Contacts of the helix formed by residues 342 - 357 (chain A) in PDB entry 1DT6
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 342 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A GLU* 3.1 25.0 - - + +
324A ILE* 4.1 14.1 - - + -
327A VAL* 3.5 20.4 - - + -
328A ILE* 3.6 29.4 - - + -
338A ASP* 3.5 14.1 - - - +
339A ARG* 3.0 14.3 + - - +
340A SER 3.3 0.4 - - - -
341A ARG* 1.3 86.3 - - - +
343A PRO* 1.3 66.3 - - - +
345A THR* 3.3 28.3 - - + +
346A ASP* 3.1 21.1 + - - +
443A PHE* 4.1 7.8 - - + -
447A THR* 4.0 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A GLU* 4.0 8.3 - - - +
339A ARG 5.1 0.4 - - - +
340A SER 4.9 4.2 - - - +
341A ARG* 3.6 8.5 - - - +
342A MET* 1.3 88.2 - - - +
344A TYR* 1.3 54.2 + - - +
346A ASP* 3.2 6.7 + - + +
347A ALA* 2.6 36.7 + - - +
410A LEU* 4.2 2.5 - - - -
415A ASN* 3.6 22.4 - - + +
416A PHE* 3.8 34.5 - - + +
417A LYS* 4.0 9.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A VAL* 3.4 40.3 - - - +
319A ARG* 3.3 51.7 + - + +
320A VAL* 3.8 10.5 - - + -
323A GLU* 2.8 22.9 + - - +
343A PRO* 1.3 78.4 - - - +
345A THR* 1.3 64.2 + - - +
347A ALA* 3.0 5.9 + - - +
348A VAL* 2.9 44.8 + - + +
406A PRO* 3.8 19.0 - - + +
410A LEU* 3.8 24.0 - - + -
415A ASN* 4.0 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A VAL* 3.5 28.4 + - + +
323A GLU* 2.6 23.2 + - - +
342A MET* 3.3 28.5 - - + +
344A TYR* 1.3 74.7 - - - +
346A ASP* 1.3 58.4 + - - +
348A VAL* 3.1 8.8 + - - +
349A ILE* 3.0 34.5 + - + +
443A PHE* 4.2 14.4 - - + -
446A LEU* 6.6 0.2 - - + -
447A THR* 3.9 22.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
339A ARG* 3.5 43.1 + - + +
342A MET 3.1 16.6 + - - +
343A PRO* 3.6 2.9 - - + +
345A THR* 1.3 76.0 - - - +
347A ALA* 1.3 67.8 + - - +
349A ILE* 3.5 11.4 + - - +
350A HIS* 2.9 58.2 + - - -
417A LYS* 3.6 19.2 - - - +
443A PHE* 5.6 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A PRO 2.6 21.4 + - - +
344A TYR 3.0 5.6 + - - +
346A ASP* 1.3 72.3 - - - +
348A VAL* 1.3 53.8 + - - +
350A HIS* 3.3 2.1 + - - +
351A GLU* 2.7 35.5 + - - +
406A PRO* 3.6 24.4 - - + +
409A PHE* 3.8 7.4 - - + +
410A LEU* 3.6 20.4 - - + -
417A LYS* 3.4 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A LEU* 4.7 4.5 - - + -
316A VAL* 3.6 22.7 - - + -
320A VAL* 4.0 11.0 - - + -
344A TYR* 2.9 40.0 + - + +
345A THR 3.3 7.0 - - - +
347A ALA* 1.3 72.1 - - - +
349A ILE* 1.3 70.8 + - + +
350A HIS 3.0 1.1 - - - -
351A GLU* 2.9 4.1 + - - +
352A ILE* 2.8 39.7 + - + +
404A PHE* 4.3 7.4 - - + -
406A PRO* 3.4 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A THR* 3.0 24.0 + - + +
346A ASP* 4.1 9.6 - - - +
348A VAL* 1.3 78.6 - - + +
350A HIS* 1.3 64.3 + - + +
352A ILE* 3.4 11.3 + - + +
353A GLN* 3.3 22.5 + - - +
439A ARG 5.6 1.1 - - - +
442A LEU* 3.9 35.0 - - + +
443A PHE* 3.3 49.8 - - + +
446A LEU* 4.0 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ARG* 6.0 1.4 + - - -
346A ASP* 2.9 46.2 + - - +
347A ALA 3.3 4.5 - - - +
349A ILE* 1.3 78.0 - - + +
351A GLU* 1.3 62.4 + - - +
