Contacts of the helix formed by residues 1346 - 1354 (chain D) in PDB entry 5NSS
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 GLY1346 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1318D SER* 4.0 27.6 - - - -
1321D SER* 4.6 2.0 - - - -
1344D LEU* 3.4 1.6 - - - +
1345D ARG* 1.3 79.0 - - - +
1347D LEU* 1.3 60.3 + - - -
1348D LYS 3.5 1.8 - - - -
1349D GLU* 3.3 10.2 + - - +
1350D ASN* 2.8 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1347 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805D GLN* 3.3 44.2 + - + +
806D ASP 6.1 0.2 - - - -
807D LEU 3.9 19.7 - - - +
808D VAL* 5.5 10.1 - - + -
1345D ARG 4.4 5.8 - - - +
1346D GLY* 1.3 73.1 - - - -
1348D LYS* 1.3 58.6 + - - +
1350D ASN* 2.9 21.9 + - - +
1351D VAL* 2.9 17.5 + - - +
1357D ILE* 3.6 33.1 - - + +
1358D PRO* 3.6 29.4 - - + +
1359D ALA* 4.7 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1348 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1276C TRP* 5.7 6.3 - - - +
1279C GLU* 4.7 4.9 - - - +
342D LEU* 5.1 13.0 - - + +
802D ASP* 5.0 4.6 + - - -
805D GLN* 4.0 26.2 - - + +
1321D SER* 4.1 9.4 - - - +
1322D ALA* 3.3 39.2 - - - +
1324D SER* 5.0 4.8 - - - -
1325D PHE* 3.5 24.4 - - - +
1346D GLY 3.5 0.2 - - - -
1347D LEU* 1.3 79.1 - - - +
1349D GLU* 1.3 57.3 + - - +
1351D VAL* 3.0 15.9 + - + +
1352D ILE* 2.9 40.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1349 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1318D SER* 4.9 2.7 - - - -
1320D ILE* 4.2 11.7 - - + +
1321D SER* 3.7 34.2 - - - +
1342D ASP* 5.2 4.0 - - + -
1344D LEU* 4.5 9.9 - - + -
1346D GLY* 3.3 17.7 + - - +
1347D LEU 3.2 0.4 - - - -
1348D LYS* 1.3 79.2 - - - +
1350D ASN* 1.3 56.7 + - - +
1352D ILE* 3.2 6.8 + - - +
1353D VAL* 2.9 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1350 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1288C GLN* 2.7 19.4 + - - +
1344D LEU* 3.0 50.6 + - - +
1346D GLY 2.8 23.7 + - - +
1347D LEU* 2.9 9.7 + - - +
1349D GLU* 1.3 74.8 - - - +
1351D VAL* 1.3 54.0 + - - +
1353D VAL* 4.5 0.7 - - - +
1354D GLY 2.9 22.0 + - - -
1355D ARG* 2.9 20.8 + - - +
1356D LEU 4.1 7.4 + - - +
1357D ILE* 4.4 2.2 - - - -
1358D PRO* 3.1 25.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1351 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1275C VAL* 5.2 4.7 - - + -
1279C GLU* 4.5 4.0 - - - +
1287C LEU* 3.7 41.5 - - + +
1288C GLN* 3.2 18.7 - - - +
1291C LEU* 3.4 41.0 - - + +
1292C THR* 4.2 0.7 - - - +
342D LEU* 5.6 2.0 - - - +
1347D LEU 2.9 14.3 + - - +
1348D LYS* 3.0 19.0 + - + +
1350D ASN* 1.3 76.3 - - - +
1352D ILE* 1.3 62.1 + - + +
1354D GLY 3.9 0.9 + - - -
1357D ILE* 3.7 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1352 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1320C PRO* 3.3 19.2 - - - +
1323C PHE* 3.7 13.5 - - + +
1326C LEU* 5.0 13.9 - - + -
341D ASN* 3.8 22.4 + - - +
342D LEU* 3.7 34.8 - - + -
1320D ILE* 4.0 37.5 - - + +
1321D SER* 4.9 2.0 - - - -
1324D SER* 5.3 4.7 - - - +
1348D LYS* 2.9 29.8 + - + +
1349D GLU* 3.2 6.3 + - - +
1350D ASN 3.2 0.2 - - - -
1351D VAL* 1.3 78.1 - - + +
1353D VAL* 1.3 63.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1353 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1318C GLY 4.1 2.1 - - - +
1319C MET* 3.7 22.6 - - + +
1320C PRO* 3.1 18.5 - - - +
1323C PHE* 5.3 2.0 - - - -
19D ALA* 5.2 9.0 - - - +
20D ILE* 5.5 6.1 - - + -
1320D ILE* 3.7 29.8 - - + -
1344D LEU* 3.6 34.5 - - + -
1349D GLU 2.9 20.4 + - - +
1350D ASN 4.4 0.7 - - - +
1352D ILE* 1.3 78.4 - - + +
1354D GLY* 1.3 58.5 + - - +
1355D ARG* 3.8 10.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1354 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1288C GLN* 3.1 26.4 - - - +
1292C THR* 3.7 18.1 + - - +
1317C PRO* 3.9 20.0 - - - +
1318C GLY 4.3 9.2 - - - -
1320C PRO* 4.2 1.6 - - - -
1350D ASN 2.9 6.1 + - - -
1352D ILE 3.3 2.6 - - - -
1353D VAL* 1.3 77.5 - - - +
1355D ARG* 1.3 64.0 + - - +
1356D LEU 3.8 0.5 + - - -
----------------------------------------------------------
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