25.2 + - - +
119A GLU* 3.9 7.4 - - - +
314A VAL* 4.1 5.6 - - + +
354A TYR* 2.8 53.6 + - + +
355A PHE* 3.5 10.8 - - + +
357A GLY* 1.3 73.4 - - - +
359A ILE* 1.3 60.2 + - - +
361A LEU* 3.3 20.6 + - - +
362A TYR 2.9 23.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A PHE* 4.1 9.6 - - + -
355A PHE* 2.6 32.7 + - + +
356A ILE* 3.5 8.3 - - - +
358A ARG* 1.3 70.1 - - - +
360A TYR* 1.3 66.3 + - - +
362A TYR* 3.0 3.9 + - - +
363A LEU* 2.9 44.7 + - + +
375A PHE* 4.1 13.9 - - + -
393A ALA* 4.3 0.4 - - + -
405A VAL* 3.8 31.9 - - + +
407A CYS* 3.9 25.1 - - + -
523A PRO* 4.0 12.1 - - + -
525A PHE* 3.9 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A LEU* 3.7 31.9 - - + -
318A HIS 4.0 16.1 + - - -
319A LEU* 4.1 24.0 - - + -
356A ILE 2.9 17.4 + - - +
357A GLY 3.6 3.4 - - - +
359A ILE* 1.3 75.8 - - - +
361A LEU* 1.3 66.3 + - + +
363A LEU* 3.4 4.7 + - - +
364A THR* 2.8 52.9 + - + +
370A PRO* 3.4 31.6 - - + +
373A LEU* 4.3 14.4 - - + -
375A PHE* 3.7 26.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A HIS* 3.7 11.7 - - + +
313A ASN 5.5 4.0 - - - +
314A VAL* 4.8 8.5 - - + -
317A LEU* 3.7 30.3 - - + -
357A GLY 2.9 19.0 + - - +
358A ARG* 3.5 37.0 - - - +
359A ILE 3.2 0.2 - - - -
360A TYR* 1.3 77.3 - - + +
362A TYR* 1.3 66.4 + - - +
364A THR* 3.0 16.8 + - - +
365A LYS* 3.1 16.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ILE* 2.8 37.8 + - - +
110A THR* 3.9 11.0 - - + -
111A TRP* 3.5 46.1 - + - +
114A HIS* 3.4 36.3 + + + -
115A PHE* 3.8 10.8 - + + -
358A ARG 2.9 8.8 + - - +
359A ILE 3.0 6.7 + - - +
361A LEU* 1.3 76.0 - - - +
363A LEU* 1.3 77.9 + - + +
365A LYS* 3.1 8.0 + - + +
366A VAL* 3.1 44.9 + - + +
525A PHE* 4.2 7.9 - + - -
527A LEU* 4.8 1.7 - - - +
530A ILE* 4.3 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ILE* 2.9 40.3 + - + +
360A TYR* 4.0 0.9 - - - +
362A TYR* 1.3 89.6 - - + +
364A THR* 1.3 62.1 + - - +
366A VAL* 3.3 9.6 + - - +
367A GLY 3.3 0.9 + - - -
368A ILE* 3.1 44.5 + - + +
373A LEU* 3.8 26.5 - - + -
375A PHE* 5.1 0.2 - - + -
393A ALA* 4.0 13.2 - - + -
404A ILE* 3.8 19.1 - - + -
405A VAL* 3.9 17.9 - - + -
530A ILE* 4.1 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A TYR* 2.8 54.8 + - + +
361A LEU* 3.0 18.2 + - - +
363A LEU* 1.3 76.8 - - - +
365A LYS* 1.3 60.6 + - - +
367A GLY* 3.4 11.3 + - - -
368A ILE 3.5 19.2 - - - +
370A PRO* 3.9 14.8 - - + -
373A LEU* 4.3 6.5 - - + -
554A PRO* 5.2 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A THR* 3.7 25.6 + - + +
113A GLN* 6.3 0.4 - - - +
114A HIS* 3.0 39.6 + - - +
361A LEU* 3.1 14.8 + - - +
362A TYR* 3.1 6.5 + - + +
364A THR* 1.3 78.8 + - - +
366A VAL* 1.3 60.1 + - - +
554A PRO* 3.4 21.5 - - - +
556A VAL* 3.7 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ILE* 3.2 32.5 - - + -
110A THR* 4.9 5.2 - - + -
362A TYR* 3.1 51.5 + - + +
363A LEU* 3.3 9.1 + - - +
365A LYS* 1.3 77.1 - - - +
367A GLY* 1.3 57.0 + - - +
368A ILE* 5.2 0.2 - - + -
530A ILE* 4.4 7.6 - - + -
534A VAL* 3.5 25.5 - - + +
554A PRO* 3.4 13.9 - - - +
557A VAL* 4.0 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A LEU 3.3 0.4 + - - -
364A THR 3.4 5.1 + - - -
365A LYS 3.3 3.8 - - - -
366A VAL* 1.3 80.5 - - - +
368A ILE* 1.3 64.5 + - - +
369A SER* 3.6 3.6 + - - -
534A VAL* 4.2 9.3 - - - +
537A HIS* 3.9 11.3 - - - +
538A THR* 3.9 14.4 + - - -
554A PRO* 3.7 18.8 - - - -
----------------------------------------------------------
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