Contacts of the helix formed by residues 1032 - 1049 (chain B) in PDB entry 2B7A
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 SER1032 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
973B ILE* 3.3 22.9 - - - +
1006B GLU 3.4 21.3 - - - -
1007B PTR 4.3 7.4 - - - -
1024B GLU* 4.5 4.9 + - - +
1030B LYS 5.3 0.6 + - - -
1031B PHE* 1.3 76.2 - - - +
1033B VAL* 1.3 64.8 + - - +
1034B ALA* 3.4 12.0 + - - +
1035B SER* 2.7 32.8 + - - -
1036B ASP* 3.1 6.9 + - - -
1110B VAL* 4.7 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1033 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968B GLY* 5.0 17.5 - - - +
971B ARG* 6.2 1.6 - - - -
972B TYR 5.1 1.6 - - - +
973B ILE* 3.4 18.9 - - + +
1001B LEU* 4.9 7.6 - - + -
1006B GLU* 4.8 2.6 + - - +
1032B SER* 1.3 74.2 - - - +
1034B ALA* 1.3 57.0 + - - +
1036B ASP* 3.1 10.1 + - - +
1037B VAL* 2.9 31.3 + - + +
1115B SER* 5.9 2.7 - - - -
1116B PHE* 4.3 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1034 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032B SER* 3.2 5.6 + - - +
1033B VAL* 1.3 81.3 - - - +
1035B SER* 1.3 56.1 + - - +
1037B VAL* 3.4 8.8 + - - +
1038B TRP 3.1 18.7 + - - -
1110B VAL* 3.4 43.7 - - + +
1113B ARG* 3.0 27.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1035 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
973B ILE* 4.5 1.2 - - - +
1022B ALA* 3.9 7.7 + - - +
1024B GLU* 3.8 12.3 - - - -
1025B SER* 3.7 22.0 - - - -
1030B LYS 4.3 1.8 - - - -
1031B PHE* 3.4 12.4 - - - +
1032B SER* 2.7 39.0 + - - -
1034B ALA* 1.3 73.7 - - - +
1036B ASP* 1.3 65.6 + - - +
1038B TRP* 3.4 3.3 + - - +
1039B SER* 3.1 25.8 + - - -
1113B ARG* 3.7 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1036 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964B MET* 3.3 27.6 - - + +
972B TYR 4.3 1.2 - - - +
973B ILE* 3.5 12.4 - - - +
974B HIS* 2.8 26.3 + - - +
975B ARG* 3.0 27.3 + - - -
976B ASP 4.7 0.3 + - - -
977B LEU* 3.6 9.8 + - + +
1032B SER 3.1 11.9 + - - +
1033B VAL* 3.1 12.6 + - - +
1035B SER* 1.3 77.5 + - - +
1037B VAL* 1.3 57.8 + - - +
1039B SER* 3.4 5.6 + - - -
1040B PHE* 2.8 28.6 + - - +
1116B PHE* 3.8 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1037 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1033B VAL* 2.9 24.4 + - + +
1034B ALA* 3.5 11.9 - - - +
1035B SER 3.3 0.4 - - - -
1036B ASP* 1.3 73.7 - - - +
1038B TRP* 1.3 64.7 + - - +
1040B PHE* 3.3 4.5 + - - +
1041B GLY 3.1 17.3 + - - -
1105B CYS* 3.4 26.3 - - + +
1113B ARG* 3.9 16.4 - - + -
1114B PRO* 3.3 29.2 - - + +
1115B SER* 4.9 0.4 - - - -
1116B PHE* 3.8 31.2 - - + +
1119B LEU* 4.2 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1038 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019B PHE 5.4 1.0 + - - -
1020B TRP 3.4 20.8 + - - -
1021B TYR 3.1 14.1 + - - -
1022B ALA* 3.6 22.0 - - + -
1023B PRO* 3.4 29.6 - - + -
1034B ALA 3.1 11.5 + - - +
1035B SER 3.5 8.5 - - - +
1036B ASP 3.3 0.2 - - - -
1037B VAL* 1.3 75.6 - - - +
1039B SER* 1.3 61.6 + - - +
1041B GLY 3.1 10.9 + - - -
1042B VAL* 3.3 16.6 + - + +
1061B PHE* 5.8 3.2 - + - -
1082B LEU* 3.7 25.8 - - + -
1087B ARG* 3.4 28.3 - - + -
1105B CYS 3.6 14.3 + - - +
1106B TRP* 3.3 54.8 + + + -
1107B ASN 3.8 5.8 - - - -
1113B ARG* 3.6 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1039 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
975B ARG 5.5 4.2 + - - -
977B LEU* 3.9 28.7 + - - +
1020B TRP* 2.7 28.0 + - - +
1021B TYR* 4.6 5.4 - - - -
1035B SER 3.1 12.6 + - - -
1036B ASP* 3.7 9.9 + - - -
1037B VAL 3.3 0.2 - - - -
1038B TRP* 1.3 77.6 - - - +
1040B PHE* 1.3 57.9 + - - +
1042B VAL* 3.0 9.2 + - - +
1043B VAL* 2.9 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1040 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957B THR* 3.5 27.4 - - + -
960B ILE* 3.9 29.6 - - + -
961B CYS* 3.2 28.0 - - - -
977B LEU* 4.1 6.2 - - + +
1036B ASP 2.8 18.2 + - - +
1037B VAL 3.4 4.0 - - - +
1038B TRP 3.2 0.2 - - - -
1039B SER* 1.3 76.6 - - - +
1041B GLY* 1.3 59.2 + - - +
1043B VAL* 3.1 15.2 + - + +
1044B LEU* 2.9 39.0 + - + +
1047B LEU* 6.6 0.2 - - + -
1101B ILE* 4.7 0.9 - - + -
1105B CYS* 3.9 7.9 - - - -
