Contacts of the helix formed by residues 1043 - 1067 (chain B) in PDB entry 2O8C
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 ASN1043 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905B LEU* 5.0 0.8 - - - +
908B GLU* 3.4 40.9 - - - +
1039B ASN 5.2 0.9 - - - +
1040B PHE 3.4 3.8 + - - +
1041B ASP 2.9 1.8 + - - -
1042B LYS* 1.3 76.8 - - + +
1044B TYR* 1.3 61.9 + - - +
1045B LYS* 3.3 3.7 + - - +
1046B ASP* 3.2 36.1 + - - +
1047B TRP* 2.9 51.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1044 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B LYS* 3.5 58.8 - - + +
647B LEU* 5.0 4.5 + - - +
703B MET 5.5 0.7 - - - -
822B LEU* 6.1 1.6 - - - -
1041B ASP* 2.9 23.0 + - - +
1042B LYS* 3.9 13.7 - - - -
1043B ASN* 1.3 73.9 - - - +
1045B LYS* 1.3 113.4 + - + +
1047B TRP* 4.3 6.7 - - - -
1048B GLN* 2.9 32.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1045 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043B ASN* 3.3 1.7 - - - +
1044B TYR* 1.3 115.6 + - + +
1046B ASP* 1.3 64.6 + - - +
1048B GLN* 4.3 1.8 - - - +
1049B SER* 2.8 29.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1046 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903B PRO* 3.6 20.3 - - + +
904B ASP 4.8 8.3 + - - +
905B LEU* 3.9 15.9 - - + +
908B GLU* 5.7 1.2 - - - +
1043B ASN* 3.2 34.3 + - - +
1044B TYR 3.3 0.2 - - - -
1045B LYS* 1.3 80.0 - - - +
1047B TRP* 1.3 66.6 + - - +
1049B SER* 3.0 8.1 + - - -
1050B ALA* 2.9 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1047 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822B LEU* 3.6 25.8 - - + -
865B PHE* 3.3 37.6 - + + -
905B LEU* 3.7 22.9 - - + -
908B GLU* 3.8 19.3 - - + -
909B LEU* 3.6 32.8 - - + -
912B TRP* 4.5 2.7 - - - -
1040B PHE* 3.0 59.3 + + - -
1041B ASP* 5.1 0.9 - - - -
1043B ASN* 2.9 44.4 + - + +
1044B TYR* 4.1 4.0 - - - +
1046B ASP* 1.3 77.6 - - - +
1048B GLN* 1.3 60.8 + - - +
1050B ALA* 3.4 0.4 + - - -
1051B VAL* 3.2 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1048 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705B ASN* 6.2 0.4 - - - +
819B GLU* 3.7 32.7 + - - +
822B LEU* 3.9 21.5 - - + +
823B SER* 5.8 0.6 + - - -
1044B TYR* 2.9 21.0 + - + +
1045B LYS* 4.3 1.8 - - - +
1047B TRP* 1.3 74.6 - - - +
1049B SER* 1.3 60.6 + - - +
1051B VAL* 3.1 11.9 + - - +
1052B GLU* 3.0 55.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1049 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901B ARG 5.5 3.8 - - - -
903B PRO* 3.9 14.2 - - - +
1045B LYS 2.8 24.1 + - - -
1046B ASP* 3.0 13.2 + - - -
1048B GLN* 1.3 76.6 - - - +
1050B ALA* 1.3 57.1 + - - +
1051B VAL 3.3 0.2 - - - -
1052B GLU* 3.8 14.4 - - - +
1053B CYS* 3.1 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1050 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865B PHE* 4.4 1.6 - - + -
868B MET* 3.6 19.1 - - - +
902B PHE* 3.7 32.3 - - + -
903B PRO* 3.7 13.2 - - + +
905B LEU* 3.9 14.4 - - + -
1046B ASP 2.9 16.4 + - - +
1047B TRP 3.7 5.6 - - - +
1049B SER* 1.3 76.5 + - - +
1051B VAL* 1.3 62.3 + - - +
1053B CYS 3.7 0.2 + - - -
1054B ILE* 3.4 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1051 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769B PHE* 3.5 20.8 - - + -
818B LEU* 3.8 26.0 - - + -
819B GLU* 3.9 25.1 - - + +
822B LEU* 4.1 10.8 - - + -
865B PHE* 3.8 10.8 - - + -
868B MET* 3.9 9.6 - - + -
1047B TRP 3.2 14.3 + - - +
1048B GLN* 3.1 22.6 + - - +
1050B ALA* 1.3 78.4 - - - +
1052B GLU* 1.3 59.4 + - + +
