Contacts of the helix formed by residues 1058 - 1080 (chain A) in PDB entry 5CXV
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 THR1058 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1014A LEU* 4.2 2.5 - - - -
1051A ARG* 4.7 5.8 - - - +
1057A ILE* 1.3 78.7 - - - +
1059A LYS* 1.3 61.0 + - - +
1060A ASP* 2.6 28.1 + - - +
1061A GLU* 2.8 32.5 + - - +
1062A ALA* 2.9 26.3 + - - +
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Residues in contact with LYS1059 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU* 3.7 38.6 - - + +
132A SER* 4.1 11.0 - - - -
135A ALA* 3.6 26.6 - - - +
1012A LEU* 5.1 3.1 - - + -
1014A LEU* 4.0 31.8 - - + +
1058A THR* 1.3 74.9 - - - +
1060A ASP* 1.3 58.2 + - - +
1062A ALA* 3.3 5.4 + - - +
1063A GLU* 2.9 29.1 + - - +
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Residues in contact with ASP1060 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A SER* 3.7 21.9 - - - +
1058A THR* 2.6 27.1 + - - +
1059A LYS* 1.3 74.4 - - - +
1061A GLU* 1.3 66.3 + - - +
1062A ALA 3.3 0.2 - - - -
1063A GLU* 3.3 14.0 + - - +
1064A LYS* 2.9 26.5 + - - +
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Residues in contact with GLU1061 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049A ILE* 3.2 33.8 - - + +
1051A ARG* 2.6 37.7 + - - -
1057A ILE* 3.3 15.5 - - + +
1058A THR* 2.8 44.2 + - - +
1060A ASP* 1.3 83.7 - - - +
1062A ALA* 1.3 58.5 + - - +
1064A LYS* 3.7 6.7 - - + +
1065A LEU* 2.9 32.4 + - - +
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Residues in contact with ALA1062 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU* 4.5 2.7 - - + -
1003A PHE* 5.4 0.9 - - - -
1012A LEU* 4.0 27.4 - - + -
1014A LEU* 4.2 1.8 - - + -
1027A GLY* 4.3 6.3 - - - -
1028A ILE* 4.9 6.5 + - + +
1057A ILE* 4.0 19.2 - - + +
1058A THR 2.9 13.3 + - - +
1059A LYS* 3.4 11.7 - - - +
1060A ASP 3.3 0.2 - - - -
1061A GLU* 1.3 74.6 - - - +
1063A GLU* 1.3 59.4 + - - +
1065A LEU* 3.8 5.0 - - - +
1066A PHE* 2.9 28.9 + - - +
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Residues in contact with GLU1063 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A THR 5.2 0.9 - - - -
129A ARG* 3.2 24.7 - - - +
130A PRO* 3.5 3.0 - - + -
131A LEU* 2.8 25.0 + - + -
132A SER* 2.7 48.1 + - - -
1003A PHE* 4.1 15.2 - - + -
1059A LYS 2.9 14.6 + - - +
1060A ASP* 3.5 11.4 - - - +
1061A GLU 3.2 0.4 - - - -
1062A ALA* 1.3 74.4 - - - +
1064A LYS* 1.3 60.0 + - - +
1066A PHE* 3.2 5.8 + - - +
1067A ASN* 2.9 40.5 + - - +
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Residues in contact with LYS1064 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1060A ASP* 2.9 17.1 + - - +
1061A GLU* 3.4 8.3 + - - +
1063A GLU* 1.3 76.4 - - - +
1065A LEU* 1.3 62.6 + - + +
1067A ASN* 3.2 10.2 + - - +
1068A GLN* 3.0 24.0 + - - +
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Residues in contact with LEU1065 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1026A ILE* 3.7 31.0 - - + +
1027A GLY* 5.2 2.0 - - - -
1028A ILE 6.1 0.9 - - - +
