Contacts of the strand formed by residues 1400 - 1405 (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 GLU1400 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1349D ASN 2.8 6.7 - - - +
1350D LEU* 3.1 4.9 - - - -
1351D SER* 2.7 44.2 + - - -
1353D ARG* 2.4 46.5 + - - +
1398D MET* 4.2 1.7 - - - +
1399D PHE* 1.3 83.5 - - - +
1401D GLY* 1.3 58.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1401 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1348D GLN 3.6 2.0 - - - -
1349D ASN* 3.1 17.9 - - - -
1350D LEU* 4.3 5.6 - - - -
1399D PHE* 4.3 10.6 - - - -
1400D GLU* 1.3 75.5 + - - +
1402D ARG* 1.3 75.3 + - - -
1403D ILE* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1402 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1346D GLN 3.9 0.5 - - - +
1347D ILE* 3.3 7.0 - - - +
1348D GLN* 2.9 69.1 + - + +
1350D LEU* 5.1 0.8 - - - +
1401D GLY* 1.3 82.9 - - - -
1403D ILE* 1.3 64.6 + - - +
1404D ILE* 4.0 9.6 - - + +
1409D ASP* 4.3 22.4 + - - +
1411D ALA* 5.9 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1403 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1345D ILE* 6.3 0.7 - - + -
1346D GLN 3.8 3.1 - - - -
1347D ILE* 3.6 31.2 - - + -
1350D LEU* 4.5 20.2 - - + -
1391D ALA* 3.9 22.4 - - + +
1392D PHE* 4.9 17.0 - - + +
1394D ARG* 5.7 4.9 - - + -
1399D PHE* 5.3 11.4 - - + -
1402D ARG* 1.3 76.0 - - - +
1404D ILE* 1.3 61.4 + - - +
1405D ILE* 4.5 20.4 - - + +
1408D ILE 4.1 0.2 - - - +
1409D ASP* 3.2 24.4 - - - +
1410D ILE* 4.9 5.3 + - + +
1421D ARG* 5.2 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1404 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1345D ILE* 3.4 2.8 - - - +
1346D GLN* 2.9 69.9 + - + +
1348D GLN* 3.9 26.2 - - - +
1402D ARG* 4.6 9.6 - - + +
1403D ILE* 1.3 79.8 - - - +
1405D ILE* 1.3 65.5 + - - +
1406D ASP 4.1 0.6 + - - +
1407D GLY* 3.6 29.8 - - - +
1408D ILE 3.7 6.1 - - - +
1409D ASP* 4.1 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1405 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1339D TRP* 3.8 24.1 - - + +
1340D PRO* 5.6 1.1 - - + -
1342D GLN 5.1 5.8 - - - +
1344D LYS 3.9 4.0 - - - +
1345D ILE* 3.6 26.2 - - + -
1392D PHE* 4.2 19.5 - - + -
1403D ILE* 4.5 12.6 - - + +
1404D ILE* 1.3 79.6 - - - +
1406D ASP* 1.3 73.4 + - + +
1407D GLY 3.4 0.2 - - - -
1408D ILE* 2.6 31.7 + - - +
1421D ARG* 3.3 37.7 - - - +
1422D LEU* 4.7 4.7 - - + -
1502D ILE* 5.6 6.7 - - + -
----------------------------------------------------------
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