Contacts of the helix formed by residues 403 - 409 (chain D) in PDB entry 5YWB
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 SER 403 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401D HIS 3.4 0.6 + - - -
402D LEU* 1.3 88.1 - - - +
404D THR* 1.3 60.0 + - - +
405D SER* 4.1 11.0 - - - -
406D ASN* 3.0 24.9 + - - +
407D LEU 3.4 0.7 + - - -
617D ALA* 3.5 11.5 + - - -
618D GLU 2.6 30.5 + - - -
619D ILE* 3.8 16.2 - - - +
729D GLU* 5.0 2.9 - - - -
1215D ARG* 4.2 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 404 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402D LEU* 4.0 1.0 + - - -
403D SER* 1.3 70.1 - - - +
405D SER* 1.3 59.3 + - - +
406D ASN 3.2 0.2 - - - -
407D LEU* 3.5 31.0 - - + -
408D SER* 2.9 28.1 + - - +
688D TRP* 5.1 6.1 - - - -
724D LEU* 5.8 2.2 - - - +
729D GLU* 4.2 16.6 + - - +
1211D LEU* 5.3 2.0 - - + +
1212D THR* 4.2 17.5 - - + +
1215D ARG* 3.8 15.6 + - - +
1480D GLU* 3.9 25.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 405 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403D SER* 3.1 9.1 - - - -
404D THR* 1.3 78.8 - - - +
406D ASN* 1.3 59.4 + - - +
408D SER* 2.7 22.8 + - - -
409D MET* 3.2 13.5 - - - +
617D ALA* 6.4 1.1 - - - -
686D PHE* 5.9 0.9 - - - -
688D TRP* 3.3 51.2 - - - +
689D THR* 5.2 2.5 - - - -
730D MET* 5.2 3.1 - - - +
2501D ADP 5.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 406 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402D LEU* 4.3 7.4 - - + +
403D SER* 3.0 15.0 + - - +
405D SER* 1.3 79.0 + - - +
407D LEU* 1.3 60.1 + - - +
409D MET* 2.8 36.4 + - - +
411D GLU* 6.3 2.3 - - + +
412D MET* 3.3 20.6 + - + +
616D SER* 4.0 10.5 - - - +
617D ALA* 3.1 51.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 407 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402D LEU* 4.4 15.3 - - + -
403D SER 3.4 3.9 + - - +
404D THR* 3.1 34.2 + - + +
406D ASN* 1.3 79.0 - - - +
408D SER* 1.3 61.7 + - - +
409D MET 3.3 6.8 - - - +
412D MET* 3.3 29.1 - - + +
413D THR* 4.8 2.3 + - - -
414D ALA* 5.0 3.8 - - + +
417D ILE* 5.0 1.1 - - + -
1208D VAL* 3.9 35.9 - - + +
1209D GLU* 4.7 9.6 - - - +
1211D LEU* 4.8 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 408 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404D THR* 2.9 13.0 + - - +
405D SER* 2.7 26.0 + - - -
407D LEU* 1.3 77.8 - - - +
409D MET* 1.3 70.4 + - - +
1476D THR* 3.0 28.2 + - - +
1479D GLY* 4.9 9.4 - - - -
1480D GLU* 3.9 26.7 - - - -
1481D ASN* 4.5 10.1 + - - +
2501D ADP 4.3 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 409 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405D SER 3.2 15.7 - - - +
406D ASN* 2.8 23.9 + - - +
407D LEU 3.3 6.9 - - - +
408D SER* 1.3 94.2 - - - +
410D GLY* 1.3 67.0 + - - +
411D GLU* 3.2 10.3 + - + +
412D MET 3.5 3.5 + - - -
413D THR* 3.8 4.9 + - - -
1476D THR* 4.4 6.5 - - + -
1481D ASN* 5.4 7.6 - - - +
----------------------------------------------------------
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