1030A HIS* 3.8 25.4 - - + +
1045A LEU* 6.1 1.3 - - + -
1048A ALA* 4.3 23.3 - - + +
1049A ILE* 5.0 13.7 - - + -
1057A ILE* 4.5 12.8 - - + -
1061A GLU 2.9 19.0 + - - +
1062A ALA* 3.9 5.4 - - - +
1064A LYS* 1.3 76.0 - - - +
1066A PHE* 1.3 58.8 + - - +
1068A GLN* 3.0 29.2 - - + +
1069A ASP* 3.0 32.3 + - - -
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Residues in contact with PHE1066 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ASN 5.5 0.4 - - - -
1002A ILE* 4.1 2.5 - - + -
1003A PHE* 3.3 50.9 - + + -
1006A LEU* 3.4 47.8 - - + -
1028A ILE* 4.0 29.1 - - + +
1062A ALA 2.9 19.7 + - - +
1063A GLU 3.7 3.4 - - - +
1064A LYS 3.2 0.2 - - - -
1065A LEU* 1.3 75.2 - - - +
1067A ASN* 1.3 68.9 + - - +
1069A ASP* 3.2 4.6 + - - +
1070A VAL* 2.9 47.0 + - + +
1103A PHE* 3.8 17.9 - + - -
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Residues in contact with ASN1067 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A THR 5.9 0.8 + - - -
1003A PHE* 5.4 2.1 - - - -
1063A GLU* 2.9 30.5 + - - +
1064A LYS* 3.6 8.1 - - - +
1066A PHE* 1.3 85.3 - - - +
1068A GLN* 1.3 63.7 + - - +
1070A VAL* 3.8 8.2 - - - +
1071A ASP* 3.0 35.2 + - - +
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Residues in contact with GLN1068 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1030A HIS* 3.0 28.5 + - - -
1064A LYS 3.0 11.1 + - - +
1065A LEU* 3.0 33.8 + - + +
1067A ASN* 1.3 75.6 - - - +
1069A ASP* 1.3 90.5 + - - +
1071A ASP* 3.5 3.7 + - - +
1072A ALA* 3.0 28.6 + - - +
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Residues in contact with ASP1069 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506A GOL 3.5 26.6 + - - -
1028A ILE 4.6 1.7 - - - +
1030A HIS* 3.2 34.6 + - - +
1065A LEU 3.0 21.4 + - - +
1066A PHE* 3.2 4.3 + - - +
1068A GLN* 1.3 103.5 + - - +
1070A VAL* 1.3 56.3 - - - +
1072A ALA* 3.2 6.5 + - - +
1073A ALA* 2.9 26.5 + - - +
1103A PHE* 3.4 27.5 - - + -
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Residues in contact with VAL1070 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002A ILE* 4.2 20.0 - - + -
1006A LEU* 4.9 0.4 - - + -
1066A PHE* 2.9 40.6 + - + +
1067A ASN* 3.3 16.4 - - - +
1069A ASP* 1.3 72.5 - - - +
1071A ASP* 1.3 71.1 + - - +
1073A ALA* 3.1 3.7 + - - +
1074A VAL* 3.0 30.0 + - + +
1099A ILE* 4.0 24.7 - - + -
1103A PHE* 3.9 10.8 - - + -
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Residues in contact with ASP1071 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067A ASN* 3.0 29.2 + - - +
1068A GLN* 4.0 3.8 - - - +
1070A VAL* 1.3 85.7 - - - +
1072A ALA* 1.3 56.1 + - - +
1074A VAL* 4.1 4.3 - - - +
1075A ARG* 2.9 32.8 + - - +
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Residues in contact with ALA1072 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506A GOL 5.3 5.4 - - - +
1068A GLN* 3.0 23.0 + - - +
1069A ASP* 3.2 7.6 + - - +
1071A ASP* 1.3 76.7 - - - +
1073A ALA* 1.3 58.3 + - - +
1075A ARG* 4.0 3.7 - - - +
1076A GLY* 2.9 26.0 + - - -
1107A GLU* 4.7 1.0 - - - +