353A GLN* 3.2 3.9 + - - -
354A ARG* 3.1 18.4 + - - +
409A PHE* 3.7 29.0 - + + -
417A LYS* 3.6 23.3 - - + +
419A SER* 5.1 4.9 - - - -
422A PHE* 3.1 54.6 - + - -
439A ARG* 3.5 20.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A ALA 2.7 20.7 + - - +
348A VAL* 2.9 5.4 + - - +
350A HIS* 1.3 73.0 - - - +
352A ILE* 1.3 57.4 + - - +
354A ARG* 2.9 27.4 + - - -
355A PHE* 2.8 28.9 + - - +
403A VAL 3.1 6.2 - - - +
404A PHE* 3.6 16.1 - - + -
405A ASP 2.9 38.9 + - - +
406A PRO* 4.0 7.9 - - + -
408A HIS* 2.7 36.8 - - - +
409A PHE* 3.5 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A THR* 4.4 6.7 - - + +
306A SER* 3.4 44.9 - - - +
309A LEU* 3.9 9.4 - - + -
310A LEU* 5.2 6.3 - - + -
348A VAL* 2.8 32.1 + - + +
349A ILE* 3.6 14.4 - - + +
350A HIS 3.2 0.2 - - - -
351A GLU* 1.3 71.1 - - - +
353A GLN* 1.3 61.8 + - + +
355A PHE* 4.7 0.2 - - - -
356A ILE* 2.9 50.0 + - + +
404A PHE* 3.5 26.7 - - + -
442A LEU* 6.3 0.2 - - + -
446A LEU* 4.6 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A THR* 4.7 9.5 + - + +
349A ILE* 3.3 13.4 + - - +
350A HIS 3.2 7.9 + - - +
352A ILE* 1.3 75.1 - - + +
354A ARG* 1.3 66.1 + - - +
356A ILE* 4.0 7.1 - - + +
357A ASP* 3.4 18.5 + - - -
358A LEU 4.7 1.0 + - - -
392A LEU* 4.0 5.4 - - - +
422A PHE* 3.8 19.3 - - + -
424A PRO* 4.2 13.3 - - + +
425A PHE* 3.5 37.9 - - - -
439A ARG* 5.0 4.0 - - - +
442A LEU* 3.7 29.7 - - + +
501A HEM 3.8 23.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A HIS 3.1 12.8 + - - +
351A GLU* 2.9 44.3 + - - +
352A ILE 3.3 0.2 - - - -
353A GLN* 1.3 79.4 - - - +
355A PHE* 1.3 77.7 + - - +
357A ASP 3.6 3.5 + - - -
392A LEU* 2.8 57.9 + - + +
393A HIS* 3.2 28.9 + - - +
398A PHE* 3.5 39.7 - - + +
401A PRO* 2.7 41.6 + - - +
403A VAL 3.5 9.7 + - - -
408A HIS* 4.0 2.9 - - - -
409A PHE* 3.9 9.9 - - + -
422A PHE* 4.4 6.4 - - + -
424A PRO* 5.6 0.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
305A TYR* 5.1 4.0 - - - -
309A LEU* 4.0 25.8 - - + -
351A GLU* 2.8 19.5 + - - +
352A ILE 4.1 1.1 - - - +
354A ARG* 1.3 90.1 - - - +
356A ILE* 1.3 73.0 + - + +
357A ASP* 3.3 1.0 + - - +
393A HIS* 3.3 22.0 + + - -
401A PRO 4.5 1.3 - - - -
402A LYS* 3.5 26.5 - - - -
403A VAL 3.9 3.6 - - - -
404A PHE* 3.6 40.4 - + + -
466A ILE* 4.9 21.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
302A THR* 3.9 33.2 - - + +
305A TYR* 3.6 49.0 + - + -
309A LEU* 3.5 28.9 - - + -
352A ILE* 2.9 30.7 + - + +
353A GLN* 4.0 7.4 - - + +
355A PHE* 1.3 76.4 - - + +
357A ASP* 1.3 73.2 + - - +
358A LEU* 3.2 19.1 + - + +
475A SER* 4.0 11.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A GLN 3.4 8.0 + - - -
354A ARG 3.6 1.8 + - - +
355A PHE 3.2 2.3 - - - +
356A ILE* 1.3 79.8 - - - +
358A LEU* 1.3 64.3 + - - +
359A LEU 3.7 3.6 + - - +
360A PRO* 3.1 33.3 - - - +
388A LEU* 4.5 0.5 - - - +
389A THR* 2.7 39.8 + - - -
392A LEU* 3.6 23.1 - - + +
393A HIS* 3.8 21.6 + - + +
475A SER* 3.3 6.1 + - - -
----------------------------------------------------------
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