Contacts of the helix formed by residues 1058 - 1077 (chain B) in PDB entry 6PUO
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 HIS1058 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1054B GLN 5.1 1.1 - - - -
1055B VAL* 4.2 20.1 + - + -
1057B GLU* 1.3 99.1 + - + +
1059B THR* 1.3 65.7 + - - +
1060B ASP* 3.1 8.7 - - - -
1061B GLN* 3.2 30.3 + - + +
1062B ILE* 3.9 21.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1059 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922B PRO* 4.0 25.6 - - + +
925B ILE* 3.3 33.8 - - - +
926B ILE* 4.8 7.4 - - + -
1055B VAL* 3.7 21.0 + - - +
1056B GLN* 4.4 13.9 - - - +
1058B HIS* 1.3 76.8 - - - +
1060B ASP* 1.3 62.6 + - - +
1061B GLN 3.2 0.4 - - - -
1062B ILE* 3.0 18.7 + - - +
1063B TRP* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1060 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1050A TYR* 6.1 1.8 - - - +
918B LYS* 6.0 3.4 - - - +
922B PRO* 4.4 13.0 - - + -
1057B GLU 3.8 7.1 - - - +
1058B HIS* 3.1 18.7 - - - -
1059B THR* 1.3 72.7 + - + +
1061B GLN* 1.3 69.4 + - - +
1063B TRP* 3.7 11.4 - - + +
1064B LYS* 2.9 49.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1061 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727B MET* 3.9 29.8 - - + +
728B LYS* 4.4 20.3 - - - +
731B SER* 4.0 24.9 + - - +
1058B HIS* 3.4 22.6 - - + +
1059B THR 3.2 0.4 - - - -
1060B ASP* 1.3 88.7 + - - +
1062B ILE* 1.3 57.5 + - + +
1064B LYS* 3.4 8.2 + - + +
1065B PHE* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1062 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727B MET* 4.9 15.3 - - + -
925B ILE* 5.4 11.0 - - + -
929B ARG* 5.3 11.9 - - - +
1058B HIS* 4.0 26.2 - - + +
1059B THR* 3.0 25.0 + - - +
1061B GLN* 1.3 76.8 - - + +
1063B TRP* 1.3 58.1 + - - +
1065B PHE* 3.3 9.2 + - + +
1066B GLN* 2.9 47.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1063 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915B THR* 2.8 27.7 + - - -
916B ILE* 4.5 6.3 - - + -
917B SER 3.3 19.9 + - - -
918B LYS* 3.8 48.9 - - + -
921B GLY* 4.3 14.7 - - - -
922B PRO* 4.1 21.3 - - + -
925B ILE* 5.4 9.3 - - + +
1059B THR 3.0 12.2 + - - +
1060B ASP* 3.7 10.5 - - + +
1061B GLN 3.3 0.2 - - - -
1062B ILE* 1.3 78.7 - - - +
1064B LYS* 1.3 85.5 + - + +
1066B GLN* 3.0 9.8 + - + -
1067B ARG* 3.0 58.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1064 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730B VAL* 4.2 7.1 - - - +
731B SER* 4.0 28.9 + - - -
736B GLN* 3.6 44.1 + - - +
739B LEU* 5.2 2.4 - - - +
918B LYS* 5.3 7.4 - - - +
1060B ASP* 2.9 36.4 + - - +
1061B GLN* 3.8 5.8 - - + +
1063B TRP* 1.3 97.8 - - + +
1065B PHE* 1.3 61.3 + - - +
1067B ARG* 3.6 14.8 + - - +
1068B HIS* 4.7 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1065 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721B ALA 4.4 3.8 - - - -
722B LEU* 3.7 34.2 - - + +
725B LYS* 4.1 39.9 - - + -
727B MET* 3.6 30.5 - - + +
730B VAL* 4.1 35.8 - - + +
731B SER* 5.8 0.4 - - - -
1061B GLN 2.9 17.6 + - - +
1062B ILE* 3.5 7.4 - - + +
1063B TRP 3.2 0.2 - - - -
1064B LYS* 1.3 78.3 - - - +
1066B GLN* 1.3 69.7 + - + +
1067B ARG 3.3 0.9 + - - -
1068B HIS* 3.8 13.2 + - - +
1069B ASP* 5.1 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1066 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925B ILE* 6.1 5.2 - - + -
1062B ILE* 2.9 32.8 + - + +
1063B TRP* 3.0 12.0 + - + +
1065B PHE* 1.3 85.9 - - + +
1067B ARG* 1.3 59.3 + - - +
1068B HIS 3.2 1.1 - - - -
1069B ASP* 2.8 34.1 - - - +
1070B LEU* 4.5 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1067 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736B GLN* 2.9 36.4 + - - +
739B LEU* 4.5 10.3 - - + +
740B THR* 2.6 44.0 + - - +
743B TRP* 5.3 7.3 - - - +
916B ILE* 5.2 9.6 - - + +
918B LYS* 6.1 1.0 - - - +
1063B TRP* 3.0 45.0 + - + +
1064B LYS* 3.7 12.3 - - - +
1065B PHE 3.2 1.2 - - - -
1066B GLN* 1.3 77.8 - - - +
1068B HIS* 1.3 64.2 + - - +
1070B LEU* 3.4 9.2 + - - +
