Contacts of the helix formed by residues 396 - 418 (chain A) in PDB entry 3L7A
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 LEU 396 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A HIS 4.4 2.2 - - - +
202A PHE* 4.6 1.1 - - + -
215A TRP* 4.0 10.1 - - + -
293A LEU* 4.8 2.2 - - + -
297A TYR* 3.7 43.3 - - + -
344A LEU* 3.9 31.6 - - + -
392A LEU* 2.8 35.4 + - + +
395A LEU* 1.3 100.4 - - + +
397A PRO* 1.4 64.9 - - - +
398A ARG 3.3 2.2 - - - -
399A HIS* 3.1 33.1 + - + +
400A LEU 3.1 10.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A TYR 3.6 21.5 - - - +
204A GLY 3.8 15.5 - - - +
205A ARG* 4.2 6.5 - - - -
206A VAL* 4.0 11.7 - - + +
215A TRP* 3.7 11.9 - - + +
392A LEU 3.5 1.8 - - - +
393A GLU* 3.6 23.1 - - + +
394A THR 4.0 2.7 - - - +
395A LEU 3.5 6.5 - - - +
396A LEU* 1.4 88.9 - - - +
398A ARG* 1.3 61.4 + - - +
400A LEU* 3.6 5.0 + - + +
401A GLN* 3.4 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A VAL* 3.7 22.6 - - + +
208A HIS* 5.1 2.6 - - - -
213A ALA* 3.7 16.6 - - - +
214A LYS 5.9 0.2 - - - +
215A TRP* 4.4 23.0 - - + +
351A ARG* 4.0 20.6 - - + -
354A VAL* 4.5 10.3 - - - +
355A ASP* 2.8 43.8 + - - +
361A TRP* 5.4 4.4 - - - -
396A LEU 3.3 0.8 - - - -
397A PRO* 1.3 79.3 - - - +
399A HIS* 1.3 60.6 + - - +
401A GLN* 3.1 39.2 + - - +
402A ILE* 3.0 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A TRP* 3.9 10.6 - + - -
297A TYR* 3.3 36.7 - + - -
344A LEU* 4.7 13.0 - - + -
347A PRO* 4.0 15.2 - - + +
348A GLU* 2.7 44.3 + - + -
351A ARG* 3.7 19.4 - - + -
392A LEU* 5.7 1.3 - - + -
396A LEU* 3.1 30.7 + - + +
398A ARG* 1.3 74.9 - - - +
400A LEU* 1.3 59.6 + - - +
402A ILE* 3.2 7.8 + - - +
403A ILE* 2.9 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A VAL* 3.8 23.1 - - + -
392A LEU* 4.3 22.3 - - + +
393A GLU* 3.8 37.0 - - + +
396A LEU 3.1 11.3 + - - +
397A PRO* 3.8 8.7 - - + +
398A ARG 3.3 0.2 - - - -
399A HIS* 1.3 76.1 - - - +
401A GLN* 1.3 57.9 + - + +
403A ILE* 3.2 8.9 + - + +
404A TYR* 2.9 62.3 + - + +
439A ILE* 4.2 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A VAL* 3.6 39.8 - - - +
208A HIS* 4.1 15.4 + - - -
397A PRO* 3.4 10.6 + - - +
398A ARG* 3.1 32.7 + - - +
400A LEU* 1.3 77.9 - - + +
402A ILE* 1.3 63.1 + - - +
404A TYR* 3.4 12.3 + - + +
405A GLU* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A PRO* 3.8 26.0 - - + +
350A MET* 4.0 12.3 - - + -
351A ARG* 3.7 40.4 - - + +
354A VAL* 6.2 0.9 - - + -
361A TRP* 3.9 19.2 - - + -
398A ARG* 3.0 49.1 + - + +
399A HIS* 3.2 8.7 + - - +
401A GLN* 1.3 76.6 - - - +
403A ILE* 1.3 56.7 + - - +
405A GLU* 3.2 4.1 + - - +
406A ILE* 2.9 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU* 4.7 9.9 - - + -
347A PRO* 4.2 24.7 - - + -
392A LEU* 4.5 17.5 - - + -
399A HIS* 2.9 25.9 + - + +
400A LEU* 3.6 6.7 - - + +
402A ILE* 1.3 74.4 - - - +
404A TYR* 1.3 65.8 + - + +
406A ILE* 3.3 9.7 + - - +
407A ASN* 3.0 22.3 + - - +
430A LEU* 4.5 15.7 - - + +
431A VAL* 5.4 1.3 - - + -
439A ILE* 4.0 40.8 - - + -
441A MET* 5.0 1.6 - - + -
444A LEU* 4.4 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A VAL* 3.3 27.9 - - - +
393A GLU* 5.4 0.3 + - - -
400A LEU* 2.9 48.5 + - + +
401A GLN* 3.6 10.5 - - + +
403A ILE* 1.3 78.2 - - + +
405A GLU* 1.3 56.4 + - - +
407A ASN* 3.3 6.3 + - + +
408A GLN* 3.0 29.0 + - - +
431A VAL* 3.7 34.3 - - + -
437A LYS* 4.0 17.5 + - - -
439A ILE* 4.6 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A TRP* 3.6 32.8 - - + -
401A GLN 3.1 13.8 + - - +
402A ILE* 3.6 7.4 - - - +
404A TYR* 1.3 73.4 - - - +
406A ILE* 1.3 64.9 + - - +
408A GLN* 3.5 29.3 + - - +
409A ARG* 2.8 56.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ILE* 4.4 6.7 - - + -
347A PRO* 4.7 5.6 - - + -
350A MET* 4.8 1.8 - - + -
361A TRP* 3.9 15.9 - - + -