1116B PHE* 3.8 18.4 - + + -
1119B LEU* 3.7 36.6 - - + -
1123B VAL* 5.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1041 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1037B VAL 3.1 7.3 + - - -
1038B TRP 3.1 9.7 + - - -
1040B PHE* 1.3 76.3 - - - +
1042B VAL* 1.3 56.8 + - - +
1044B LEU* 3.4 5.4 + - - -
1045B TYR 3.0 22.0 + - - -
1102B MET* 3.5 10.0 - - - +
1105B CYS* 3.8 20.0 - - - -
1106B TRP* 3.3 21.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1042 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019B PHE 4.0 8.1 - - - +
1020B TRP* 3.4 37.5 - - + +
1038B TRP* 3.3 24.9 + - + +
1039B SER* 3.0 9.6 + - - +
1041B GLY* 1.3 73.7 - - - +
1043B VAL* 1.3 59.5 + - - +
1045B TYR* 3.2 4.4 + - - +
1046B GLU* 2.8 28.3 + - - +
1057B PRO* 3.7 23.6 - - + -
1061B PHE* 6.0 1.1 - - + -
1088B LEU* 4.2 9.2 - - + -
1106B TRP* 3.4 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1043 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
960B ILE* 5.0 10.3 - - + -
977B LEU* 3.7 12.3 - - + +
978B ALA* 3.6 35.2 - - - +
979B THR* 4.1 8.5 - - + -
982B ILE* 3.8 24.7 - - + -
1039B SER 2.9 18.4 + - - +
1040B PHE* 3.1 15.7 + - + +
1042B VAL* 1.3 75.7 - - - +
1044B LEU* 1.3 56.9 + - - +
1046B GLU* 3.2 11.8 + - - +
1047B LEU* 2.9 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1044 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
954B LEU* 4.7 2.9 - - + -
957B THR* 3.6 33.2 - - + +
1040B PHE* 2.9 25.5 + - + +
1041B GLY* 3.6 9.2 - - - +
1043B VAL* 1.3 72.9 - - - +
1045B TYR* 1.3 65.8 + - - +
1047B LEU* 3.4 7.3 + - + +
1048B PHE* 3.2 46.3 + - + +
1098B ILE* 4.0 14.1 - - + +
1101B ILE* 3.7 36.6 - - + -
1102B MET* 3.9 19.6 - - + +
1123B VAL* 5.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1045 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1041B GLY 3.0 10.9 + - - +
1042B VAL* 3.2 7.6 - - - +
1044B LEU* 1.3 74.3 - - - +
1046B GLU* 1.3 70.2 + - - +
1048B PHE* 3.2 3.6 + - - -
1049B THR* 3.1 43.6 + - + +
1055B LYS* 2.5 33.1 + - - +
1057B PRO* 4.1 20.9 - - + -
1060B GLU* 3.3 20.8 + - - +
1088B LEU* 3.8 30.3 - - + -
1089B PRO* 3.2 25.4 - - + +
1091B PRO* 3.7 11.4 - - + +
1102B MET* 3.4 35.6 - - + -
1106B TRP* 4.0 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1046 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938B ARG* 4.5 6.8 - - - -
978B ALA* 3.6 2.4 - - - +
979B THR* 2.6 47.7 + - + -
1020B TRP* 2.8 44.6 + - + +
1042B VAL 2.8 17.2 + - - +
1043B VAL* 3.2 14.9 - - - +
1045B TYR* 1.3 73.9 - - - +
1047B LEU* 1.3 63.0 + - - +
1049B THR* 2.6 26.4 + - - -
1050B TYR 3.3 4.7 + - - -
1051B ILE* 3.5 18.5 - - + +
1057B PRO* 4.3 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1047 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937B LEU* 3.6 31.4 - - + -
941B LEU* 3.4 27.1 - - + +
953B LEU* 3.6 30.8 - - + +
956B TYR* 4.9 5.2 - - + -
957B THR* 3.3 34.3 - - + +
960B ILE* 5.8 2.5 - - + -
979B THR* 4.0 10.8 - - + -
1043B VAL* 2.9 25.7 + - + +
1044B LEU* 3.6 13.9 - - + +
1045B TYR 3.2 0.2 - - - -
1046B GLU* 1.3 76.3 - - - +
1048B PHE* 1.3 64.8 + - + +
1050B TYR* 3.1 16.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1048 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
950B HIS* 3.5 44.1 + + + -
953B LEU* 3.9 28.3 - - + -
954B LEU* 4.0 16.8 - - + -
957B THR* 4.9 0.7 - - - -
1044B LEU* 3.2 32.8 + - + +
1045B TYR 3.2 3.0 + - - -
1047B LEU* 1.3 79.7 - - + +
1049B THR* 1.3 59.4 + - - +
1050B TYR* 3.3 11.3 - - - -
1091B PRO* 3.4 28.7 - - + +
1092B ASP 4.2 10.2 + - - +
1094B CYS* 3.8 21.7 - - + +
1095B PRO* 4.0 11.7 - - + -
1098B ILE* 3.6 25.4 - - + -
1102B MET* 5.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1049 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1045B TYR* 3.1 45.6 + - + +
1046B GLU* 2.6 24.3 + - - -
1048B PHE* 1.3 76.7 - - - +
1050B TYR* 1.3 69.3 + - - +
1051B ILE* 3.1 11.2 + - - -
1052B GLU* 3.2 20.3 + - - +
1055B LYS* 4.0 24.1 + - + +
1056B SER* 5.6 1.4 - - - -
1057B PRO* 6.1 0.2 - - - +
1091B PRO* 3.8 16.2 - - + -
1092B ASP 5.9 0.7 - - - +
----------------------------------------------------------
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