Contacts of the helix formed by residues 1088 - 1099 (chain A) in PDB entry 6CNB
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 ALA1088 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894A GLU 5.6 1.6 - - - +
895A ASP* 6.4 0.2 - - - -
896A LEU 3.8 11.9 - - - +
897A SER* 4.5 2.5 - - - +
1086A GLY 3.5 1.8 + - - -
1087A THR* 1.3 74.6 - - - +
1089A ILE* 1.3 64.2 + - - +
1090A GLY 3.3 1.2 + - - -
1091A ALA* 4.3 10.9 - - + +
1092A ILE* 3.6 25.6 + - - +
1423A ILE* 3.9 34.2 - - + +
1424A GLY* 5.5 0.2 - - - -
1071B ILE* 4.4 13.5 - - + +
1072B ALA 4.6 2.9 + - - +
1074B GLY* 5.6 0.8 - - - -
88F TYR* 4.3 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1089 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896A LEU 3.2 5.7 + - - +
897A SER* 4.6 0.2 - - - +
898A CYS* 4.2 8.3 - - + +
904A VAL* 4.8 5.4 - - + -
916A TYR* 3.3 38.1 - - + +
922A ASP* 5.3 4.0 - - - +
923A PRO* 5.8 2.0 - - + -
1083A LEU* 3.5 39.9 - - + -
1087A THR* 3.4 32.0 + - + +
1088A ALA* 1.3 72.5 - - - +
1090A GLY* 1.3 60.8 + - - +
1092A ILE* 3.9 7.8 - - + +
1093A GLY* 2.9 25.8 + - - -
1354A HIS* 5.0 7.2 - - + +
1357A LEU* 4.0 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1090 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893A LEU* 3.5 34.5 - - - +
896A LEU* 3.0 28.6 + - - +
1089A ILE* 1.3 77.2 - - - +
1091A ALA* 1.3 63.1 + - - +
1093A GLY* 2.8 12.3 + - - -
1094A ALA* 2.9 12.3 + - - +
1357A LEU* 4.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1091 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890A MET* 5.6 1.1 - - - -
893A LEU 4.9 0.4 - - - -
894A GLU* 3.9 15.2 + - - +
1088A ALA* 3.8 9.0 + - + +
1089A ILE 3.5 0.2 - - - -
1090A GLY* 1.3 73.4 - - - +
1092A ILE* 1.3 64.0 + - - +
1094A ALA* 3.1 7.2 + - - +
1095A GLN* 3.0 26.7 + - - +
1068B ASP* 4.1 13.0 - - - +
1071B ILE* 4.0 18.4 - - + +
1072B ALA* 3.8 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1092 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A ARG* 3.9 23.3 - - - +
544A PRO* 3.9 25.7 - - + +
922A ASP* 5.9 4.0 - - - +
923A PRO* 5.9 0.9 - - + -
924A LEU* 6.1 3.4 - - + -
1087A THR* 4.2 16.8 - - + -
1088A ALA 3.6 16.1 + - - +
1089A ILE* 4.2 9.0 - - + +
1090A GLY 3.4 0.2 - - - -
1091A ALA* 1.3 75.3 - - - +
1093A GLY* 1.3 63.4 + - - +
1095A GLN* 3.8 3.9 - - - +
1096A SER* 2.9 26.2 + - - -
1354A HIS* 3.8 20.4 - - + +
1072B ALA* 3.9 29.6 - - + +
87F LYS* 6.3 0.2 - - - +
88F TYR* 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1093 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893A LEU* 4.0 9.0 - - - -
1089A ILE 2.9 13.4 + - - -
1090A GLY 2.8 10.1 + - - -
1092A ILE* 1.3 77.2 - - - +
1094A ALA* 1.3 62.2 + - - +
1096A SER* 3.2 17.6 + - - -
1097A ILE* 3.4 15.1 + - - +
1354A HIS* 4.3 19.1 - - - +
