Contacts of the helix formed by residues 396 - 422 (chain A) in PDB entry 4IE6
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 TRP 396 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLY* 3.5 41.5 - - - -
104A CYS 3.9 9.0 - - - -
105A THR* 4.0 5.6 - - + -
114A PHE* 3.5 43.7 - + + +
115A THR* 2.9 27.0 + - - -
331A LEU* 4.2 12.6 - - + -
378A TRP* 3.9 13.5 - + - -
382A PHE* 3.5 25.6 - + + -
389A TYR* 5.5 7.2 - - + -
393A THR* 4.8 8.0 - - + +
394A ASP 3.1 0.8 - - - -
395A TRP* 1.3 98.4 - + + +
397A CYS* 1.3 59.3 + - - +
399A PRO* 3.4 15.0 - - + +
400A MET* 2.8 45.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A PHE* 5.1 4.7 - - - -
383A TRP* 6.5 0.4 - - - -
387A ASN* 5.9 4.9 - - - -
394A ASP* 3.0 24.4 + - + +
396A TRP* 1.3 78.6 - - - +
398A GLN* 1.3 59.8 + - - +
400A MET* 3.9 3.3 - - - +
401A ALA* 3.1 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A ASP 4.4 0.8 + - - -
395A TRP 4.4 0.4 + - - -
397A CYS* 1.3 76.5 - - - +
399A PRO* 1.3 92.9 - - + +
400A MET 3.0 0.2 + - - -
401A ALA* 3.1 8.1 + - + +
402A GLN* 2.9 49.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A LEU* 3.6 38.3 - - + +
335A LEU* 6.4 0.2 - - + -
395A TRP* 2.8 35.0 - - + +
396A TRP* 3.4 18.2 - - + +
398A GLN* 1.3 103.1 - - + +
400A MET* 1.3 56.0 + - - +
402A GLN* 3.3 7.4 + - + +
403A LEU* 3.0 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A PHE* 3.3 36.1 - - + -
378A TRP* 4.1 19.1 - - + +
379A LEU* 3.9 23.6 - - - +
382A PHE* 3.6 48.9 - - + -
383A TRP* 4.8 11.0 - - + +
396A TRP* 2.8 33.0 + - + +
397A CYS* 4.0 3.6 - - - +
399A PRO* 1.3 71.3 - - - +
401A ALA* 1.3 60.8 + - - +
402A GLN 3.2 1.3 - - - -
403A LEU* 3.9 11.6 - - + +
404A GLU* 2.9 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A CYS* 3.1 15.5 + - - +
398A GLN* 3.5 13.0 - - + +
400A MET* 1.3 78.7 - - - +
402A GLN* 1.3 56.6 + - - +
404A GLU* 3.3 7.2 + - - +
405A ALA* 3.0 28.2 + - - +
473A ARG* 5.8 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A LEU* 3.8 33.7 - - + +
398A GLN* 2.9 39.6 + - - +
399A PRO* 3.7 5.9 - - - +
401A ALA* 1.3 78.7 - - - +
403A LEU* 1.3 58.9 + - - +
405A ALA* 3.4 6.1 + - - +
406A LEU* 3.0 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A LEU* 3.9 17.0 - - + -
334A ILE* 4.1 22.2 - - + +
335A LEU* 3.6 26.9 - - + -
338A CYS* 4.2 19.3 - - - -
374A VAL* 3.9 13.2 - - + +
378A TRP* 4.5 9.4 - - + -
379A LEU* 4.0 10.4 - - + +
399A PRO* 3.0 22.2 + - + +
400A MET* 4.0 28.7 - - + +
402A GLN* 1.3 74.6 - - - +
404A GLU* 1.3 59.0 + - - +
406A LEU* 3.9 4.9 - - + +
407A TRP* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A LEU* 3.8 17.9 - - + +
383A TRP* 4.2 7.3 + - - -
400A MET 2.9 19.1 + - - +
401A ALA* 3.6 7.2 - - - +
402A GLN 3.2 0.2 - - - -
403A LEU* 1.3 75.9 - - - +
405A ALA* 1.3 58.4 + - - +
407A TRP* 3.3 15.5 + - + +
408A LYS* 2.9 25.3 + - + +
473A ARG* 2.8 46.2 + - - +
474A PRO* 4.1 18.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A ALA 3.0 16.4 + - - +