1054B ILE 3.7 0.2 + - - -
1055B ALA* 3.1 25.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1052 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819B GLU* 5.5 2.5 - - - +
1048B GLN* 3.0 42.0 + - - +
1049B SER* 3.8 12.6 + - - +
1050B ALA 3.3 0.2 - - - -
1051B VAL* 1.3 77.4 - - + +
1053B CYS* 1.3 66.3 + - - +
1055B ALA* 3.0 9.2 + - - +
1056B VAL* 3.0 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1053 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890B VAL* 3.4 48.0 - - - +
900B GLY 5.1 1.6 - - - -
901B ARG 3.7 22.2 - - - -
902B PHE* 3.5 30.7 - - + -
1049B SER 3.1 19.4 + - - +
1050B ALA 3.8 1.1 - - - +
1051B VAL 3.5 0.2 - - - -
1052B GLU* 1.3 75.3 - - - +
1054B ILE* 1.3 58.3 + - + +
1056B VAL* 3.1 7.3 + - - +
1057B LEU* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1054 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767B THR* 4.5 0.9 - - + -
769B PHE* 3.7 17.5 - - + -
812B LEU* 3.7 23.3 - - + -
815B LEU* 4.0 6.7 - - + -
868B MET* 3.3 45.1 - - + +
871B ILE* 3.7 23.8 - - + -
872B ILE* 5.0 6.5 - - + -
890B VAL 5.6 0.4 - - - +
902B PHE* 4.5 9.6 - - + -
1050B ALA 3.4 13.9 + - - +
1051B VAL 4.2 0.7 - - - +
1052B GLU 3.3 0.4 - - - -
1053B CYS* 1.3 76.7 - - + +
1055B ALA* 1.3 59.9 + - - +
1057B LEU* 3.7 11.7 - - + +
1058B ASP* 2.8 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1055 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769B PHE* 3.7 31.0 - - + +
770B GLY* 4.2 4.8 - - - -
773B LEU* 3.6 16.2 - - + -
1051B VAL* 3.1 17.0 + - + +
1052B GLU* 3.0 14.5 + - - +
1054B ILE* 1.3 75.5 - - - +
1056B VAL* 1.3 63.5 + - - +
1058B ASP* 3.4 2.9 + - - +
1059B VAL* 3.1 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1056 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773B LEU* 3.7 18.4 - - + -
777B TRP* 4.3 17.7 - - + -
886B ILE* 4.3 15.0 - - + -
890B VAL* 3.7 24.7 - - + -
1052B GLU* 3.0 16.0 + - + +
1053B CYS 3.4 6.7 - - - +
1055B ALA* 1.3 75.8 - - - +
1057B LEU* 1.3 57.4 + - - +
1059B VAL* 3.2 3.6 + - - +
1060B LEU* 2.9 46.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1057 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798B LEU* 4.7 6.5 - - + -
808B VAL* 4.3 8.5 - - + -
812B LEU* 5.4 4.7 - - + -
871B ILE* 3.9 28.0 - - + -
872B ILE* 5.6 0.4 - - + -
875B MET* 4.1 14.6 - - - -
887B LEU* 3.9 18.8 - - + -
890B VAL* 4.4 4.7 - - + +
891B ILE* 3.8 33.2 - - + -
1053B CYS 3.0 13.8 + - - +
1054B ILE* 3.3 15.0 + - + +
1056B VAL* 1.3 75.3 - - - +
1058B ASP* 1.3 57.6 + - - +
1060B LEU* 3.6 4.2 + - + +
1061B LEU* 3.1 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1058 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765B CYS* 3.3 15.3 - - - +
766B HIS* 3.2 25.1 + - - -
767B THR* 2.8 42.4 + - + +
770B GLY* 3.4 4.8 - - - -
812B LEU* 3.7 23.3 - - + +
1054B ILE 2.8 17.0 + - - +
1055B ALA 3.6 5.2 - - - +
1057B LEU* 1.3 75.3 - - - +
1059B VAL* 1.3 58.9 + - - +
1061B LEU* 3.3 3.4 + - - +
1062B CYS* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1059 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765B CYS* 4.3 1.6 - - - -
770B GLY 3.3 26.7 - - - +
773B LEU* 3.8 19.1 - - + -
774B LEU* 3.8 23.6 - - + +
777B TRP* 3.7 35.2 - - + -
1055B ALA 3.1 16.2 + - - +
1056B VAL* 3.7 3.6 - - - +
1058B ASP* 1.3 74.9 - - - +
1060B LEU* 1.3 60.1 + - - +
1062B CYS* 3.1 9.0 + - - +
1063B LEU* 2.8 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1060 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777B TRP* 3.8 25.1 - - + -
