Contacts of the helix formed by residues 1071 - 1088 (chain A) in PDB entry 1DJO
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 THR1071 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1069A SER 4.0 8.7 - - - +
1070A ILE* 1.3 86.3 - - - +
1072A ASN* 1.3 66.0 + - - +
1073A ASP* 3.6 11.2 + - - +
1074A ASP* 3.1 39.6 + - - +
1075A LEU* 3.2 12.4 + - - +
3232B ASN* 3.3 15.5 - - - +
3262B ARG* 4.0 23.1 - - - +
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Residues in contact with ASN1072 (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 THR* 1.3 75.5 - - - +
1073A ASP* 1.3 61.1 + - - +
1075A LEU* 3.3 14.2 + - - +
1076A LEU* 3.1 31.4 + - + +
1221A LEU* 4.0 24.3 + - + +
1222A PRO 4.3 6.9 + - - -
1223A GLN* 5.2 3.2 - - - +
1314A ARG* 3.1 21.0 + - - +
1318A MET* 3.7 26.9 - - - +
3231B GLY 5.2 0.2 - - - -
3232B ASN* 3.0 30.5 + - - +
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Residues in contact with ASP1073 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1071A THR* 3.2 10.8 + - - +
1072A ASN* 1.3 78.2 - - - +
1074A ASP* 1.3 62.5 + - - +
1076A LEU* 3.8 15.3 - - - +
1077A LYS* 3.0 30.1 + - - +
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Residues in contact with ASP1074 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1063A MET* 3.9 24.1 - - - +
1065A ILE* 3.8 19.2 - - - +
1069A SER 4.5 1.4 - - - +
1070A ILE* 3.7 16.0 - - + -
1071A THR* 3.1 34.0 + - - +
1073A ASP* 1.3 78.1 - - - +
1075A LEU* 1.3 58.7 + - - +
1077A LYS* 3.4 7.1 + - - +
1078A LEU* 2.9 30.7 + - - +
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Residues in contact with LEU1075 (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 ILE* 4.4 11.9 - - + -
1071A THR 3.2 9.5 + - - +
1072A ASN* 3.5 24.5 - - - +
1073A ASP 3.3 0.2 - - - -
1074A ASP* 1.3 80.2 - - - +
1076A LEU* 1.3 53.0 + - + +
1078A LEU* 3.2 5.5 + - + +
1079A GLY* 2.7 33.6 + - - -
1105A GLU* 5.8 1.3 - - + -
1106A THR* 3.6 38.6 - - + +
1109A PHE* 3.7 41.4 - - + -
1221A LEU* 5.8 2.7 - - + -
1314A ARG* 5.6 1.1 - - - +
1315A ILE* 4.3 24.0 - - + -
1318A MET* 4.7 4.3 - - + -
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Residues in contact with LEU1076 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1072A ASN* 3.1 14.0 + - + +
1073A ASP* 3.8 16.8 - - - +
1075A LEU* 1.3 77.7 - - - +
1077A LYS* 1.3 58.0 + - - +
1079A GLY* 3.3 0.7 + - - +
1080A LYS* 2.9 45.5 + - + +
1109A PHE* 4.8 1.6 - - + -
1215A ILE* 4.1 15.2 - - + +
1218A ILE* 3.8 29.8 - - + +
1219A SER 3.4 20.9 - - - +
1220A SER* 3.9 5.2 - - - -
1221A LEU* 3.2 37.5 - - + +
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Residues in contact with LYS1077 (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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1062A VAL* 3.4 44.2 + - + +
1063A MET* 4.4 7.0 - - + +
1073A ASP 3.0 20.0 + - - +
1074A ASP* 3.6 7.2 - - - +
1076A LEU* 1.3 76.0 - - - +
1078A LEU* 1.3 61.8 + - - +
1080A LYS* 4.2 5.6 - - - +
1081A ARG* 3.3 24.3 + - + +
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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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1015A LEU* 4.5 9.4 - - + -
1017A THR* 3.9 27.1 - - + -
1062A VAL* 5.0 6.3 - - + -
1063A MET* 4.4 10.3 - - + -
1070A ILE* 5.7 3.8 - - + -
1074A ASP 2.9 17.9 + - - +
1075A LEU* 3.6 5.8 - - + +
1077A LYS* 1.3 77.3 - - - +
1079A GLY* 1.3 66.3 + - - +
1081A ARG* 3.4 4.4 + - + +
1082A VAL* 3.1 36.1 + - + +
1096A ILE* 4.1 21.1 - - + -
1098A HIS* 4.5 6.5 - - + +
1106A THR* 4.0 26.9 - - + -
1110A LEU* 5.0 2.9 - - + -
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Residues in contact with GLY1079 (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 LEU 2.7 19.8 + - - -
1076A LEU 3.8 1.3 - - - -
1078A LEU* 1.3 75.1 - - - +
1080A LYS* 1.3 56.1 + - - +
1082A VAL 3.4 0.5 + - - -
1083A ALA* 3.1 16.5 + - - +
1109A PHE* 4.5 2.2 - - - -
1110A LEU* 3.9 10.3 - - - +
1114A GLN* 2.6 33.2 + - - -
1215A ILE* 3.8 14.3 - - - +