402A GLN* 3.7 7.4 - - - +
404A GLU* 1.3 74.4 - - - +
406A LEU* 1.3 65.9 + - + +
408A LYS* 3.2 7.8 + - - +
409A LYS* 3.1 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A LEU* 4.0 24.9 - - + +
338A CYS* 3.8 35.7 - - + -
339A GLN* 5.5 0.9 - - - +
342A LEU* 3.5 26.0 - - + +
402A GLN* 3.0 34.2 + - + +
403A LEU* 3.9 5.8 - - - +
405A ALA* 1.3 77.2 - - + +
407A TRP* 1.3 62.1 + - - +
409A LYS* 3.4 7.4 + - - +
410A MET* 3.1 29.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A HIS* 3.3 23.9 + + - -
374A VAL* 4.1 12.5 - - + +
375A GLU* 2.8 43.0 + - + -
379A LEU* 3.6 10.8 - - + -
403A LEU 3.0 19.0 + - - +
404A GLU* 3.4 14.4 - - + +
406A LEU* 1.3 74.1 - - - +
408A LYS* 1.3 78.4 + - + +
410A MET* 3.0 13.3 + - - +
411A GLU* 2.9 50.8 + - + -
449A ARG* 4.0 0.9 - - - -
474A PRO* 3.5 35.0 - - + -
476A TRP* 3.4 31.6 - + - -
483A MET* 3.8 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A GLU* 2.9 15.5 + - + +
405A ALA* 3.2 11.4 + - - +
407A TRP* 1.3 82.2 - - + +
409A LYS* 1.3 67.7 + - - +
411A GLU* 3.1 7.3 + - + +
412A GLY* 3.0 16.6 + - - -
482A SER 5.7 1.8 - - - +
483A MET* 4.2 27.4 - - + -
484A PRO* 5.3 5.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU* 3.7 31.2 - - + -
345A VAL* 4.7 12.6 - - + -
349A VAL 5.1 1.9 + - - -
350A ASP* 3.0 28.4 + - - +
351A ASN 2.7 33.5 + - - +
354A VAL* 3.7 25.4 - - + +
405A ALA 3.1 12.2 + - - +
406A LEU* 3.5 9.6 - - - +
408A LYS* 1.3 74.4 - - - +
410A MET* 1.3 54.5 + - - +
412A GLY* 2.7 23.9 + - - -
413A VAL* 2.9 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A CYS* 3.7 52.3 - - + +
341A ALA* 4.1 8.5 - - + -
342A LEU* 4.1 15.9 - - + -
367A GLY 4.9 1.3 - - - +
370A ILE* 4.1 7.9 - - + -
371A HIS* 3.5 46.3 + - + +
374A VAL* 4.2 11.0 - - - -
406A LEU* 3.1 17.8 + - + +
407A TRP* 3.0 8.8 + - - +
409A LYS* 1.3 72.6 - - - +
411A GLU* 1.3 67.1 + - - +
413A VAL* 2.9 20.5 + - + +
414A THR* 3.0 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A HIS* 2.6 30.6 + - - -
407A TRP* 2.9 39.3 + - + +
408A LYS 3.1 7.8 + - - +
410A MET* 1.3 73.3 - - - +
412A GLY* 1.3 62.9 + - - +
414A THR* 4.7 0.7 - - - -
415A ASN* 3.1 23.0 + - - +
445A ARG* 4.5 3.2 + - - -
449A ARG* 2.9 28.5 + - - -
476A TRP* 3.7 15.7 - - - -
483A MET* 3.9 10.7 - - + +
484A PRO* 4.0 16.4 - - + +
485A LEU* 3.5 26.0 - - + +
489A LEU* 5.4 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A VAL* 4.1 22.6 - - - +
408A LYS 3.0 7.6 + - - -
409A LYS* 2.7 11.3 + - - -
411A GLU* 1.3 77.4 - - - +
413A VAL* 1.3 60.5 - - - -
415A ASN* 3.3 8.3 + - - +
416A ALA* 3.0 20.6 + - - +
484A PRO* 4.2 11.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ALA 5.5 3.1 - - - +
342A LEU* 4.5 7.4 - - + -
344A ASN* 5.5 3.1 - - + +
345A VAL* 3.3 33.4 - - + -
354A VAL* 4.0 8.5 - - + +
356A LEU* 3.7 21.1 - - + -
364A LEU* 5.5 2.9 - - + -
367A GLY* 5.9 7.0 - - - -
368A GLU* 4.0 12.8 - - - +
409A LYS 2.9 15.5 + - - +
410A MET* 2.9 16.4 + - + +
412A GLY* 1.3 70.0 - - - +