791B ARG* 4.6 14.6 - - + +
794B ALA* 3.9 24.7 - - + -
795B ILE* 4.4 6.1 - - + +
798B LEU* 3.6 16.1 - - + +
886B ILE* 4.6 6.7 - - + -
887B LEU* 3.9 31.6 - - + -
890B VAL* 4.9 0.7 - - + -
1056B VAL* 2.9 37.8 + - + +
1057B LEU* 4.0 4.7 - - - +
1059B VAL* 1.3 75.9 - - - +
1061B LEU* 1.3 57.3 + - - +
1063B LEU* 3.3 8.3 + - + +
1064B ALA* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1061 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766B HIS* 6.0 2.5 - - + -
798B LEU* 3.7 24.9 - - + -
805B ILE* 3.8 37.5 - - + -
808B VAL* 4.3 18.2 - - + -
809B VAL* 4.3 15.0 - - + -
812B LEU* 3.8 26.7 - - + -
875B MET* 6.4 0.4 - - + -
1057B LEU* 3.1 30.4 + - + +
1058B ASP* 3.7 4.9 - - - +
1060B LEU* 1.3 73.4 - - - +
1062B CYS* 1.3 65.2 + - - +
1064B ALA* 3.3 3.4 + - + +
1065B ASN* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1062 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762B VAL* 3.3 25.1 - - - +
764B THR* 3.1 39.3 + - - +
765B CYS* 3.7 22.9 - - - +
774B LEU* 3.8 12.8 - - - -
1058B ASP 2.9 14.6 + - - +
1059B VAL* 3.3 9.4 - - - +
1061B LEU* 1.3 77.2 - - - +
1063B LEU* 1.3 61.4 + - - +
1065B ASN* 3.5 2.0 + - - +
1066B TYR* 3.4 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1063 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762B VAL* 4.1 18.8 - - + -
774B LEU* 4.6 3.4 - - + -
777B TRP* 3.8 36.1 - - + -
791B ARG* 5.5 0.2 - - - -
795B ILE* 3.8 13.9 - - + -
1059B VAL* 2.8 22.7 + - + +
1060B LEU* 3.8 9.4 - - + +
1062B CYS* 1.3 74.1 - - - +
1064B ALA* 1.3 63.2 + - - +
1066B TYR* 3.6 5.2 + - - +
1067B SER* 2.8 29.1 + - - -
1153B MET* 5.4 1.1 - - + -
1156B MET* 3.9 30.3 - - + +
1157B GLY 4.7 4.9 - - - +
1158B CYS* 3.9 24.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1064 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795B ILE* 3.7 31.8 - - + +
798B LEU* 4.1 17.0 - - + -
799B MET* 4.1 11.8 - - + +
805B ILE* 5.7 2.7 - - + -
1060B LEU 2.9 16.9 + - - +
1061B LEU* 3.6 7.2 - - + +
1062B CYS 3.3 0.2 - - - -
1063B LEU* 1.3 78.7 - - - +
1065B ASN* 1.3 57.0 + - - +
1067B SER* 3.2 4.9 + - - -
1068B ARG* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1065 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764B THR* 4.2 25.6 + - + +
1061B LEU 3.1 16.5 + - - +
1062B CYS 3.8 4.9 - - - +
1063B LEU 3.3 0.2 - - - -
1064B ALA* 1.3 75.6 - - - +
1066B TYR* 1.3 63.4 + - - +
1068B ARG* 3.2 28.1 + - - +
1069B GLY 3.9 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1066 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761B ARG* 3.9 46.0 - - + -
762B VAL* 4.5 27.4 - - + +
764B THR* 6.1 1.7 - - + +
1062B CYS 3.4 11.0 + - - +
1063B LEU* 3.9 8.1 - - - +
1064B ALA 3.3 0.4 - - - -
1065B ASN* 1.3 77.6 - - - +
1067B SER* 1.3 60.1 - - - +
1068B ARG 3.1 2.7 + - - -
1069B GLY* 3.5 4.5 + - - -
1074B MET* 3.4 28.8 - - + +
1097B PRO* 3.9 17.3 + - - +
1153B MET* 3.7 19.5 - - + +
1158B CYS* 3.6 19.1 - - - -
1159B TYR 3.6 18.2 - - - -
1161B PRO* 3.2 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1067 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795B ILE* 3.6 12.9 - - - +
799B MET* 4.4 9.6 - - - +
1063B LEU 2.8 22.4 + - - -
1064B ALA 3.5 6.1 - - - -
1065B ASN 3.2 0.2 - - - -
1066B TYR* 1.3 75.6 - - - +
1068B ARG* 1.3 61.9 + - - +
1069B GLY* 3.3 0.7 - - - -
1074B MET* 4.1 16.1 - - - +
1158B CYS* 3.5 5.9 - - - -
1159B TYR* 3.3 54.6 + - - -
----------------------------------------------------------
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