Contacts of the helix formed by residues 345 - 363 (chain A) in PDB entry 3DYQ
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 PRO 345 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ASN 4.0 4.9 - - - +
344A ILE* 1.3 93.7 - - + +
346A PRO* 1.3 77.5 - - + +
347A ASP* 4.5 6.3 - - + +
348A GLY* 2.9 9.0 + - - +
349A PHE* 2.9 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ILE 3.8 1.1 - - - +
345A PRO* 1.3 87.8 - - + +
347A ASP* 1.3 58.3 + - - +
349A PHE* 3.1 10.0 + - + +
350A LYS* 2.8 50.6 + - - +
308B ARG* 4.4 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A PRO* 3.1 5.2 + - + +
346A PRO* 1.3 78.8 - - - +
348A GLY* 1.3 57.2 + - - +
350A LYS* 3.4 18.2 + - - +
351A GLN* 3.0 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A THR* 6.1 1.6 - - - -
344A ILE* 3.8 11.2 - - - -
345A PRO* 2.9 11.9 + - - +
347A ASP* 1.3 74.9 - - - +
349A PHE* 1.3 66.3 + - - +
351A GLN* 3.0 12.8 + - - +
352A ILE* 2.9 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A PHE* 4.1 28.3 - + - -
333A LEU* 5.5 4.3 - - + -
339A ASN* 5.3 6.1 - - - -
341A PHE* 3.9 39.5 - + + +
344A ILE* 3.7 9.0 - - + +
345A PRO 2.9 12.8 + - - +
346A PRO* 3.1 12.5 + - + +
348A GLY* 1.3 76.9 - - - +
350A LYS* 1.3 57.8 + - + +
352A ILE* 3.2 8.2 + - - +
353A ARG* 2.8 56.8 + - - +
308B ARG* 3.6 44.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A PRO* 2.8 37.2 + - - +
347A ASP* 3.7 17.7 + - - +
349A PHE* 1.3 83.4 - - + +
351A GLN* 1.3 60.9 + - - +
353A ARG* 3.8 6.5 - - - +
354A GLN* 3.1 25.8 + - - +
305B ILE* 6.0 6.1 - - + -
306B ASN* 4.9 15.0 - - - +
308B ARG* 5.0 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A SER* 5.5 0.5 + - - -
280A THR* 3.5 27.0 + - + +
281A ASP* 5.6 1.0 - - - +
284A ILE* 3.9 5.9 - - + +
347A ASP* 3.0 15.9 + - - +
348A GLY* 3.4 14.4 - - - +
350A LYS* 1.3 77.0 - - - +
352A ILE* 1.3 61.9 + - - +
354A GLN* 3.6 4.8 + - - +
355A GLY* 3.1 19.8 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
228A PHE* 5.0 3.1 - - + -
280A THR* 4.1 20.2 - - + -
283A LEU* 3.8 18.8 - - + -
284A ILE* 3.9 15.1 - - + +
341A PHE* 3.7 32.1 - - + -
344A ILE* 3.8 33.0 - - + -
348A GLY* 2.9 26.8 + - - +
349A PHE* 3.6 6.3 - - - +
351A GLN* 1.3 73.1 - - - +
353A ARG* 1.3 62.1 + - - +
355A GLY* 3.2 1.6 + - - -
356A MET* 2.8 49.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A PHE* 3.1 60.8 - - + +
349A PHE* 2.8 40.0 + - + +
350A LYS* 3.8 8.1 - - - +
351A GLN 3.3 0.2 - - - -
352A ILE* 1.3 77.4 - - - +
354A GLN* 1.3 64.9 + - - +
356A MET* 3.7 1.7 - - - +
357A ILE* 2.9 42.1 + - + +
312B ALA* 3.3 18.0 + - - +
313B VAL* 3.9 15.0 - - - +
316B ASN* 3.6 11.3 + - - +
317B ASP* 2.8 42.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
350A LYS 3.1 15.1 + - - +
351A GLN* 3.8 5.4 - - - +
353A ARG* 1.3 79.5 - - - +
355A GLY* 1.3 64.5 + - - +
357A ILE* 3.2 14.2 + - - +
358A THR* 2.9 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ILE* 3.6 21.3 - - - -
351A GLN 3.1 14.9 + - - -
352A ILE 3.6 2.9 - - - -
354A GLN* 1.3 78.1 - - - +
356A MET* 1.3 63.2 + - - +
358A THR* 3.2 6.5 + - - -