414A THR* 1.3 68.8 + - - +
416A ALA* 2.9 15.3 + - - +
417A VAL* 2.9 15.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A GLU* 2.8 32.9 + - - +
371A HIS* 3.1 12.8 + - - -
410A MET 3.0 7.5 + - - -
411A GLU 3.9 0.7 - - - -
413A VAL* 1.3 74.5 - - - +
415A ASN* 1.3 64.2 + - - +
417A VAL* 2.9 6.7 + - + +
418A LEU* 2.9 33.6 + - + +
438A ILE* 6.4 1.3 - - + -
442A LEU* 6.2 2.9 - - + -
445A ARG* 3.1 23.2 + - - +
485A LEU* 3.7 19.5 - - + -
489A LEU* 6.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ASP 5.8 2.0 + - - -
411A GLU 3.1 11.9 + - - +
412A GLY* 3.3 10.5 + - - +
414A THR* 1.3 77.5 - - - +
416A ALA* 1.3 63.4 + - - +
418A LEU* 2.9 13.6 + - - +
419A HIS* 3.0 43.0 + - - -
484A PRO* 3.8 29.4 + - + +
485A LEU* 3.4 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A VAL 3.7 22.7 - - - +
355A SER* 5.3 0.2 - - - -
356A LEU* 3.7 23.8 - - + +
359A PHE* 4.4 3.4 - - + -
412A GLY 3.0 11.4 + - - +
413A VAL* 2.9 13.4 + - - +
415A ASN* 1.3 72.6 - - - +
417A VAL* 1.3 62.3 + - - +
419A HIS* 3.3 10.0 + - - +
420A GLU* 3.0 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LEU* 3.6 11.0 - - + -
359A PHE* 4.5 2.9 - - + -
364A LEU* 3.5 35.4 - - + -
368A GLU* 4.4 9.6 - - + +
413A VAL* 2.9 24.8 + - + +
414A THR* 2.9 8.7 + - + +
416A ALA* 1.3 75.2 - - - +
418A LEU* 1.3 63.4 + - + +
420A GLU* 3.3 7.6 + - + +
421A VAL* 3.0 21.8 + - + +
434A ILE* 3.8 26.7 - - + -
438A ILE* 4.0 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A THR* 2.9 26.2 + - + +
415A ASN* 2.9 9.1 + - - +
417A VAL* 1.3 80.3 - - + +
419A HIS* 1.3 65.1 + - + +
421A VAL* 3.5 11.6 + - + +
422A LYS* 3.4 30.3 + - + +
435A LEU* 6.0 2.2 - - + -
438A ILE* 4.6 19.1 - - + -
485A LEU* 3.7 28.0 - - + -
492A ILE* 4.6 21.5 - - + +
496A LEU* 6.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ASN* 3.0 42.5 + - - +
416A ALA* 3.7 10.8 - - - +
418A LEU* 1.3 77.7 + - + +
420A GLU* 1.3 64.9 + - - +
422A LYS* 3.1 20.9 + - - +
423A ARG* 3.4 10.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A PHE* 3.3 59.2 - - + +
416A ALA 3.0 7.2 + - - +
417A VAL 3.5 7.2 - - - +
419A HIS* 1.3 77.3 - - - +
421A VAL* 1.3 63.2 + - - +
423A ARG* 2.9 61.1 + - - +
426A LEU* 3.4 17.7 - - + +
434A ILE* 4.3 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A VAL* 3.0 18.8 + - + +
418A LEU* 3.8 13.5 - - + +
419A HIS 3.3 0.2 - - - -
420A GLU* 1.3 75.6 - - - +
422A LYS* 1.3 59.5 + - + +
423A ARG 3.3 3.7 + - - +
426A LEU* 4.1 9.7 - - - +
431A ARG* 3.7 27.6 - - + +
434A ILE* 3.3 40.4 - - + -
435A LEU* 3.8 28.0 - - + -
438A ILE* 5.0 2.9 - - + -
499A GLN* 4.3 17.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A LEU* 3.4 15.7 + - - +
419A HIS* 3.1 15.6 + - - +
420A GLU 3.1 1.0 - - - -
421A VAL* 1.3 82.9 - - + +
423A ARG* 1.3 60.7 + - - +
424A GLU* 3.8 1.4 + - - -
495A GLU* 4.1 25.8 + - - -
499A GLN* 5.3 7.4 - - - +
----------------------------------------------------------
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