Contacts of the helix formed by residues 1059 - 1080 (chain E) in PDB entry 5B2G
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 THR1059 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015E LEU* 4.6 1.6 - - - -
1058E ILE* 1.3 78.3 - - - +
1060E LYS* 1.3 63.7 + - - +
1061E ASP* 3.8 7.7 + - - +
1062E GLU* 3.5 32.2 + - - +
1063E ALA* 3.1 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1060 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008E ARG* 4.0 31.7 + - - +
1013E LEU* 6.2 0.7 - - - -
1015E LEU* 4.8 13.9 - - + +
1059E THR* 1.3 72.6 - - - +
1061E ASP* 1.3 67.2 + - - +
1063E ALA* 3.9 4.8 - - - +
1064E GLU* 2.9 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1061 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059E THR* 3.3 7.9 + - - +
1060E LYS* 1.3 86.0 + - - +
1062E GLU* 1.3 59.8 + - + +
1064E GLU* 4.1 5.7 - - - +
1065E LYS* 3.0 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1062 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1050E ILE* 5.1 13.0 - - + +
1052E ARG* 5.0 14.2 + - - +
1058E ILE* 5.3 8.2 - - + +
1059E THR* 3.5 27.2 + - - +
1061E ASP* 1.3 80.7 - - + +
1063E ALA* 1.3 58.4 + - - +
1065E LYS* 3.9 4.3 - - - +
1066E LEU* 2.9 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1063 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1013E LEU* 6.2 2.5 - - + -
1015E LEU* 5.2 5.6 - - + -
1028E GLY* 4.8 8.7 - - - -
1029E ILE* 4.0 14.5 + - + +
1058E ILE* 3.8 25.2 - - + +
1059E THR 3.1 20.3 + - - +
1060E LYS* 3.9 5.8 - - - +
1062E GLU* 1.3 77.6 - - - +
1064E GLU* 1.3 58.3 + - - +
1066E LEU* 3.5 9.4 + - - +
1067E PHE* 3.1 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1064 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004E PHE* 3.4 44.2 - - + +
1008E ARG* 6.3 0.9 - - - +
1029E ILE* 4.5 7.2 - - + -
1060E LYS* 2.9 19.7 + - - +
1061E ASP* 4.2 5.4 - - - +
1063E ALA* 1.3 76.0 - - - +
1065E LYS* 1.3 73.2 + - - +
1067E PHE* 3.3 8.8 + - + +
1068E ASN* 2.8 44.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1065 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1061E ASP* 3.0 27.9 + - + +
1062E GLU* 4.0 4.5 - - - +
1064E GLU* 1.3 90.9 + - - +
1066E LEU* 1.3 64.3 + - - +
1067E PHE 3.2 0.2 - - - -
1068E ASN* 3.3 28.5 + - + +
1069E GLN* 3.1 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1066 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027E ILE* 4.9 19.3 - - + +
1028E GLY* 5.4 2.7 - - - -
1029E ILE 5.0 7.9 - - - +
1031E HIS* 4.3 12.8 - - + +
1033E LEU* 5.7 5.6 - - + -
1049E ALA 5.3 1.8 - - - +
1050E ILE* 3.5 31.4 - - + -
1058E ILE* 6.4 1.1 - - + -
1062E GLU 2.9 20.5 + - - +
1063E ALA* 3.7 8.5 - - - +
1065E LYS* 1.3 76.3 - - - +
1067E PHE* 1.3 64.5 + - - +
1069E GLN* 3.6 6.1 + - - +
1070E ASP* 2.8 59.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1067 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003E ILE* 4.9 4.7 - - + -
1004E PHE* 5.1 10.1 - - + -
1007E LEU* 3.1 51.4 - - + -
1029E ILE* 3.7 48.0 - - + -
1063E ALA 3.1 14.7 + - - +
1064E GLU* 3.4 9.9 - - + +
1065E LYS 3.2 0.2 - - - -
1066E LEU* 1.3 79.8 - - - +
1068E ASN* 1.3 69.6 + - - +
1070E ASP* 3.2 10.4 + - + +
1071E VAL* 2.9 50.5 + - + +
1104E PHE* 3.8 29.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1068 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003E ILE* 5.2 8.9 - - - +
1004E PHE* 6.1 1.6 - - - +
1064E GLU* 2.8 27.2 + - - +
1065E LYS* 3.3 33.8 + - + +
1067E PHE* 1.3 86.7 - - - +
1069E GLN* 1.3 60.6 + - + +
1071E VAL* 3.2 9.4 + - - +
1072E ASP* 3.0 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1069 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1065E LYS* 3.1 23.1 + - - +
1066E LEU* 4.0 7.1 - - - +
1067E PHE 3.4 0.2 - - - -
1068E ASN* 1.3 76.3 - - + +
1070E ASP* 1.3 61.1 + - - +
