Contacts of the helix formed by residues 400 - 413 (chain A) in PDB entry 4I5L
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 400 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A LEU* 4.1 27.8 - - + -
369A PHE* 3.7 33.0 - - + -
370A LEU* 5.3 2.9 - - + -
388A LEU* 5.3 1.8 - - + -
391A VAL* 4.3 29.8 - - + -
395A ILE* 4.4 12.1 - - + -
396A GLY 4.0 9.2 - - - +
397A ILE* 3.1 11.0 + - + +
399A GLN* 1.3 83.7 - - + +
401A SER* 1.3 56.4 + - - +
402A GLN* 3.1 10.3 - - - +
403A SER* 2.8 29.7 + - - +
404A LEU* 3.0 26.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A ILE 3.4 4.2 + - - -
398A ARG* 2.7 37.8 + - - +
399A GLN 3.6 0.4 - - - -
400A LEU* 1.3 76.2 - - - +
402A GLN* 1.3 58.0 + - - +
404A LEU* 3.9 9.5 - - - +
405A LEU* 2.9 33.8 + - - +
434A LEU* 3.9 11.8 - - - +
438A PHE* 3.7 31.0 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
398A ARG 4.5 2.3 - - - +
399A GLN* 2.8 32.8 + - - +
400A LEU* 3.0 11.1 + - - +
401A SER* 1.3 79.1 + - - +
403A SER* 1.3 77.2 + - - +
405A LEU* 4.6 3.3 - - - +
406A PRO* 3.1 21.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A PHE* 4.8 2.7 - - - -
370A LEU* 3.4 31.9 - - - +
373A LEU* 3.4 20.4 - - - +
400A LEU* 2.8 8.0 + - - -
402A GLN* 1.3 97.0 + - - +
404A LEU* 1.3 62.5 + - - +
405A LEU 3.3 0.4 - - - -
406A PRO* 3.5 14.9 - - - +
407A ALA* 3.9 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A PHE* 3.9 13.2 - - + -
373A LEU* 3.8 28.7 - - + -
385A ILE* 4.0 13.7 - - + -
388A LEU* 4.3 27.4 - - + -
397A ILE* 4.4 10.3 - - + -
400A LEU* 3.0 46.2 + - + +
401A SER* 3.3 7.4 + - - +
403A SER* 1.3 77.6 - - - +
405A LEU* 1.3 58.1 + - - +
407A ALA* 3.2 4.5 + - - +
408A ILE* 2.8 46.6 + - + +
430A LEU* 5.6 1.8 - - + -
434A LEU* 5.1 5.8 - - + -
438A PHE* 6.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A SER 2.9 16.2 + - - +
402A GLN* 4.6 3.4 - - - +
404A LEU* 1.3 75.5 - - - +
406A PRO* 1.4 71.2 - - + +
408A ILE* 3.1 7.3 + - - -
409A VAL* 2.9 41.7 + - + +
438A PHE* 4.4 11.2 - - + -
442A LYS* 3.5 53.8 - - + +
443A LEU* 4.0 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A GLN 3.1 21.5 - - - +
403A SER* 3.5 11.7 - - - +
405A LEU* 1.4 93.6 - - + +
407A ALA* 1.3 56.5 + - - +
409A VAL* 3.9 7.8 - - + +
410A GLU* 3.0 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A LEU* 3.8 45.5 - - + +
381A ARG* 4.7 6.9 + - - +
385A ILE* 4.0 9.2 - - + -
403A SER 3.9 3.6 - - - +
404A LEU 3.2 8.5 + - - +
405A LEU 3.2 0.6 - - - -
406A PRO* 1.3 80.1 - - - +
408A ILE* 1.3 63.5 + - - +
410A GLU* 3.4 6.3 + - - +
411A LEU* 3.2 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ILE* 4.2 16.6 - - + -
404A LEU* 2.8 41.6 + - + +
405A LEU* 3.6 6.5 - - + +
407A ALA* 1.3 76.2 - - - +
409A VAL* 1.3 63.2 + - - +
411A LEU* 3.3 4.3 + - - +
412A ALA* 2.9 22.1 + - + +
423A ILE* 4.4 10.7 - - + +
427A MET* 4.0 21.8 - - + -
430A LEU* 4.2 24.0 - - + -
434A LEU* 4.5 16.8 - - + -
438A PHE* 5.9 0.7 - - + -
443A LEU* 4.1 12.8 - - + -
446A LEU* 4.0 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A LEU* 2.9 38.3 + - + +
406A PRO* 3.9 7.4 - - + +
408A ILE* 1.3 75.9 - - - +
410A GLU* 1.3 63.3 + - - +
412A ALA* 3.1 12.5 + - - +
413A GLU* 3.3 37.7 + - - +
442A LYS 5.6 0.9 - - - +
446A LEU* 4.1 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ARG* 3.3 33.7 + - - +
406A PRO* 3.0 22.1 + - - +
407A ALA* 3.9 2.9 - - - +
408A ILE 3.3 0.2 - - - -
409A VAL* 1.3 78.1 - - - +
411A LEU* 1.3 61.1 + - - +
413A GLU* 3.5 4.7 + - - +
414A ASP* 3.3 21.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
378A PRO* 3.8 24.2 - - + +
381A ARG* 3.9 26.0 - - + +
382A LEU* 3.9 23.8 - - + -
385A ILE* 3.7 30.5 - - + -
407A ALA 3.2 11.0 + - - +
408A ILE 3.7 6.1 - - - +
410A GLU* 1.3 73.8 - - - +
412A ALA* 1.3 63.7 + - - +
413A GLU 3.1 1.7 + - - -
414A ASP* 3.3 18.3 + - - +
419A VAL* 3.7 23.9 - - + +
420A ARG* 3.9 6.9 - - - -
423A ILE* 3.7 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ILE* 2.9 13.7 + - + +
409A VAL 3.1 9.4 + - - +
411A LEU* 1.3 76.9 - - - +
413A GLU* 1.3 62.4 + - + +
414A ASP 3.5 0.2 - - - -
420A ARG* 3.2 14.5 - - - +
423A ILE* 3.8 10.5 - - + +
446A LEU* 3.9 21.5 - - + -
450A TRP* 3.0 46.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A VAL* 3.3 35.0 + - - +
410A GLU* 3.5 6.1 + - - +
412A ALA* 1.3 82.8 - - + +
414A ASP* 1.3 66.9 + - - +
415A ALA* 3.4 2.8 + - - -
420A ARG* 4.2 3.6 - - - +
446A LEU* 4.3 10.7 - - + +
----------------------------------------------------------
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