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Residues in contact with ALA1073 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506A GOL 5.3 4.7 + - - +
1069A ASP 2.9 13.2 + - - +
1070A VAL* 3.1 13.7 + - - +
1072A ALA* 1.3 77.8 - - - +
1074A VAL* 1.3 57.5 + - - +
1076A GLY 3.5 0.3 + - - -
1077A ILE* 2.9 32.7 + - + +
1099A ILE* 4.7 11.4 - - + +
1102A VAL* 4.2 19.6 - - + +
1103A PHE* 4.3 15.5 - - + +
1107A GLU* 3.8 4.2 - - - +
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Residues in contact with VAL1074 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1070A VAL* 3.0 22.8 + - + +
1071A ASP* 4.2 3.8 - - - +
1073A ALA* 1.3 71.8 - - - +
1075A ARG* 1.3 69.8 + - - +
1077A ILE* 3.0 7.8 + - + +
1078A LEU* 2.9 34.2 + - + +
1087A TYR* 3.5 32.8 - - + +
1099A ILE* 3.6 32.1 - - + -
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Residues in contact with ARG1075 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1071A ASP 2.9 19.1 + - - +
1072A ALA* 4.0 4.0 - - - +
1074A VAL* 1.3 76.9 - - - +
1076A GLY* 1.3 64.2 + - - +
1078A LEU* 3.3 10.9 + - - +
1079A ARG* 3.0 21.4 + - - +
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Residues in contact with GLY1076 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1072A ALA 2.9 16.8 + - - -
1075A ARG* 1.3 74.9 - - - +
1077A ILE* 1.3 65.4 + - - +
1079A ARG* 2.9 10.1 + - - +
1080A ASN* 2.9 22.3 + - - +
1107A GLU* 2.9 24.5 - - - +
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Residues in contact with ILE1077 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1073A ALA 2.9 20.0 + - - +
1074A VAL* 3.0 12.7 + - - +
1076A GLY* 1.3 74.5 - - - +
1078A LEU* 1.3 64.1 + - - +
1080A ASN* 3.1 25.6 + - - +
1083A LEU* 4.2 17.9 - - + +
1084A LYS 3.7 5.8 + - - +
1087A TYR* 3.8 38.1 - - + -
1098A LEU* 4.4 10.3 - - + -
1099A ILE* 4.2 26.7 - - + -
1102A VAL* 3.6 36.3 - - + -
1107A GLU* 3.2 2.4 + - - +
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Residues in contact with LEU1078 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1074A VAL* 2.9 33.1 + - + +
1075A ARG* 3.8 8.1 - - - +
1077A ILE* 1.3 75.0 - - - +
1079A ARG* 1.3 59.3 + - - +
1084A LYS* 3.3 35.8 + - + +
1087A TYR* 3.6 36.3 - - + +
1088A ASP* 3.9 11.4 - - - +
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Residues in contact with ARG1079 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1075A ARG 3.0 12.5 + - - +
1076A GLY* 2.9 13.0 + - - +
1078A LEU* 1.3 78.9 - - - +
1080A ASN* 1.3 61.6 + - - +
1081A ALA* 3.6 2.9 + - - +
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Residues in contact with ASN1080 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1076A GLY 2.9 13.9 + - - +
1077A ILE 3.1 7.6 + - - +
1079A ARG* 1.3 76.7 - - - +
1081A ALA* 1.3 63.3 + - - +
1082A LYS* 2.7 34.2 + - - +
1083A LEU* 3.0 25.6 + - + +
1084A LYS* 3.1 25.2 + - - +
1107A GLU* 4.2 29.0 + - - +
1108A THR* 5.3 1.4 + - - +
1111A ALA* 4.9 5.3 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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