Contacts of the helix formed by residues 1059 - 1081 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A PRO* 6.0 6.1 - - + -
1015B LEU* 4.0 1.8 - - - -
1052B ARG* 5.6 4.7 - - - +
1058B ILE* 1.3 77.3 - - - +
1060B LYS* 1.3 66.0 + - - +
1061B ASP* 3.0 14.0 + - - +
1062B GLU* 3.0 44.7 + - - +
1063B ALA* 3.1 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1060 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B LEU* 3.9 39.6 + - + +
174B THR* 5.2 3.6 - - - +
178B LYS* 4.6 9.9 - - - +
1013B LEU* 6.2 2.7 - - + -
1015B LEU* 3.7 31.1 - - + +
1059B THR* 1.3 73.4 - - - +
1061B ASP* 1.3 68.1 + - - +
1063B ALA* 3.1 5.2 + - - +
1064B GLU* 2.9 26.3 + - - +
2001B PO4 3.6 36.8 + - - +
1131C VAL* 6.1 1.4 - - - +
1154C ARG* 2.9 41.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1061 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A THR* 4.3 23.7 + - - +
174B THR* 2.8 28.6 + - - +
1059B THR* 3.0 11.6 + - - +
1060B LYS* 1.3 78.7 - - - +
1062B GLU* 1.3 57.7 + - + +
1064B GLU* 2.8 30.6 - - - +
1065B LYS* 2.9 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1062 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A PRO* 6.0 1.2 - - - +
1050B ILE* 3.4 39.9 - - + +
1052B ARG* 3.4 29.5 + - - -
1058B ILE* 4.0 12.0 - - + +
1059B THR* 3.0 32.0 + - - +
1061B ASP* 1.3 76.5 - - + +
1063B ALA* 1.3 57.3 + - - +
1065B LYS* 3.5 19.9 - - + +
1066B LEU* 2.9 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1063 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B LEU* 4.9 6.3 - - + -
1013B LEU* 6.2 2.7 - - + -
1015B LEU* 4.4 9.2 - - + -
1028B GLY* 4.9 12.6 - - - -
1029B ILE* 5.5 8.2 + - + +
1058B ILE* 3.9 21.0 - - + +
1059B THR 3.1 11.2 + - - +
1060B LYS* 3.1 14.6 + - - +
1062B GLU* 1.3 77.6 - - - +
1064B GLU* 1.3 57.8 - - - +
1066B LEU* 3.2 7.3 + - - +
1067B PHE* 2.9 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1064 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B THR 4.6 2.2 - - - +
171B ARG* 3.2 16.9 - - - +
172B PRO* 3.1 32.6 - - + +
173B LEU* 3.1 26.0 + - + +
174B THR* 2.6 30.0 + - - -
1004B PHE* 5.4 4.5 - - + -
1029B ILE* 5.9 1.3 - - - -
1060B LYS 2.9 12.2 + - - +
1061B ASP* 2.8 30.0 - - - +
1063B ALA* 1.3 72.5 - - - +
1065B LYS* 1.3 70.3 + - + +
1067B PHE* 3.0 9.7 + - - +
1068B ASN* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1065 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1061B ASP* 2.9 45.3 + - - +
1062B GLU* 3.5 19.6 - - + +
1064B GLU* 1.3 82.6 - - + +
1066B LEU* 1.3 63.3 + - + +
1068B ASN* 3.2 8.9 + - - +
1069B GLN* 2.9 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1066 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027B ILE* 5.2 4.0 - - + -
1031B HIS* 4.7 22.9 - - + +
1046B LEU* 5.0 7.2 - - + -
1049B ALA* 4.9 16.8 - - + +
1050B ILE* 3.9 28.3 - - + -
1058B ILE* 4.5 17.0 - - + -
1062B GLU 2.9 25.0 + - - +
1063B ALA* 3.2 5.6 + - - +
1065B LYS* 1.3 76.7 - - + +
1067B PHE* 1.3 56.9 + - - +
1069B GLN* 3.3 27.4 - - - +
1070B ASP* 2.8 41.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1067 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B PRO* 5.6 0.4 - - + -
259B LYS* 5.0 5.4 - - + -
1003B ILE* 4.7 2.9 - - + -
1004B PHE* 3.5 50.0 - + + -
1007B LEU* 3.6 36.6 - - + -
1029B ILE* 3.7 41.1 - - + +
1063B ALA 2.9 12.5 + - - +
1064B GLU* 3.0 11.8 + - - +
1066B LEU* 1.3 74.3 - - - +
1068B ASN* 1.3 81.7 + - - +
1070B ASP* 3.2 8.7 + - - +
1071B VAL* 2.9 46.9 + - + +
1104B PHE* 4.2 6.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1068 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ILE* 4.6 5.0 + - - +
170B THR* 3.3 30.1 + - - +
172B PRO* 4.6 6.1 - - - +
259B LYS* 3.1 43.0 + - - +
1064B GLU 2.9 27.9 + - - -
1065B LYS* 3.6 8.8 - - - +
1067B PHE* 1.3 86.0 - - - +
1069B GLN* 1.3 63.9 + - - +
1071B VAL* 3.1 3.5 + - - -
1072B ASP* 2.9 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1069 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1031B HIS* 5.1 5.5 - - - -
1049B ALA* 5.4 9.7 + - - +
1065B LYS 2.9 12.1 + - - +
1066B LEU* 3.3 34.0 - - - +
1068B ASN* 1.3 76.4 - - - +
1070B ASP* 1.3 65.5 + - - +
1072B ASP* 3.4 6.3 + - - +
