Contacts of the helix formed by residues 1318 - 1325 (chain D) in PDB entry 6RIP
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 SER1318 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1316D THR* 3.7 8.7 - - - +
1317D GLU* 1.3 76.6 - - - +
1319D PHE* 1.3 65.2 + - - +
1320D ILE 2.9 2.6 + - - -
1321D SER* 3.0 17.6 + - - -
1322D ALA 3.9 0.9 + - - -
1341D ARG 5.6 0.4 - - - -
1342D ASP* 2.4 44.2 + - - +
1343D GLU 4.4 3.8 - - - -
1344D LEU 4.8 0.9 - - - -
1345D ARG 5.8 1.1 - - - -
1349D GLU* 2.9 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1319 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1337C ILE* 5.1 6.5 - - + -
20D ILE* 4.1 20.9 - - + -
22D ILE* 3.6 42.6 - - + -
1316D THR 5.4 1.6 - - - -
1317D GLU 2.9 10.0 + - - +
1318D SER* 1.3 71.0 - - - +
1320D ILE* 1.3 84.6 + - + +
1322D ALA* 3.0 11.5 + - - +
1323D ALA* 2.9 20.4 + - + +
1331D VAL* 3.9 10.1 - - + +
1332D LEU* 4.7 17.5 - - + -
1335D ALA* 4.2 22.9 - - + -
1340D LYS* 4.8 14.4 - - + -
1342D ASP* 3.9 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1320 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1323C PHE* 5.5 6.1 - - + -
1337C ILE* 6.3 1.3 - - + -
20D ILE* 3.6 31.4 - - + -
338D PHE* 4.6 13.2 - - + -
1318D SER* 2.9 4.2 + - - +
1319D PHE* 1.3 104.2 - - + +
1321D SER* 1.3 63.6 + - - +
1323D ALA* 3.7 4.8 - - + +
1324D SER* 2.9 26.1 + - - +
1342D ASP* 3.9 15.3 - - - +
1344D LEU* 5.5 1.3 - - + -
1348D LYS* 5.8 0.7 - - + -
1349D GLU* 4.2 17.3 - - + +
1352D ILE* 4.3 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1321 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805D GLN* 4.6 8.3 + - - -
806D ASP* 4.9 4.9 + - - -
1313D SER 5.5 0.7 - - - -
1316D THR* 4.7 18.4 - - - +
1318D SER* 3.0 9.7 + - - -
1320D ILE* 1.3 76.9 - - - +
1322D ALA* 1.3 67.5 + - - +
1324D SER* 3.0 15.2 + - - -
1325D PHE* 3.0 14.2 + - - +
1348D LYS* 4.6 14.5 + - - +
1349D GLU* 2.6 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1322 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1313D SER 4.8 6.3 + - - +
1314D LEU* 4.1 23.3 - - + +
1316D THR* 5.4 1.9 - - - +
1318D SER 3.9 0.8 + - - +
1319D PHE* 3.0 13.2 + - - +
1321D SER* 1.3 77.2 - - - +
1323D ALA* 1.3 54.3 + - - +
1324D SER 2.7 0.9 + - - -
1325D PHE* 2.3 45.6 + - - +
1327D GLU 3.9 4.3 - - - +
1331D VAL* 3.4 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1323 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D PHE* 3.4 34.5 - - + +
1319D PHE* 2.9 19.4 + - + +
1320D ILE* 3.3 7.8 + - - +
1322D ALA* 1.3 72.4 - - - +
1324D SER* 1.3 60.7 + - - +
1327D GLU 4.1 10.7 + - - +
1328D THR* 3.6 13.9 + - + -
1331D VAL* 4.1 3.5 - - + +
1332D LEU* 3.6 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1324 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D PHE* 3.5 26.7 - - - +
339D ARG* 4.3 13.3 - - - +
343D LEU* 4.0 13.2 - - - +
798D ARG* 3.8 13.7 + - - -
1320D ILE* 2.9 14.6 + - - +
1321D SER 3.4 8.1 - - - -
1322D ALA 2.7 5.1 + - - -
1323D ALA* 1.3 77.7 - - - +
1325D PHE* 1.3 58.4 + - - -
1326D GLN 3.8 1.4 + - - -
1348D LYS* 3.7 26.6 + - - +
1352D ILE* 4.1 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1325 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795D TYR* 5.9 0.4 - + - -
798D ARG* 4.3 15.9 - - - +
799D ARG* 3.8 29.6 - - + -
802D ASP* 3.3 37.5 - - + +
1309D ILE 6.0 0.2 - - - -
1310D THR* 4.6 6.7 - - - -
1313D SER* 3.0 38.1 - - - -
1314D LEU* 3.7 10.4 - - + +
1321D SER 3.0 11.5 + - - +
1322D ALA* 2.3 29.9 + - - +
1324D SER* 1.3 69.8 - - - +
1326D GLN* 1.3 98.6 + - + +
1327D GLU* 3.1 12.1 - - - +
1348D LYS* 5.0 0.2 - - - +
----------------------------------------------------------
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