1357A LEU* 5.3 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1094 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886A SER* 5.1 3.5 - - - +
889A LEU* 4.2 17.6 - - + +
890A MET* 4.0 40.2 - - + +
893A LEU* 3.6 15.5 - - + +
1090A GLY 2.9 8.8 + - - +
1091A ALA* 3.1 5.4 + - - +
1093A GLY* 1.3 74.1 - - - +
1095A GLN* 1.3 59.0 + - - +
1096A SER 2.9 6.1 + - - -
1097A ILE* 2.9 15.1 + - - +
1098A GLY* 3.0 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1095 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A SER 4.9 1.1 - - - +
480A LEU 3.1 25.1 + - - +
481A HIS* 3.1 20.0 - - - +
482A ARG* 4.2 23.1 - - + +
544A PRO* 5.8 4.0 - - + +
886A SER* 4.7 14.9 + - - -
890A MET* 3.4 18.3 - - + +
1091A ALA 3.0 16.5 + - - +
1092A ILE* 3.8 3.6 - - - +
1094A ALA* 1.3 75.7 - - - +
1096A SER* 1.3 57.0 + - - +
1098A GLY* 3.8 4.9 + - - +
1099A GLU* 3.1 20.8 - - - +
1065B MET* 4.8 13.0 + - - +
1068B ASP* 3.0 31.2 + - - +
1069B CYS* 5.7 1.1 - - - -
1072B ALA* 5.3 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1096 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A PRO* 6.0 2.7 - - - -
545A LYS* 3.2 28.6 + - - +
1092A ILE* 2.9 20.7 + - - -
1093A GLY 3.2 6.3 - - - -
1094A ALA 2.9 0.4 + - - -
1095A GLN* 1.3 75.8 - - - +
1097A ILE* 1.3 59.5 + - - +
1098A GLY 3.2 5.0 + - - -
1099A GLU* 3.7 15.3 - - - +
1348A MET* 5.4 1.0 - - - +
1350A VAL* 3.2 17.0 - - - +
1354A HIS* 2.7 33.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1097 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885A MET* 4.2 17.9 - - + +
889A LEU* 4.1 19.7 - - + -
893A LEU* 5.8 1.6 - - + -
1093A GLY 3.4 14.3 + - - +
1094A ALA* 2.9 6.2 + - - +
1096A SER* 1.3 77.4 - - - +
1098A GLY* 1.3 65.4 + - - +
1099A GLU 3.6 7.0 + - - +
1126A ILE* 5.3 4.9 - - + -
1130A ILE* 5.2 5.6 - - + -
1339A ILE* 5.5 2.5 - - + -
1343A MET* 4.0 25.5 - - + +
1350A VAL* 4.2 10.1 - - + -
1354A HIS* 5.0 5.8 - - + +
1355A ILE* 3.7 28.7 - - + -
1358A LEU* 3.9 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1098 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A LEU 5.3 4.3 - - - -
882A THR* 3.9 15.8 - - - +
885A MET* 4.8 8.3 - - - +
886A SER* 3.2 31.4 + - - -
889A LEU* 5.5 1.6 - - - -
1094A ALA 3.0 12.8 + - - -
1095A GLN* 3.8 4.5 + - - -
1096A SER 3.2 2.6 - - - -
1097A ILE* 1.3 81.0 - - - +
1099A GLU* 1.3 61.8 + - - +
1100A PRO 3.9 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1099 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A LEU* 4.6 27.0 + - + +
481A HIS* 3.9 25.2 + - + +
545A LYS* 2.7 42.5 + - - +
882A THR* 5.3 0.4 - - - -
1095A GLN 3.1 22.6 - - - +
1096A SER 3.7 5.8 - - - +
1097A ILE 3.9 7.2 - - - +
1098A GLY* 1.3 70.5 - - - +
1100A PRO* 1.3 72.1 - - + +
1348A MET* 3.8 14.9 - - - +
----------------------------------------------------------
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