1072E ASP* 3.3 6.2 + - - +
1073E ALA* 2.9 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1070 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1031E HIS* 3.0 58.1 + - + +
1066E LEU* 2.8 32.7 + - - +
1067E PHE* 3.5 9.0 - - - +
1069E GLN* 1.3 79.8 - - - +
1071E VAL* 1.3 57.8 + - - +
1073E ALA* 3.9 6.1 - - - +
1074E ALA* 2.9 30.5 + - - +
1104E PHE* 4.9 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1071 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007E LEU* 5.1 2.5 - - + -
1067E PHE* 2.9 53.0 + - + +
1068E ASN* 3.5 13.0 - - - +
1069E GLN 3.1 0.2 - - - -
1070E ASP* 1.3 78.0 - - - +
1072E ASP* 1.3 66.4 + - - +
1074E ALA* 3.6 5.3 - - - +
1075E VAL* 3.0 33.0 + - + +
1100E ILE* 3.9 30.5 - - + -
1104E PHE* 4.9 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1072 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1068E ASN* 3.0 19.2 + - - +
1069E GLN* 3.3 6.0 + - - +
1071E VAL* 1.3 82.5 - - - +
1073E ALA* 1.3 64.3 + - - +
1075E VAL* 4.1 4.6 - - - +
1076E ARG* 3.1 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1073 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1069E GLN 2.9 17.3 + - - +
1070E ASP* 3.9 7.6 - - - +
1072E ASP* 1.3 75.0 - - - +
1074E ALA* 1.3 58.2 + - - +
1076E ARG* 3.9 4.4 - - - +
1077E GLY* 2.9 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1074 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1070E ASP 2.9 20.4 + - - +
1071E VAL* 3.6 8.1 - - - +
1072E ASP 3.3 0.2 - - - -
1073E ALA* 1.3 75.4 - - - +
1075E VAL* 1.3 64.9 + - + +
1077E GLY* 3.2 2.7 + - - -
1078E ILE* 3.0 30.1 + - + +
1100E ILE* 5.4 5.2 - - + -
1103E VAL* 5.4 4.4 - - + +
1104E PHE* 5.0 15.3 - - + -
1108E GLU* 4.6 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1075 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1071E VAL* 3.0 24.8 + - + +
1072E ASP* 4.1 5.6 - - - +
1074E ALA* 1.3 76.4 - - - +
1076E ARG* 1.3 59.2 + - + +
1078E ILE* 3.0 17.0 + - + +
1079E LEU* 3.0 41.4 + - + +
1088E TYR* 4.3 24.9 - - + +
1100E ILE* 3.4 43.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1076 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1072E ASP* 3.1 22.4 + - + +
1073E ALA* 4.2 4.7 - - - +
1075E VAL* 1.3 78.9 - - + +
1077E GLY* 1.3 61.4 + - - +
1079E LEU* 3.2 32.3 + - + +
1080E ARG* 3.3 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1077 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1073E ALA 2.9 17.8 + - - -
1074E ALA* 3.5 5.6 - - - -
1075E VAL 3.1 0.4 - - - -
1076E ARG* 1.3 78.9 - - - +
1078E ILE* 1.3 58.8 + - - +
1080E ARG* 3.6 27.7 + - - +
1108E GLU* 3.3 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1078 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1074E ALA* 3.0 21.4 + - + +
1075E VAL* 3.2 19.5 - - + +
1077E GLY* 1.3 77.4 - - - +
1079E LEU* 1.3 59.9 + - + +
1080E ARG 2.8 21.3 - - - +
1082E ALA 4.7 1.4 + - - -
1083E LYS 5.0 0.3 + - - -
1084E LEU* 3.6 43.7 + - + +
1085E LYS 5.1 0.9 + - - -
1100E ILE* 5.4 6.3 - - + -
1103E VAL* 3.2 45.8 - - + -
1108E GLU* 3.9 16.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1079 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1075E VAL* 3.0 34.7 + - + +
1076E ARG* 3.2 31.1 + - + +
1078E ILE* 1.3 79.4 - - + +
1080E ARG* 1.3 60.7 + - + +
1082E ALA* 3.8 8.9 + - - +
1085E LYS* 3.9 59.7 + - + +
1088E TYR* 4.8 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1080 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1076E ARG 3.3 15.2 + - - +
1077E GLY* 3.8 19.9 + - - +
1078E ILE 2.8 16.6 - - - +
1079E LEU* 1.3 75.0 - - + +
1081E ASN* 1.3 67.1 + - + +
1082E ALA 3.1 8.1 + - - -
1083E LYS 4.7 0.5 + - - -
1108E GLU* 4.9 2.4 - - - +
----------------------------------------------------------
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