1073B ALA* 2.9 33.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1070 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1029B ILE 4.1 8.3 - - - +
1030B GLY 5.4 0.7 - - - +
1031B HIS* 3.0 48.9 + - - +
1066B LEU* 2.8 28.8 + - - +
1067B PHE* 3.6 5.1 - - - +
1069B GLN* 1.3 78.5 - - - +
1071B VAL* 1.3 57.9 + - - +
1073B ALA* 3.7 6.4 - - - +
1074B ALA* 2.9 30.5 + - - +
1104B PHE* 3.7 20.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1071 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B GLU* 4.4 2.5 - - - +
259B LYS* 3.9 20.2 - - + +
1003B ILE* 3.7 25.8 - - + -
1007B LEU* 4.6 1.1 - - + -
1067B PHE* 2.9 61.4 + - + +
1068B ASN* 3.1 8.0 + - - +
1070B ASP* 1.3 74.4 - - - +
1072B ASP* 1.3 66.7 + - - +
1074B ALA* 3.2 5.3 + - - +
1075B VAL* 2.9 37.0 + - + +
1100B ILE* 4.6 4.0 - - + +
1104B PHE* 4.0 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1072 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B GLU* 5.6 0.2 - - - +
259B LYS* 2.7 37.4 + - - -
1068B ASN* 2.9 14.6 + - - +
1069B GLN* 3.9 4.9 + - - +
1071B VAL* 1.3 76.1 - - - +
1073B ALA* 1.3 59.2 + - - +
1075B VAL* 3.1 10.5 + - - +
1076B ARG* 2.9 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1073 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1069B GLN* 2.9 21.5 + - + +
1070B ASP* 3.7 8.3 - - - +
1072B ASP* 1.3 77.6 - - - +
1074B ALA* 1.3 56.1 + - - +
1076B ARG* 3.4 7.7 + - - +
1077B GLY* 2.9 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1074 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1070B ASP 2.9 18.5 + - - +
1071B VAL* 3.2 4.5 + - - +
1073B ALA* 1.3 76.6 - - - +
1075B VAL* 1.3 57.6 + - - +
1077B GLY* 3.1 4.4 + - - -
1078B ILE* 2.9 32.0 + - - +
1100B ILE* 4.9 8.3 - - + +
1103B VAL* 3.9 27.1 - - + +
1104B PHE* 4.6 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1075 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B GLU* 4.3 19.5 - - - +
1071B VAL* 2.9 28.1 + - + +
1072B ASP* 3.5 11.9 - - - +
1074B ALA* 1.3 73.2 - - - +
1076B ARG* 1.3 66.5 + - - +
1078B ILE* 2.9 20.6 + - + +
1079B LEU* 2.9 33.9 + - + +
1088B TYR* 5.0 13.5 - - + +
1100B ILE* 4.6 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1076 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1072B ASP 2.9 12.5 + - - +
1073B ALA* 3.6 11.2 - - - +
1075B VAL* 1.3 75.0 - - - +
1077B GLY* 1.3 57.1 + - - +
1079B LEU* 4.3 5.3 - - - +
1080B ARG* 2.9 35.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1077 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1073B ALA 2.9 14.0 + - - -
1074B ALA* 3.3 6.1 - - - -
1075B VAL 3.1 0.4 - - - -
1076B ARG* 1.3 77.5 - - - +
1078B ILE* 1.3 62.6 + - - +
1080B ARG* 3.8 4.6 - - - +
1081B ASN* 3.3 21.3 + - - +
1084B LEU* 4.6 2.3 - - - +
1103B VAL* 5.6 2.5 - - - -
1108B GLU* 5.1 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1078 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1074B ALA 2.9 17.0 + - - +
1075B VAL* 2.9 14.9 + - + +
1077B GLY* 1.3 74.8 - - - +
1079B LEU* 1.3 68.5 + - + +
1081B ASN 3.3 17.2 + - - +
1084B LEU* 3.5 27.5 - - + +
1085B LYS 3.8 1.4 + - - -
1088B TYR* 3.8 42.0 - - + -
1099B LEU* 4.3 16.8 - - + -
1100B ILE* 4.4 20.6 - - + +
1103B VAL* 3.7 32.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1079 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1075B VAL* 2.9 34.3 + - + +
1076B ARG* 4.3 4.5 - - - +
1078B ILE* 1.3 80.4 - - + +
1080B ARG* 1.3 62.3 + - - +
1081B ASN 3.2 8.3 + - - +
1085B LYS* 4.0 27.5 - - + +
1088B TYR* 3.8 33.0 - - + -
1089B ASP* 4.6 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1080 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1076B ARG 2.9 21.8 + - - +
1077B GLY* 3.8 6.5 - - - +
1078B ILE 3.3 0.2 - - - -
1079B LEU* 1.3 77.5 - - - +
1081B ASN* 1.3 59.1 + - - +
1082B ALA 3.8 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1081 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1077B GLY 3.3 6.8 + - - +
1078B ILE 3.3 12.1 + - - +
1079B LEU 3.1 8.2 - - - +
1080B ARG* 1.3 79.6 - - - +
1082B ALA* 1.3 66.1 + - - +
1083B LYS* 3.0 33.1 + - - +
1084B LEU* 3.4 26.3 + - + +
1085B LYS* 3.3 18.7 + - - +
1108B GLU* 5.7 6.4 - - + +
1112B ALA* 5.0 10.9 - - - +
----------------------------------------------------------
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