Contacts of the helix formed by residues 333 - 354 (chain A) in PDB entry 4DVQ
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 333 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A GLU* 2.8 47.2 + - - +
330A LEU* 3.2 6.3 - - - +
332A ARG* 1.3 88.9 + - - +
334A PRO* 1.4 59.3 - - - +
335A ASP* 3.2 14.1 - - - +
336A VAL* 2.9 20.0 + - + +
337A GLN 2.9 23.0 + - - -
422A ARG* 6.0 0.9 - - - +
423A TYR* 4.0 23.5 + - + +
106G LEU* 5.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU 3.6 6.0 - - - +
331A ALA 3.8 10.1 - - - +
332A ARG 3.3 9.2 - - - +
333A ASN* 1.4 89.3 - - - +
335A ASP* 1.3 54.3 + - - +
337A GLN* 3.2 10.5 + - + +
338A GLN* 2.8 31.6 + - - +
341A ARG* 5.0 1.4 + - - -
473A VAL 5.9 0.7 - - - +
478A GLN* 5.3 3.6 - - - +
280E PHE* 6.3 3.1 - - + -
106G LEU* 3.5 26.2 - - + -
107G HIS* 5.8 1.1 - - - +
138G ARG* 6.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ASN* 3.4 19.6 - - - +
334A PRO* 1.3 76.5 - - - +
336A VAL* 1.3 71.9 + - - +
338A GLN* 3.4 6.8 + - - +
339A ILE* 3.3 29.1 + - + +
106G LEU* 3.6 32.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU* 4.3 7.6 - - + -
333A ASN* 2.9 18.4 + - + +
335A ASP* 1.3 88.3 + - - +
337A GLN* 1.3 67.0 + - - +
339A ILE* 3.3 11.6 + - + +
340A LEU* 3.0 32.1 + - + +
423A TYR* 3.8 21.5 - - + +
424A ASN* 5.5 0.7 - - - -
425A PRO* 3.6 33.2 - - + -
426A GLN* 5.6 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU* 3.2 43.4 - - + +
331A ALA 4.0 0.2 + - - -
333A ASN 2.9 5.1 + - - -
334A PRO* 3.2 12.9 + - + +
336A VAL* 1.3 79.0 - - - +
338A GLN* 1.3 50.9 + - - +
340A LEU* 3.2 5.4 + - - +
341A ARG* 2.7 65.8 + - - +
468A LEU* 3.7 17.5 - - + +
471A PHE 3.9 1.2 + - - -
472A LEU* 3.5 2.2 - - - +
473A VAL* 2.9 52.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A PRO 2.8 16.8 + - - +
335A ASP* 3.7 8.1 - - - +
336A VAL 3.1 0.2 - - - -
337A GLN* 1.3 73.8 - - - +
339A ILE* 1.3 61.3 + - + +
341A ARG* 2.8 41.3 + - - +
342A GLN* 2.9 37.7 + - - +
345A LEU* 6.1 1.6 - - - +
472A LEU* 4.6 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A ASP* 3.3 16.7 + - + +
336A VAL* 3.6 14.4 - - + +
338A GLN* 1.3 77.7 - - + +
340A LEU* 1.3 64.9 + - + +
342A GLN* 3.2 17.0 + - - +
343A GLU* 3.2 11.4 + - - +
364A LEU* 4.1 26.7 - - + -
426A GLN* 3.8 28.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU* 3.4 39.3 - - + -
336A VAL* 3.0 23.2 + - + +
337A GLN 3.5 5.4 - - - +
339A ILE* 1.3 76.5 - - + +
341A ARG* 1.3 61.6 + - - +
343A GLU* 3.4 7.8 + - - +
344A SER* 3.2 25.8 + - - -
364A LEU* 3.4 46.7 - - + +
365A LEU* 3.4 16.6 - - + +
368A ALA* 4.0 15.7 - - + -
425A PRO* 5.1 3.4 - - + -
468A LEU* 3.7 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A PRO 5.0 1.0 + - - -
337A GLN* 2.7 48.2 + - - +
338A GLN* 2.8 38.0 + - - +
340A LEU* 1.3 72.0 - - - +
342A GLN* 1.3 65.2 + - - +
344A SER* 3.2 1.4 + - - +
345A LEU* 3.0 40.0 + - + +
468A LEU* 3.3 41.8 + - + +
471A PHE 2.8 28.5 + - - -
472A LEU* 3.0 24.2 - - - +
502A ILE* 3.7 18.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A GLN* 2.9 22.7 + - - +
339A ILE* 3.2 10.3 + - - +
341A ARG* 1.3 74.8 - - - +
343A GLU* 1.3 58.4 + - - +
345A LEU* 3.8 7.2 - - + +
346A ALA* 2.8 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ILE 3.2 11.1 + - - +
340A LEU* 3.6 10.3 - - - +
341A ARG 3.1 0.4 - - - -
342A GLN* 1.3 79.6 - - - +
