Contacts of the helix formed by residues 1059 - 1081 (chain D) in PDB entry 4DAJ
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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015D LEU* 3.4 7.1 - - - +
1052D ARG* 5.0 5.8 - - - +
1057D VAL* 6.2 0.9 - - + -
1058D ILE* 1.3 76.2 - - - +
1060D LYS* 1.3 65.2 + - - +
1061D ASP* 3.7 10.8 + - - +
1062D GLU* 2.7 42.1 + - - +
1063D ALA* 3.1 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1060 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D LEU* 3.3 45.4 + - + +
174D THR* 4.7 3.1 - - - +
177D ALA* 5.2 4.6 - - - +
178D LYS* 3.1 39.3 - - - +
1013D LEU* 6.0 5.2 - - + -
1015D LEU* 3.5 25.6 - - + +
1059D THR* 1.3 72.1 - - - +
1061D ASP* 1.3 67.9 + - - +
1063D ALA* 3.0 3.8 - - - +
1064D GLU* 2.9 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1061 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C THR* 5.2 10.0 - - - +
171D ARG* 5.7 1.9 - - - -
174D THR* 2.9 37.6 + - - +
1059D THR* 3.2 9.8 + - - +
1060D LYS* 1.3 76.6 + - - +
1062D GLU* 1.3 70.2 + - + +
1063D ALA 3.0 0.7 + - - -
1064D GLU* 3.0 12.0 - - - +
1065D LYS* 2.9 44.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1062 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1050D ILE* 3.6 26.3 - - + +
1052D ARG* 3.3 29.5 + - - -
1058D ILE* 3.0 30.6 - - + +
1059D THR* 2.7 37.7 + - - +
1061D ASP* 1.3 76.7 - - + +
1063D ALA* 1.3 57.9 + - - +
1065D LYS* 3.2 14.8 + - + +
1066D LEU* 2.9 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1063 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D LEU* 3.8 13.2 - - + -
1013D LEU* 5.9 2.0 - - + -
1015D LEU* 4.0 6.5 - - + -
1028D GLY* 4.7 11.3 - - - -
1029D ILE* 5.1 7.1 + - + +
1058D ILE* 3.9 22.1 - - + +
1059D THR 3.1 13.5 + - - +
1060D LYS* 3.0 13.2 + - - +
1061D ASP 3.0 0.4 - - - -
1062D GLU* 1.3 77.2 - - - +
1064D GLU* 1.3 58.2 + - - +
1066D LEU* 3.1 7.2 + - - +
1067D PHE* 2.9 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1064 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D THR 4.3 2.9 - - - +
171D ARG* 3.2 28.6 - - - +
172D PRO* 3.2 14.8 - - + -
173D LEU* 2.8 47.0 + - + +
174D THR* 3.0 27.4 + - - -
1060D LYS 2.9 10.0 + - - +
1061D ASP* 3.0 23.7 - - - +
1063D ALA* 1.3 72.6 - - - +
1065D LYS* 1.3 64.1 + - + +
1067D PHE* 3.2 9.4 - - - +
1068D ASN* 2.7 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1065 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D ARG* 6.3 1.3 - - - +
1061D ASP* 2.9 40.3 + - - +
1062D GLU* 3.4 15.1 - - + +
1064D GLU* 1.3 82.8 - - + +
1066D LEU* 1.3 62.2 + - + +
1068D ASN* 3.4 7.2 + - - +
1069D GLN* 2.9 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1066 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027D ILE* 5.3 4.0 - - + +
1031D HIS* 5.1 24.7 - - + +
1046D LEU* 5.1 8.7 - - + -
1049D ALA* 4.6 21.1 - - + +
1050D ILE* 3.6 33.2 - - + -
1058D ILE* 4.9 12.3 - - + -
1062D GLU 2.9 15.6 + - - +
1063D ALA* 3.5 7.9 - - - +
1065D LYS* 1.3 72.9 - - + +
1067D PHE* 1.3 70.4 + - - +
1069D GLN* 3.2 26.7 + - - +
1070D ASP* 2.9 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1067 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D PRO* 5.0 1.3 - - + -
259D LYS* 4.9 2.9 - - - -
1003D ILE* 4.4 1.8 - - + -
1004D PHE* 3.3 56.1 - + + -
1007D LEU* 3.7 34.5 - - + -
1029D ILE* 3.7 38.9 + - + +
1063D ALA 2.9 12.3 + - - +
1064D GLU* 3.2 11.4 - - - +
1066D LEU* 1.3 80.2 - - - +
1068D ASN* 1.3 92.8 + - - +
1070D ASP* 2.9 18.9 + - - +
1071D VAL* 2.9 32.7 + - + +
1104D PHE* 4.8 3.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1068 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D ILE 4.6 7.3 - - - +
170D THR* 3.5 24.9 + - - -
172D PRO* 4.1 8.1 - - - +
259D LYS* 3.2 34.4 + - - +
1064D GLU 2.7 29.3 + - - +
1065D LYS* 3.9 6.7 - - - +
1067D PHE* 1.3 95.0 - - - +
1069D GLN* 1.3 62.6 + - - +
1071D VAL* 3.1 7.4 + - - +
1072D ASP* 2.9 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1069 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1031D HIS* 5.7 4.0 - - - -
1049D ALA* 5.2 6.7 + - - +
1065D LYS 2.9 13.2 + - - +
1066D LEU* 3.4 33.3 - - - +
1068D ASN* 1.3 76.4 - - - +
1070D ASP* 1.3 70.8 + - - +
1072D ASP* 3.2 6.7 + - - +