365A TRP* 3.7 45.5 - - + -
402A ILE* 2.9 34.6 + - + +
403A ILE* 3.3 10.1 + - - +
405A GLU* 1.3 75.8 - - - +
407A ASN* 1.3 57.7 + - - +
409A ARG* 3.4 3.7 + - - +
410A PHE* 2.9 29.2 + - + +
430A LEU* 4.0 18.2 - - + -
444A LEU* 4.1 20.2 - - + -
447A ALA* 4.7 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A ILE 3.0 13.3 + - - +
404A TYR* 3.5 13.0 + - - +
405A GLU 3.3 0.2 - - - -
406A ILE* 1.3 77.0 - - - +
408A GLN* 1.3 56.4 + - - +
410A PHE* 3.3 4.1 + - - +
411A LEU* 2.8 44.7 + - - +
429A SER* 3.3 22.0 + - - -
430A LEU* 2.8 45.4 + - + +
431A VAL* 3.8 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A TYR 3.0 17.8 + - - +
405A GLU* 3.8 30.9 + - - +
407A ASN* 1.3 76.3 - - - +
409A ARG* 1.3 60.5 + - - +
411A LEU* 3.9 5.3 - - - +
412A ASN* 3.1 46.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A TRP* 3.3 43.8 - - - +
362A ASP* 3.2 27.9 + - - -
405A GLU* 2.8 44.1 + - - +
406A ILE* 3.9 3.6 - - - +
408A GLN* 1.3 78.3 - - - +
410A PHE* 1.3 62.9 + - - +
412A ASN* 3.5 11.2 + - - +
413A ARG* 3.3 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A TRP* 6.2 2.5 - + + -
406A ILE* 2.9 20.2 + - + +
407A ASN* 3.7 4.9 - - - +
409A ARG* 1.3 73.7 - - - +
411A LEU* 1.3 70.7 + - + +
413A ARG* 3.1 39.0 + - - +
414A VAL* 3.1 34.5 + - + +
428A MET* 4.0 13.7 - - + -
430A LEU* 4.5 14.4 - - + -
447A ALA* 4.0 27.6 - - + -
471A PHE* 3.7 38.4 - + - -
474A LEU* 3.8 22.4 - - + -
475A GLU* 4.2 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ASN* 2.8 45.5 + - - +
408A GLN* 4.1 4.5 - - - +
410A PHE* 1.3 76.9 - - + +
412A ASN* 1.3 60.5 + - - +
414A VAL* 3.6 13.2 - - + +
415A ALA* 2.9 31.0 + - - +
425A LEU* 3.6 42.2 - - + +
428A MET* 4.3 6.3 - - + +
429A SER* 4.0 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A GLN* 3.1 35.7 + - - +
409A ARG* 3.6 11.3 - - - +
410A PHE 3.2 0.2 - - - -
411A LEU* 1.3 79.6 - - - +
413A ARG* 1.3 61.6 + - + +
415A ALA* 3.8 7.3 - - - +
416A ALA* 3.2 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A TRP* 5.9 4.0 - - - +
409A ARG 3.3 13.7 + - - +
410A PHE* 3.1 38.4 + - - +
412A ASN* 1.3 75.9 - - + +
414A VAL* 1.3 64.2 + - - +
416A ALA* 3.4 6.5 + - - +
417A ALA* 3.1 24.1 + - - +
447A ALA 5.5 2.4 + - - -
474A LEU* 4.3 16.1 - - + +
475A GLU* 3.2 30.3 + - - +
478A LYS* 5.2 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A PHE* 3.1 26.4 + - + +
411A LEU* 3.2 13.4 + - + +
413A ARG* 1.3 74.4 - - - +
415A ALA* 1.3 57.7 + - - +
417A ALA* 3.1 1.7 + - - -
418A PHE* 2.9 33.9 + - + +
421A ASP 5.8 0.2 - - - +
424A ARG* 4.0 18.4 - - + -
425A LEU* 3.7 19.5 - - + +
428A MET* 3.7 41.5 - - + -
474A LEU* 4.0 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A LEU 2.9 16.0 + - - +
412A ASN* 3.8 9.6 - - - +
413A ARG 3.3 0.2 - - - -
414A VAL* 1.3 76.8 - - - +
416A ALA* 1.3 59.2 + - - +
418A PHE 4.6 4.3 - - - -
419A PRO* 3.2 29.0 - - - +
420A GLY 5.9 0.4 - - - +
425A LEU* 3.8 21.1 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
412A ASN 3.2 16.8 + - - +
413A ARG* 3.8 7.4 - - - +
414A VAL 3.2 0.4 - - - -
415A ALA* 1.3 77.9 - - - +
417A ALA* 1.3 60.1 + - - +
419A PRO* 3.9 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ARG 3.1 16.7 + - - +
416A ALA* 1.3 77.4 - - - +
418A PHE* 1.3 85.6 + - + +
419A PRO* 3.5 6.8 - - - +
474A LEU* 3.7 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A VAL* 2.9 21.3 + - + +
415A ALA* 3.5 6.2 - - - +
417A ALA* 1.3 91.1 - - + +
419A PRO* 1.3 67.4 - - - +
420A GLY 3.3 0.3 + - - -
421A ASP* 3.1 24.5 + - + +
424A ARG* 3.6 60.3 - - - +
425A LEU* 6.1 0.5 - - - +
428A MET* 5.7 0.4 - - - -
473A GLU* 4.2 22.4 - - + -
474A LEU* 3.9 28.5 - - + -
----------------------------------------------------------
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