344A SER* 1.3 62.0 + - - +
346A ALA* 3.7 5.4 - - - +
347A ALA* 3.3 23.4 + - - +
361A GLU 3.9 10.8 - - - +
362A LEU* 3.6 17.7 - - + +
363A PRO* 3.0 16.5 - - - +
364A LEU* 2.8 41.3 + - + +
365A LEU* 3.0 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A LEU 3.2 16.7 + - - -
341A ARG 3.2 2.4 + - - -
343A GLU* 1.3 77.7 + - - +
345A LEU* 1.3 60.2 + - - +
347A ALA 3.3 0.2 + - - -
348A ALA* 2.9 30.7 + - - +
362A LEU* 3.8 12.4 - - - +
365A LEU* 4.0 13.9 - - - +
465A HIS* 3.1 41.8 + - - -
468A LEU* 4.5 10.0 - - - +
469A LYS* 4.5 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A GLN* 6.1 1.6 - - - +
341A ARG* 3.0 42.3 + - + +
342A GLN* 4.0 6.1 - - + +
344A SER* 1.3 76.7 - - - +
346A ALA* 1.3 62.6 + - - +
347A ALA 2.9 1.7 + - - -
348A ALA* 3.2 18.0 + - + +
349A ALA 4.6 0.9 + - - -
469A LYS* 4.0 33.4 - - + +
502A ILE* 5.5 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A GLN* 2.8 33.5 + - - +
343A GLU* 3.7 7.6 - - - +
345A LEU* 1.3 76.3 - - - +
347A ALA* 1.3 58.0 + - + +
348A ALA 3.6 0.2 - - - -
349A ALA* 5.3 1.6 + - - +
----------------------------------------------------------
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 GLU 3.3 18.7 + - - +
344A SER 3.6 1.6 - - - +
345A LEU 3.0 0.4 - - - -
346A ALA* 1.3 77.0 - - + +
348A ALA* 1.3 64.3 + - - +
349A ALA 3.3 2.5 - - - -
350A SER* 3.1 22.9 + - - +
351A ILE* 3.2 16.2 + - + +
361A GLU* 4.1 30.5 - - + +
362A LEU* 4.2 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A SER 2.9 15.9 + - - +
345A LEU* 3.2 13.8 + - + +
347A ALA* 1.3 77.9 - - - +
349A ALA* 1.3 58.8 + - - +
351A ILE* 3.2 2.3 + - - +
352A SER* 2.8 33.9 + - - +
465A HIS* 4.3 10.2 + - - -
469A LYS* 3.6 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A LEU 4.6 1.0 + - - -
346A ALA 5.3 2.4 + - - +
347A ALA 3.3 0.4 - - - -
348A ALA* 1.3 79.6 - - - +
350A SER* 1.3 63.4 + - - +
352A SER* 3.2 16.6 + - - -
353A GLU* 3.3 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A ALA* 3.1 21.2 + - - -
349A ALA* 1.3 77.9 - - - +
351A ILE* 1.3 56.9 + - - +
353A GLU* 3.5 5.6 + - - +
354A HIS 3.0 25.7 + - - +
357A LYS* 3.3 36.7 + - - +
361A GLU* 3.6 17.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ASP* 4.8 5.2 - - - +
166A ARG* 3.7 6.1 + - - +
347A ALA* 3.2 21.1 + - + +
348A ALA 3.2 5.6 + - - +
350A SER* 1.3 74.7 - - - +
352A SER* 1.3 67.0 + - - +
354A HIS 3.6 4.7 - - - -
355A PRO* 3.1 31.6 - - + +
357A LYS* 4.4 4.9 - - + -
358A ALA* 3.8 37.9 - - + +
361A GLU* 4.7 2.9 - - + -
362A LEU* 3.8 24.7 - - + -
462A LEU* 4.8 4.9 - - + -
465A HIS* 3.6 34.8 - - + +
466A HIS* 5.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ARG* 3.6 31.4 + - - +
348A ALA 2.8 14.9 + - - -
349A ALA* 3.2 10.5 + - - -
351A ILE* 1.3 79.2 - - - +
353A GLU* 1.3 60.8 + - - +
355A PRO* 4.4 4.2 - - - +
469A LYS* 4.4 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ALA 3.3 11.5 + - - +
350A SER* 3.9 8.8 - - - +
352A SER* 1.3 79.1 - - - +
354A HIS* 1.3 88.9 + - + +
355A PRO* 4.0 3.9 - - - +
357A LYS* 5.0 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A SER 3.0 15.8 + - - +
351A ILE* 3.2 7.5 - - - +
353A GLU* 1.3 104.8 + - + +
355A PRO* 1.3 70.6 - - + +
356A GLN* 3.1 13.9 - - + +
357A LYS* 3.1 44.5 + - + +
----------------------------------------------------------
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