1073D ALA* 2.9 21.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1070 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1029D ILE 4.1 4.0 - - - +
1030D GLY 5.1 0.7 - - - -
1031D HIS* 3.5 45.8 + - - +
1066D LEU* 2.9 20.5 + - - +
1067D PHE 3.0 9.9 - - - +
1069D GLN* 1.3 81.0 - - - +
1071D VAL* 1.3 55.0 + - - +
1073D ALA* 2.9 12.3 - - - +
1074D ALA* 2.9 29.1 + - - +
1104D PHE* 3.4 27.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1071 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259D LYS* 3.8 17.5 - - + -
1003D ILE* 3.4 29.2 - - + -
1007D LEU* 4.7 6.3 - - + -
1067D PHE* 2.9 53.3 + - + +
1068D ASN* 3.1 10.5 + - - +
1070D ASP* 1.3 76.5 - - - +
1072D ASP* 1.3 65.8 + - - +
1074D ALA* 2.9 8.7 + - - +
1075D VAL* 2.9 32.4 + - + +
1100D ILE* 5.1 2.7 - - + -
1104D PHE* 4.7 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1072 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D GLU* 4.2 10.4 - - - +
259D LYS* 3.6 19.4 + - - -
1068D ASN 2.9 13.5 + - - +
1069D GLN* 3.6 9.2 - - - +
1071D VAL* 1.3 76.9 - - - +
1073D ALA* 1.3 61.4 + - - +
1075D VAL* 4.4 7.8 - - - +
1076D ARG* 2.8 65.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1073 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1069D GLN* 2.9 15.6 + - + +
1070D ASP* 2.9 19.3 + - - +
1072D ASP* 1.3 77.2 - - - +
1074D ALA* 1.3 54.3 + - - +
1076D ARG* 3.8 7.4 - - - +
1077D GLY* 2.9 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1074 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1070D ASP 2.9 11.4 + - - +
1071D VAL* 3.5 7.9 - - - +
1073D ALA* 1.3 73.4 - - - +
1075D VAL* 1.3 66.7 + - - +
1077D GLY* 3.0 3.7 + - - -
1078D ILE* 2.9 26.9 + - - +
1100D ILE* 4.1 11.4 - - + +
1103D VAL* 3.5 24.0 - - + +
1104D PHE* 3.8 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1075 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003D ILE* 5.7 0.2 - - + -
1071D VAL* 2.9 32.3 + - + +
1072D ASP* 3.8 8.5 - - - +
1074D ALA* 1.3 75.3 - - - +
1076D ARG* 1.3 60.5 + - + +
1078D ILE* 2.7 32.5 + - + +
1079D LEU* 3.0 25.4 + - + +
1088D TYR* 5.2 10.5 - - + +
1100D ILE* 4.0 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1076 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1072D ASP* 2.8 57.7 + - - +
1073D ALA* 3.9 5.4 - - - +
1075D VAL* 1.3 79.5 - - + +
1077D GLY* 1.3 56.6 + - - +
1079D LEU* 3.9 7.5 - - - +
1080D ARG* 2.9 42.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1077 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1073D ALA 2.9 15.2 + - - -
1074D ALA* 3.3 7.4 - - - -
1075D VAL 2.9 1.2 - - - -
1076D ARG* 1.3 78.0 - - - +
1078D ILE* 1.3 57.2 + - - +
1080D ARG* 4.2 3.6 - - - -
1081D ASN* 3.3 10.6 + - - +
1084D LEU* 3.6 2.5 - - - +
1103D VAL* 5.1 0.9 - - - -
1108D GLU* 3.0 45.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1078 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1074D ALA 2.9 18.1 + - - +
1075D VAL* 2.7 15.3 + - + +
1077D GLY* 1.3 71.7 - - - -
1079D LEU* 1.3 63.4 + - + +
1081D ASN 3.5 4.4 - - - +
1084D LEU* 3.5 19.5 - - + +
1085D LYS* 3.0 20.8 + - - -
1088D TYR* 3.3 44.0 - - + -
1099D LEU* 4.3 5.8 - - + -
1100D ILE* 3.5 45.8 - - + +
1103D VAL* 4.0 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1079 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1075D VAL* 3.0 28.8 + - + +
1076D ARG* 4.0 6.3 - - - +
1078D ILE* 1.3 79.8 - - + +
1080D ARG* 1.3 67.6 + - + +
1081D ASN 3.8 0.2 - - - +
1085D LYS* 3.8 44.6 - - + +
1088D TYR* 4.3 24.2 - - + -
1089D ASP* 4.6 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1080 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1076D ARG* 2.9 26.5 + - + +
1077D GLY* 5.3 1.6 - - - -
1079D LEU* 1.3 78.1 - - + +
1081D ASN* 1.3 66.0 + - - +
1082D ALA* 3.3 3.5 + - - -
1108D GLU* 3.6 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1081 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1077D GLY 3.3 16.5 + - - +
1078D ILE 3.5 2.1 + - - +
1079D LEU 3.4 0.4 - - - +
1080D ARG* 1.3 79.8 - - - +
1082D ALA* 1.3 64.0 + - - +
1083D LYS* 2.5 36.3 + - - +
1084D LEU* 2.8 23.8 + - + -
1085D LYS* 3.3 22.3 + - - +
1108D GLU* 2.9 36.7 + - + +
1109D THR* 5.3 0.6 - - - +
1112D ALA* 3.8 18.2 - - - +
----------------------------------------------------------
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