1071B ILE* 3.1 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1068 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718B LEU* 4.8 11.4 - - + +
722B LEU* 3.5 47.8 - - + +
730B VAL* 5.8 3.1 - - + -
739B LEU* 4.2 29.2 - - + +
1064B LYS 4.7 1.3 + - - +
1065B PHE 3.8 6.8 + - - +
1066B GLN 3.2 1.8 - - - -
1067B ARG* 1.3 79.7 - - - +
1069B ASP* 1.3 67.8 + - + +
1071B ILE* 3.1 9.5 + - - +
1072B GLU* 2.9 40.8 + - + +
1109B LEU* 4.9 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1069 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1065B PHE 5.1 0.6 - - - +
1066B GLN* 2.8 34.2 - - - +
1068B HIS* 1.3 84.5 - - + +
1070B LEU* 1.3 62.5 + - - +
1072B GLU* 3.9 4.7 - - - +
1073B GLU* 2.9 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1070 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743B TRP* 4.8 2.4 - - + -
799B PHE* 5.7 4.5 - - + -
912B HIS* 4.5 20.9 - - + +
915B THR* 3.8 23.1 - - - +
916B ILE* 3.7 33.9 - - + +
1066B GLN 4.6 3.6 - - - +
1067B ARG* 3.6 11.2 - - - +
1068B HIS 3.2 0.2 - - - -
1069B ASP* 1.3 84.7 + - - +
1071B ILE* 1.3 66.6 + - - +
1073B GLU* 4.1 13.0 - - - +
1074B TYR* 3.7 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1071 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739B LEU* 4.2 25.6 - - + +
742B VAL* 4.1 26.5 - - + -
743B TRP* 3.6 45.2 - - + +
795B PRO* 5.4 1.8 - - + +
916B ILE* 4.5 11.0 - - + -
1067B ARG* 3.1 37.1 + - + +
1068B HIS* 3.1 10.4 + - - +
1070B LEU* 1.3 80.2 - - - +
1072B GLU* 1.3 58.9 + - - +
1073B GLU 3.4 0.3 + - - -
1074B TYR* 3.5 2.1 + - - +
1075B HIS* 3.0 25.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1072 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1068B HIS* 2.9 36.3 + - + +
1069B ASP* 3.2 6.0 + - - +
1071B ILE* 1.3 75.6 - - - +
1073B GLU* 1.3 59.7 + - - +
1075B HIS* 3.3 9.7 + - - +
1076B GLY* 3.0 24.4 + - - -
1109B LEU* 4.5 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1073 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846B GLN* 2.5 43.3 + - + +
1069B ASP 2.9 15.9 + - - +
1070B LEU* 4.1 21.2 - - - +
1072B GLU* 1.3 76.7 - - - +
1074B TYR* 1.3 66.0 + - - +
1076B GLY* 3.1 4.2 + - - -
1077B ARG* 3.0 40.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1074 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743B TRP* 4.3 12.8 - + + -
795B PRO* 3.8 24.9 - - + +
798B VAL* 5.1 9.4 - - + +
799B PHE* 3.5 49.6 - + + -
802B ASN* 4.2 12.3 + - + +
912B HIS* 6.2 1.2 - + - -
1070B LEU* 3.7 40.0 + - + +
1071B ILE 3.5 3.4 + - - +
1073B GLU* 1.3 83.3 - - + +
1075B HIS* 1.3 65.5 + - - +
1077B ARG* 3.4 63.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1075 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742B VAL* 4.5 24.7 + - + +
795B PRO* 4.4 13.9 - - + +
1071B ILE 3.0 15.3 + - - +
1072B GLU* 3.5 12.1 - - - +
1073B GLU 3.2 0.2 - - - -
1074B TYR* 1.3 78.9 - - - +
1076B GLY* 1.3 61.2 + - - +
1077B ARG 3.5 4.0 + - - +
1105B ARG* 4.9 4.0 + - - -
1106B HIS* 3.3 41.3 + + + +
1108B GLN* 4.0 22.2 - - + +
1109B LEU* 4.7 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1076 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845B ARG* 3.9 16.5 + - - -
849B TYR* 6.0 5.7 - - - -
1072B GLU 3.0 14.3 + - - -
1073B GLU* 3.1 5.1 + - - -
1075B HIS* 1.3 78.2 - - - +
1077B ARG* 1.3 62.0 + - - +
1078B PRO* 3.7 5.5 - - - +
1105B ARG* 6.1 1.3 - - - -
1106B HIS* 4.4 16.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1077 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798B VAL* 4.7 12.0 - - + +
802B ASN* 3.1 32.8 + - - +
842B GLU* 4.4 24.7 + - - +
843B GLU* 6.0 0.4 + - - -
845B ARG* 4.6 3.1 - - - +
846B GLN* 3.3 28.9 - - - +
1073B GLU* 3.0 23.0 + - + +
1074B TYR* 3.4 48.7 + - - +
1075B HIS 3.3 4.9 - - - +
1076B GLY* 1.3 79.8 - - - +
1078B PRO* 1.3 84.4 - - + +
1079B ALA* 3.7 1.9 + - - +
1080B ALA 5.7 1.1 - - - -
1085B ILE* 5.4 4.3 - - + -
----------------------------------------------------------
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