Contacts of the helix formed by residues 1351 - 1363 (chain A) in PDB entry 6CNC
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 ASP1351 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A LYS 3.6 10.4 - - - +
546A SER* 3.8 19.4 - - - +
674A LYS* 5.3 3.9 + - - -
923A PRO* 3.4 30.3 - - + +
926A MET* 3.6 18.2 - - + +
930A ALA* 4.7 6.1 + - - +
1340A ASN* 5.3 2.6 - - - -
1349A SER* 3.6 10.4 + - - -
1350A VAL* 1.3 87.8 - - - +
1352A PRO* 1.3 73.7 - - + +
1353A ARG* 3.3 6.6 + - + +
1355A ILE* 3.9 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926A MET* 5.6 0.2 - - + -
930A ALA* 4.5 16.2 - - + -
1336A ILE* 6.2 1.8 - - + -
1340A ASN* 4.3 21.0 - - - +
1351A ASP* 1.3 90.0 - - + +
1353A ARG* 1.3 86.7 + - + +
1355A ILE* 3.4 5.1 + - + +
1356A GLN* 2.9 27.3 + - + +
204E THR* 3.9 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
913A GLN* 5.5 0.2 - - - +
916A TYR* 3.5 36.5 + - + +
917A GLY* 4.5 13.6 + - - -
919A ASP* 2.5 38.5 + - - +
921A LEU 3.7 8.3 + - - -
923A PRO* 4.0 30.7 - - + -
926A MET* 3.6 24.5 - - + +
930A ALA* 4.0 8.3 + - - +
932A PRO* 5.7 1.0 - - - +
1351A ASP* 3.2 5.4 - - + -
1352A PRO* 1.3 99.9 - - - +
1354A HIS* 1.3 64.6 + - + +
1356A GLN* 2.8 22.7 + - - +
1357A LEU* 2.9 11.6 + - - +
204E THR* 3.8 18.3 - - - -
205E SER* 4.2 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A PRO 3.6 22.4 - - - -
545A LYS 3.8 5.2 - - - -
893A LEU* 6.1 0.2 - - - +
916A TYR* 3.7 17.7 - - - -
922A ASP* 5.3 0.2 + - - -
923A PRO* 3.2 26.0 - - + +
1089A ILE* 4.7 5.8 - - + +
1092A ILE* 3.8 15.0 - - + +
1093A GLY* 4.3 25.7 - - - +
1096A SER* 2.8 33.2 + - - +
1097A ILE* 4.8 2.9 - - + +
1350A VAL* 3.5 21.3 + - + -
1351A ASP 4.1 1.0 + - - -
1353A ARG* 1.3 78.6 - - + +
1355A ILE* 1.3 59.2 + - + +
1357A LEU* 3.3 7.6 + - - +
1358A LEU* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1097A ILE* 4.0 25.8 - - + -
1336A ILE* 3.3 36.7 - - + +
1339A ILE* 3.7 22.7 - - + -
1340A ASN* 4.3 8.7 - - + +
1343A MET* 3.5 32.3 - - + -
1350A VAL* 4.2 5.2 - - + -
1351A ASP 3.9 13.9 + - - +
1352A PRO* 3.4 9.5 + - + +
1353A ARG 3.1 1.0 - - - -
1354A HIS* 1.3 72.7 - - - +
1356A GLN* 1.3 66.9 + - - +
1358A LEU* 3.1 7.1 + - + +
1359A GLY 2.9 19.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
913A GLN* 4.3 11.6 + - - +
917A GLY* 3.2 31.5 + - - +
1332A ARG* 4.1 11.4 + - - +
1336A ILE* 3.7 29.4 - - + +
1352A PRO* 2.9 20.2 + - + +
1353A ARG* 2.8 18.0 + - - +
1355A ILE* 1.3 71.5 - - - +
1357A LEU* 1.3 62.4 + - - +
1359A GLY* 3.0 5.0 + - - -
1360A ASP* 2.9 20.5 + - - +
202E SER* 4.7 8.7 + - - -
204E THR* 3.3 33.8 + - - +
208E TYR* 4.4 16.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893A LEU* 3.6 27.1 - - + -
896A LEU* 3.5 35.0 - - + -
904A VAL* 4.8 6.5 - - + -
912A VAL* 5.7 1.1 - - + -