359A LEU* 2.9 29.0 + - - +
394A LYS* 5.5 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ILE* 4.2 22.2 - - + +
287A THR* 3.7 42.4 - - + +
288A ALA* 4.3 5.6 - - + +
291A CYS* 4.5 7.9 - - - -
329A ALA* 4.8 1.6 - - + -
330A PHE* 3.9 27.8 - - + -
333A LEU* 4.5 6.7 - - + -
341A PHE* 4.2 5.2 - - - -
352A ILE* 2.8 39.8 + - + +
353A ARG 3.7 3.8 - - - +
355A GLY* 1.3 72.7 - - - +
357A ILE* 1.3 61.9 + - - +
359A LEU 3.2 0.2 + - - -
360A ILE* 2.8 50.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A CYS* 3.6 22.4 - - - -
330A PHE* 4.2 5.8 - - + -
353A ARG* 2.9 53.8 + - + +
354A GLN* 3.2 13.7 + - - +
356A MET* 1.3 75.5 - - - +
358A THR* 1.3 64.1 + - - +
360A ILE* 4.2 0.2 - - - +
361A LEU* 3.0 46.7 + - + +
316B ASN* 3.5 41.5 - - + +
317B ASP* 4.7 3.1 - - + +
318B ILE* 4.6 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A GLN* 2.9 34.4 + - - +
355A GLY* 3.2 9.6 + - - -
357A ILE* 1.3 77.4 - - - +
359A LEU* 1.3 61.5 + - + +
361A LEU* 3.8 6.3 - - - +
362A ALA* 3.0 25.8 + - - +
367A ARG* 5.1 1.6 + - - -
391A THR* 3.9 17.1 - - + +
395A MET* 3.9 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ILE* 3.8 22.0 - - + -
285A LEU* 3.9 34.1 - - + -
288A ALA* 3.9 13.9 - - + -
355A GLY* 2.9 19.8 + - - +
356A MET 3.9 2.2 - - - +
358A THR* 1.3 80.2 - - + +
360A ILE* 1.3 66.7 + - - +
362A ALA* 2.9 19.3 + - - +
363A THR* 3.5 10.0 + - - +
391A THR* 4.3 3.1 - - + +
394A LYS* 3.7 16.6 - - + +
395A MET* 3.6 36.6 - - + +
398A ILE* 3.7 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ALA* 4.0 25.8 - - + +
291A CYS* 4.3 22.0 - - + +
292A HIS* 3.9 23.6 - - + +
322A GLU* 3.6 27.4 - - + +
325A HIS* 4.1 4.9 - - + -
326A CYS* 3.9 27.8 - - + -
329A ALA* 4.8 2.0 - - + -
356A MET* 2.8 36.8 + - + +
357A ILE 4.2 1.3 - - - +
359A LEU* 1.3 71.1 - - - +
361A LEU* 1.3 60.9 + - - +
363A THR* 2.7 30.9 + - - -
398A ILE* 4.7 1.3 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
319A SER* 4.5 9.0 + - - +
322A GLU* 3.9 10.9 - - + +
323A ASN* 3.7 46.0 - - - +
326A CYS* 5.3 2.0 - - + -
357A ILE* 3.0 41.1 + - + +
358A THR* 3.9 5.6 - - - +
360A ILE* 1.3 76.8 - - + +
362A ALA* 1.3 59.7 + - - +
363A THR 3.1 1.5 + - - -
364A ASP* 3.4 19.1 + - - +
367A ARG* 3.4 19.2 + - - +
316B ASN* 5.2 1.1 - - - +
318B ILE* 3.8 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A THR 3.0 17.9 + - - +
359A LEU* 2.9 10.1 + - - +
361A LEU* 1.3 77.0 - - - +
363A THR* 1.3 58.7 + - - +
364A ASP 3.2 6.5 + - - +
367A ARG* 3.9 9.2 - - - +
371A ILE* 3.3 27.0 - - + +
395A MET* 3.7 35.2 - - + +
398A ILE* 4.8 2.0 - - + -
399A LYS* 3.6 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A HIS* 4.4 19.1 + - + -
322A GLU* 3.8 11.5 - - - +
359A LEU 3.6 14.6 - - - +
360A ILE* 2.7 18.4 + - - +
361A LEU 3.1 0.6 - - - -
362A ALA* 1.3 76.5 - - - +
364A ASP* 1.3 63.7 + - - +
365A MET* 3.1 8.0 + - - +
398A ILE* 4.0 33.0 - - + +
399A LYS* 4.5 7.4 + - - +
402A ASP* 3.9 20.1 - - + +
900A PCG 3.9 15.1 + - - +
902A NA 4.1 7.2 - - - -
----------------------------------------------------------
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