Contacts of the helix formed by residues 518 - 526 (chain D) in PDB entry 2IHU
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 ASP 518 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524C GLU 5.4 0.7 - - - +
525C ALA* 2.8 22.5 + - - +
516D GLY 4.3 0.4 - - - -
517D VAL* 1.3 73.3 - - - +
519D PHE* 1.3 56.4 + - - +
520D VAL* 3.2 14.3 + - - +
521D ALA* 3.2 31.2 + - + +
522D LEU* 2.9 26.2 + - - +
556D GLU* 4.0 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 519 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ARG* 5.0 0.7 - - - -
463D ASP* 3.6 42.0 - - + -
466D PHE* 3.7 32.8 - + - -
467D HIS* 4.0 18.8 - - + -
473D LEU* 5.5 0.2 - - - +
487D VAL* 4.1 12.1 - - + -
489D ASN* 3.8 8.7 - - - -
517D VAL* 3.4 38.8 + - + -
518D ASP* 1.3 70.1 - - - +
520D VAL* 1.3 59.6 + - - +
522D LEU* 3.6 14.9 - - + +
523D ALA* 3.0 29.3 + - - +
554D LEU* 3.5 19.1 - - + +
556D GLU* 2.8 27.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 520 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518D ASP* 3.2 8.3 + - - +
519D PHE* 1.3 76.6 - - - +
521D ALA* 1.3 63.3 + - - +
523D ALA* 3.3 3.6 + - - +
524D GLU* 3.1 36.9 + - - +
530D ALA* 3.6 29.1 - - + +
531D THR* 3.5 32.3 - - - +
532D ARG* 3.7 11.0 - - + +
554D LEU* 4.6 0.2 - - - -
556D GLU* 3.9 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 521 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521C ALA* 4.4 9.7 - - + +
525C ALA* 3.8 16.8 - - + +
518D ASP* 3.2 25.7 + - + +
520D VAL* 1.3 77.4 - - - +
522D LEU* 1.3 60.5 + - - +
524D GLU* 3.4 7.9 + - - +
525D ALA* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 522 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522C LEU* 3.7 24.2 - - + -
525C ALA* 3.6 10.0 - - + +
526C ASN* 3.8 22.0 - - - +
466D PHE* 4.5 0.2 - - + -
467D HIS* 3.7 30.3 - - + +
470D SER* 3.7 19.5 - - - +
473D LEU* 4.3 10.1 - - + -
517D VAL* 4.7 2.2 - - + -
518D ASP 2.9 17.4 + - - +
519D PHE* 3.6 24.0 - - + +
520D VAL 3.3 0.2 - - - -
521D ALA* 1.3 73.6 - - - +
523D ALA* 1.3 63.2 + - - +
525D ALA* 3.3 10.7 + - - +
526D ASN* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 523 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473D LEU* 3.9 13.2 - - + +
519D PHE 3.0 18.8 + - - +
520D VAL 3.3 4.7 + - - +
522D LEU* 1.3 75.3 - - - +
524D GLU* 1.3 58.0 + - - +
526D ASN* 3.0 15.6 + - - +
527D GLY 3.3 0.3 + - - -
528D VAL* 2.9 37.8 + - + +
530D ALA* 3.7 13.5 - - + -
554D LEU* 3.8 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 524 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518C ASP* 5.4 0.7 - - - +
520D VAL* 3.1 24.7 + - - +
521D ALA* 4.0 7.1 - - - +
522D LEU 3.3 0.2 - - - -
523D ALA* 1.3 72.7 - - - +
525D ALA* 1.3 65.2 + - - +
527D GLY* 3.1 12.9 + - - -
528D VAL 3.3 15.9 - - - +
529D ASP* 3.9 10.5 - - - +
530D ALA 3.4 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 525 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516C GLY 4.0 1.2 - - - +
517C VAL* 3.4 6.8 - - - -
518C ASP* 2.8 55.2 + - - +
521C ALA* 3.9 7.3 - - + +
522C LEU* 3.6 25.8 - - + +
521D ALA 2.9 18.3 + - - +
522D LEU 3.6 6.5 - - - +
523D ALA 3.3 0.2 - - - -
524D GLU* 1.3 76.3 - - - +
526D ASN* 1.3 57.2 + - - +
527D GLY 3.3 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 526 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C HIS* 2.8 29.1 + - - -
516C GLY 4.1 12.2 - - - +
517C VAL* 4.3 3.3 - - - +
522C LEU* 3.6 19.3 - - - +
470D SER 4.6 2.2 + - - -
471D SER* 3.5 1.6 - - - +
473D LEU* 3.7 30.9 - - + +
474D GLU* 3.4 25.3 + - - +
477D ALA* 3.6 16.6 - - - +
522D LEU* 2.9 23.8 + - - +
523D ALA 3.0 9.7 + - - +
525D ALA* 1.3 76.6 - - - +
527D GLY* 1.3 61.2 + - - +
528D VAL* 4.6 0.7 - - + -
----------------------------------------------------------
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