913A GLN* 3.9 16.7 + - - +
916A TYR* 3.6 29.6 - - + -
1089A ILE* 4.3 19.1 - - + +
1090A GLY* 4.5 4.0 - - - -
1093A GLY* 5.2 2.5 - - - -
1353A ARG 2.9 11.7 + - - +
1354A HIS* 3.7 10.8 - - + +
1355A ILE 3.2 0.2 - - - -
1356A GLN* 1.3 74.7 - - - +
1358A LEU* 1.3 65.1 + - - +
1360A ASP* 2.8 14.4 + - + +
1361A VAL* 2.9 12.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889A LEU* 4.0 23.3 - - + -
893A LEU* 4.8 8.5 - - + -
1097A ILE* 3.5 27.6 - - + -
1130A ILE* 4.0 31.9 - - + -
1335A ILE* 5.4 3.8 - - + -
1339A ILE* 5.2 11.9 - - + -
1354A HIS 2.9 12.4 + - - +
1355A ILE* 3.1 14.3 + - + +
1357A LEU* 1.3 78.1 - - - +
1359A GLY* 1.3 63.7 + - - +
1361A VAL* 3.2 17.6 - - + +
1362A MET* 2.9 29.3 + - + +
1371A ILE* 5.5 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1332A ARG* 3.3 19.8 - - - +
1335A ILE* 4.1 13.0 - - - +
1336A ILE* 3.6 19.3 - - - +
1355A ILE 2.9 11.5 + - - -
1356A GLN 3.0 4.9 + - - -
1358A LEU* 1.3 77.3 - - - +
1360A ASP* 1.3 57.4 + - - +
1362A MET* 3.4 4.7 + - - +
1363A THR* 3.0 22.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
912A VAL* 2.8 43.9 - - + +
913A GLN* 3.1 20.9 - - + +
1332A ARG* 3.8 13.7 - - - +
1356A GLN 2.9 11.3 + - - +
1357A LEU* 2.8 14.3 + - + +
1359A GLY* 1.3 73.7 - - - +
1361A VAL* 1.3 65.7 + - + +
1362A MET 3.1 1.3 - - - -
1363A THR 2.7 31.5 - - - +
1364A TYR* 3.4 8.1 - - - +
176E PRO* 5.5 1.2 - - - +
212E ARG* 4.5 5.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892A SER* 5.5 3.4 - - - +
893A LEU* 3.6 36.1 - - + -
896A LEU* 3.7 22.0 - - + -
906A THR* 6.0 0.4 - - + -
912A VAL* 4.1 14.6 - - + -
1357A LEU* 2.9 14.8 + - + +
1358A LEU* 3.2 26.0 - - + +
1360A ASP* 1.3 76.0 - - - +
1362A MET* 1.3 63.4 + - - +
1364A TYR* 4.0 13.2 - - - +
1369A LEU 5.0 0.3 - - - +
1378A LYS* 3.6 30.1 + - - +
1380A ARG* 6.2 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1129A ILE 3.4 7.9 - - - +
1130A ILE* 3.1 49.1 - - + +
1132A ALA* 4.8 2.0 - - - -
1319A VAL* 5.4 4.5 - - - -
1335A ILE* 3.3 29.6 - - + -
1358A LEU* 2.9 24.1 + - + +
1359A GLY* 3.6 6.5 - - - +
1361A VAL* 1.3 83.3 - - + +
1363A THR* 1.3 60.0 + - - +
1364A TYR* 3.6 3.3 + - - +
1367A GLU 4.2 2.6 - - - +
1368A VAL* 4.0 22.7 - - + -
1369A LEU 3.6 34.9 + - - +
1371A ILE* 5.4 2.5 - - + -
1378A LYS* 5.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1319A VAL* 5.8 0.7 - - - +
1328A ILE* 3.7 39.9 - - + -
1332A ARG* 4.2 17.8 + - + +
1335A ILE* 5.8 1.0 - - - +
1359A GLY 3.0 13.9 + - - -
1360A ASP* 2.7 20.1 - - - +
1362A MET* 1.3 73.7 - - - +
1364A TYR* 1.3 56.8 + - - +
1365A LYS 4.3 3.1 - - - +
1366A GLY 4.1 12.1 - - - +
1367A GLU 4.7 1.6 - - - -
1368A VAL* 3.1 25.2 - - + +
212E ARG* 3.3 21.8 + - - +
----------------------------------------------------------
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