Contacts of the helix formed by residues 489 - 502 (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 LEU 489 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A GLU* 5.4 1.6 - - - +
418A LEU* 6.6 0.2 - - + -
442A LEU* 4.1 15.7 - - + +
445A ARG* 3.7 40.6 - - + +
446A GLN* 3.0 19.3 - - + +
449A ARG* 3.8 13.2 - - - +
485A LEU* 5.0 10.3 - - + -
486A PRO* 3.2 34.5 - - + +
488A ASP* 1.3 69.8 - - - +
490A THR* 1.3 63.9 + - - +
491A ASP 3.2 3.4 - - - -
492A ILE* 2.9 24.9 + - + +
493A VAL* 2.9 24.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A GLN* 3.4 20.0 + - - +
450A ARG* 5.5 2.6 - - - -
488A ASP* 2.9 20.7 + - - -
489A LEU* 1.3 76.6 - - - +
491A ASP* 1.3 65.4 + - - +
493A VAL* 4.1 5.2 - - - +
494A SER* 3.1 25.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A ASP 4.4 6.1 + - - +
489A LEU 3.2 1.2 - - - -
490A THR* 1.3 80.2 - - - +
492A ILE* 1.3 61.6 + - - +
494A SER* 2.4 24.3 + - - -
495A GLU* 3.1 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A LEU* 4.6 23.1 - - + -
485A LEU* 6.1 1.1 - - + -
486A PRO* 6.2 3.6 - - + -
489A LEU* 2.9 20.3 + - + +
491A ASP* 1.3 79.6 - - - +
493A VAL* 1.3 63.3 - - + +
495A GLU* 3.2 10.5 + - - +
496A LEU* 3.0 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A LEU* 4.1 13.5 - - + -
442A LEU* 4.1 30.7 - - + +
443A THR* 4.3 9.6 - - - +
446A GLN* 4.7 5.4 - - + -
489A LEU* 2.9 29.9 + - + +
490A THR* 4.1 5.8 - - - +
492A ILE* 1.3 72.3 - - + +
494A SER* 1.3 65.8 + - - +
496A LEU* 3.2 7.8 + - - +
497A ARG* 3.1 57.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A THR* 3.1 17.4 + - - -
491A ASP* 2.4 27.3 + - - -
493A VAL* 1.3 78.7 - - - +
495A GLU* 1.3 64.2 + - - +
497A ARG* 3.2 14.0 + - - +
498A GLY* 3.0 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A LYS* 4.1 23.7 + - - -
491A ASP 3.1 9.0 + - - +
492A ILE* 3.5 11.7 - - - +
494A SER* 1.3 81.9 + - - +
496A LEU* 1.3 61.9 + - - +
498A GLY* 3.2 3.3 + - - +
499A GLN* 3.1 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A LEU* 6.2 4.5 - - + -
435A LEU* 4.0 25.7 - - + +
438A ILE* 6.3 2.0 - - + -
439A LEU* 3.9 21.5 - - + -
492A ILE 3.0 12.9 + - - +
493A VAL* 3.2 9.4 + - - +
495A GLU* 1.3 77.1 - - - +
497A ARG* 1.3 61.9 + - - +
499A GLN* 3.4 13.8 + - - +
500A LEU* 3.1 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 497 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A LEU* 3.8 23.2 - - + +
443A THR* 3.1 30.7 + - - +
493A VAL* 3.1 36.2 + - - +
494A SER* 3.5 11.5 - - - +
496A LEU* 1.3 72.0 - - - +
498A GLY* 1.3 66.3 + - - +
499A GLN 3.0 2.0 - - - -
500A LEU* 2.9 19.1 + - - +
501A LEU* 2.9 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 498 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A SER 3.0 14.4 + - - -
495A GLU* 3.2 4.0 + - - -
497A ARG* 1.3 75.2 - - - +
499A GLN* 1.3 60.9 + - - +
501A LEU* 3.4 8.6 + - - +
502A GLU* 3.2 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 499 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A VAL* 4.3 17.9 - - - +
422A LYS* 5.3 9.5 - - - +
431A ARG* 2.4 49.1 + - - +
432A ASN* 4.5 0.2 + - - -
435A LEU* 4.0 10.1 - - + +
495A GLU* 3.1 33.4 + - + +
496A LEU* 3.4 12.7 - - - +
497A ARG 3.0 0.4 - - - -
498A GLY* 1.3 72.5 - - - +
500A LEU* 1.3 58.1 + - - +
501A LEU 3.0 1.8 - - - -
502A GLU* 2.7 51.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 500 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A ASN* 3.2 49.5 + - + +
435A LEU* 3.9 10.5 - - + -
436A THR* 3.6 26.7 - - + +
439A LEU* 4.3 21.5 - - + -
496A LEU 3.1 8.0 + - - +
497A ARG* 2.9 10.8 + - - +
499A GLN* 1.3 79.3 - - - +
501A LEU* 1.3 58.5 + - - +
502A GLU 3.4 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 501 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A ARG 2.9 11.4 + - - +
498A GLY* 3.7 11.0 - - - +
500A LEU* 1.3 75.5 - - - +
502A GLU* 1.3 67.5 + - - +
503A ALA* 3.4 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A ARG* 3.5 22.2 + - - +
498A GLY 3.2 16.3 + - - +
499A GLN* 2.7 43.4 + - - +
500A LEU 4.5 2.6 - - - +
501A LEU* 1.3 72.5 - - - +
503A ALA* 1.3 64.8 + - - +
----------------------------------------------------------
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