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Residues in contact with LYS1080 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1076A LEU* 2.9 33.3 + - + +
1077A LYS* 4.2 4.9 - - - +
1079A GLY* 1.3 73.2 - - - +
1081A ARG* 1.3 66.6 + - - +
1083A ALA* 3.2 6.2 + - - +
1084A GLU* 3.1 33.0 + - - +
1215A ILE* 3.2 25.9 + - + -
1216A LYS* 4.7 8.1 + - - +
1218A ILE 3.1 28.0 + - - -
1219A SER* 5.0 6.9 - - - +
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Residues in contact with ARG1081 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015A LEU* 4.2 19.1 - - + -
1060A GLU* 2.6 46.6 + - - -
1062A VAL* 4.4 13.2 - - + -
1077A LYS* 3.3 23.4 + - + +
1078A LEU* 3.7 6.5 - - - +
1079A GLY 3.4 0.2 - - - -
1080A LYS* 1.3 78.4 - - - +
1082A VAL* 1.3 61.8 + - - +
1084A GLU* 2.5 42.9 + - - +
1085A LEU* 2.8 59.2 - - + +
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Residues in contact with VAL1082 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015A LEU* 3.9 17.7 - - + -
1078A LEU* 3.1 34.3 + - + +
1079A GLY 3.5 0.4 - - - +
1081A ARG* 1.3 76.8 - - - +
1083A ALA* 1.3 62.2 + - - +
1085A LEU* 3.4 1.1 + - - +
1086A ALA* 3.0 23.6 + - + +
1094A ILE* 3.9 16.1 - - + +
1096A ILE* 4.0 11.7 - - + -
1110A LEU* 4.2 6.3 - - + -
1114A GLN* 3.4 34.1 - - + +
1120A ILE* 3.9 18.8 - - + -
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Residues in contact with ALA1083 (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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1079A GLY 3.1 6.5 + - - +
1080A LYS* 3.2 10.0 + - - +
1082A VAL* 1.3 76.8 - - - +
1084A GLU* 1.3 59.9 + - - +
1086A ALA* 3.7 4.6 + - - +
1087A ASP* 3.1 33.3 + - - +
1114A GLN* 3.3 8.7 + - - +
1215A ILE* 3.5 31.2 - - + -
1216A LYS* 4.5 17.7 - - + -
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Residues in contact with GLU1084 (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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1080A LYS* 3.1 23.6 + - - +
1081A ARG* 2.5 48.3 + - - +
1083A ALA* 1.3 75.3 - - - +
1085A LEU* 1.3 66.4 + - - +
1087A ASP* 3.2 17.8 + - - +
1088A SER* 3.4 10.2 + - - -
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Residues in contact with LEU1085 (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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1013A VAL* 4.4 22.7 - - + -
1015A LEU* 4.8 7.4 - - + -
1058A ARG* 5.7 3.1 - - - +
1060A GLU* 4.6 4.0 - - - +
1081A ARG* 2.8 72.4 + - + +
1082A VAL* 4.0 1.3 - - - +
1084A GLU* 1.3 75.3 - - - +
1086A ALA* 1.3 61.9 + - - +
1088A SER* 3.3 13.5 + - - -
1091A VAL* 3.2 42.4 - - + +
1094A ILE* 4.0 18.2 - - + -
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Residues in contact with ALA1086 (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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1082A VAL* 3.0 18.6 + - + +
1083A ALA* 3.9 7.6 - - - +
1084A GLU 3.2 0.2 - - - -
1085A LEU* 1.3 76.9 - - - +
1087A ASP* 1.3 60.5 + - - +
1094A ILE* 4.0 12.9 - - + +
1114A GLN* 5.4 0.2 - - - +
1116A THR* 4.0 35.9 + - + +
1118A LYS* 2.9 35.8 + - + +
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Residues in contact with ASP1087 (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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1083A ALA 3.1 13.2 + - - +
1084A GLU* 3.2 11.5 + - - +
1086A ALA* 1.3 78.9 - - - +
1088A SER* 1.3 60.9 + - - +
1089A ASN* 3.7 9.9 + - - +
1116A THR* 6.1 0.3 - - - -
1118A LYS* 4.7 0.4 + - - -
1216A LYS* 2.6 37.9 + - - -
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Residues in contact with SER1088 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1084A GLU 3.4 7.6 + - - -
1085A LEU* 3.3 18.1 + - - +
1086A ALA 3.2 0.8 - - - +
1087A ASP* 1.3 79.8 - - - +
1089A ASN* 1.3 57.0 + - - +
1090A ASP* 3.2 28.5 + - - +
1091A VAL* 3.6 10.7 + - - +
1118A LYS* 2.6 31.2 + - - -
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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
------------------------------------------------------------
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