Contacts of the strand formed by residues 353 - 359 (chain D) in PDB entry 1D00
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 VAL 353 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C ARG* 5.6 0.2 - - - +
386C TYR* 3.9 15.6 + - + -
349D THR* 2.9 26.3 + - - +
351D ASP* 3.1 26.6 + - - +
352D GLY* 1.3 81.0 - - - +
354D PHE* 1.3 63.9 + - - +
355D ILE* 5.2 0.2 - - + -
493D LYS* 4.1 25.6 - - - +
494D ALA 3.6 4.3 - - - +
495D ILE* 4.6 17.7 - - + -
496D VAL 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 354 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C TYR* 3.5 13.0 - - - -
347D ALA* 4.0 20.6 - - + -
349D THR* 4.1 4.3 - - + -
353D VAL* 1.3 75.7 - - - +
355D ILE* 1.3 67.2 + - - +
356D TRP* 3.5 25.4 - + + -
378D SER* 3.9 17.0 - - - -
379D PRO* 3.6 33.9 - - + -
380D ALA 4.5 3.4 - - - -
381D PHE* 3.4 53.4 - + + -
392D LEU* 4.1 13.0 - - + -
492D ILE 3.8 0.3 - - - +
493D LYS* 3.2 5.7 - - - +
494D ALA* 2.8 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 355 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C TYR* 2.9 60.1 + - + -
418C ASN* 4.2 9.9 - - - +
421C LEU* 4.8 7.0 - - + -
353D VAL* 5.2 0.7 - - + -
354D PHE* 1.3 84.6 - - - +
356D TRP* 1.3 62.8 + - - +
357D LYS* 3.9 1.8 + - + +
435D LEU* 4.6 10.8 - - + -
491D PHE* 3.9 30.5 - - + -
492D ILE 3.3 6.3 - - - +
493D LYS* 3.8 33.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 356 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354D PHE* 3.5 17.5 - + + -
355D ILE* 1.3 71.8 - - - +
357D LYS* 1.3 72.2 + - - +
358D ILE* 3.6 27.0 + - + +
376D ILE* 3.9 16.8 - - + -
377D PHE 3.6 8.3 + - - -
378D SER* 3.3 38.8 - - - +
379D PRO* 3.8 21.8 - - + +
392D LEU* 4.1 16.8 - - + -
394D ILE* 3.5 38.6 - - + -
409D LEU* 6.0 0.9 - - + -
490D ILE 3.7 0.2 - - - +
491D PHE* 3.4 3.1 - - - -
492D ILE* 2.5 61.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 357 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C PRO* 3.2 39.5 + - + +
418C ASN* 5.5 1.1 - - - +
355D ILE* 3.9 3.7 + - + +
356D TRP* 1.3 80.1 + - - +
358D ILE* 1.3 60.9 + - - +
359D SER* 3.6 24.4 + - - +
489D ALA* 4.3 14.6 - - + -
490D ILE 3.5 7.4 - - - +
491D PHE* 3.7 28.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 358 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356D TRP* 3.8 54.7 - - + +
357D LYS* 1.3 73.5 - - - +
359D SER* 1.3 66.6 + - - +
361D PHE* 4.2 14.7 - - + +
364D LYS* 4.1 18.4 - - + +
376D ILE* 5.3 4.7 - - + -
394D ILE* 4.1 17.7 - - + -
396D LEU* 5.1 8.1 - - + -
489D ALA* 3.2 6.0 - - - -
490D ILE* 2.9 45.4 + - + +
492D ILE* 4.1 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 359 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357D LYS* 3.6 30.0 + - - +
358D ILE* 1.3 71.4 - - - +
360D ASP* 1.3 67.2 + - - +
361D PHE 3.0 4.0 + - - -
364D LYS* 2.7 34.8 + - - +
488D ASP 3.9 7.0 - - - -
489D ALA* 4.1 3.2 - - - +
----------------------------------------------------------
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