Contacts of the helix formed by residues 1102 - 1114 (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 THR1102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1067A SER* 2.9 41.9 + - - +
1068A GLU* 4.2 4.7 - - - -
1070A ILE* 3.7 11.3 - - + +
1098A HIS* 3.4 9.0 + - - -
1101A ASP* 1.3 79.9 - - - +
1103A LEU* 1.3 64.7 + - - +
1104A GLU* 3.2 3.4 - - - +
1105A GLU* 2.9 43.1 + - - +
1106A THR* 3.3 10.3 + - - -
3230B TYR 4.8 0.4 - - - -
3231B GLY* 4.4 9.6 - - - +
3254B THR* 4.0 14.1 - - + -
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Residues in contact with LEU1103 (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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1098A HIS* 3.6 31.4 - - - +
1099A GLY 3.3 12.3 + - - +
1100A THR* 3.4 17.0 + - - +
1102A THR* 1.3 77.7 - - - +
1104A GLU* 1.3 60.9 + - - +
1105A GLU 3.1 0.2 + - - -
1106A THR* 3.3 1.4 + - - -
1107A ALA* 2.9 37.1 + - + +
1122A VAL* 3.5 30.2 - - + +
1123A VAL* 4.0 2.9 - - - -
1124A GLY* 4.0 17.7 - - - +
1159A VAL* 4.4 15.7 - - + -
1161A MET* 4.5 5.8 - - - -
1171A VAL* 5.1 2.2 - - + -
1182A PHE* 4.0 20.2 - - + -
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Residues in contact with GLU1104 (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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1100A THR 4.7 0.4 + - - +
1101A ASP 4.4 7.2 - - - +
1102A THR* 4.6 4.5 - - - -
1103A LEU* 1.3 84.4 - - - +
1105A GLU* 1.3 73.4 + - + +
1107A ALA* 4.1 3.1 - - - -
1108A TYR* 3.5 11.4 + - - +
1171A VAL* 3.4 21.3 - - - +
1172A SER* 2.9 24.7 + - - -
1173A LYS* 3.0 31.9 + - - +
1182A PHE* 4.5 5.3 - - + -
1309A ASN* 3.4 9.2 + - - -
1311A GLU* 3.0 28.1 - - + +
1312A LYS* 2.8 30.0 + - - +
3282B HIS* 5.0 4.9 - - - -
3283B VAL* 5.8 0.2 - - - +
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Residues in contact with GLU1105 (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* 5.4 1.0 - - + +
1075A LEU* 5.3 2.0 - - + -
1101A ASP 4.8 0.7 - - - +
1102A THR* 2.9 27.8 + - - +
1104A GLU* 1.3 89.5 - - + +
1106A THR* 1.3 66.3 + - - +
1108A TYR* 3.3 2.2 + - - +
1109A PHE* 3.0 22.9 + - - +
1311A GLU* 3.6 32.6 - - + +
1312A LYS* 5.5 1.1 - - - -
1314A ARG* 4.2 10.9 + - - -
1315A ILE* 3.8 25.7 - - + +
3230B TYR* 3.8 5.4 - - - +
3231B GLY* 3.1 35.8 + - - -
3254B THR* 4.4 4.5 - - - +
3282B HIS* 5.3 0.5 - - - -
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Residues in contact with THR1106 (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* 3.9 5.0 - - - +
1075A LEU* 3.6 27.6 - - + +
1078A LEU* 4.0 16.4 - - + -
1096A ILE* 5.9 1.1 - - + -
1098A HIS* 2.7 43.1 + - + -
1102A THR* 3.3 3.5 + - - -
1103A LEU 3.9 3.8 - - - -
1105A GLU* 1.3 78.0 - - - +
1107A ALA* 1.3 64.5 + - - +
1109A PHE* 3.3 1.4 + - - +
1110A LEU* 3.1 42.0 + - + +
1122A VAL* 5.6 4.3 - - + -
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Residues in contact with ALA1107 (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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1103A LEU* 2.9 28.0 + - + +
1104A GLU* 4.2 3.4 - - - +
1106A THR* 1.3 77.9 - - - +
1108A TYR* 1.3 60.5 + - - +
1110A LEU* 3.7 1.0 + - - +
1111A ASN* 3.2 21.8 + - - +
1122A VAL* 4.2 25.5 - - + +
1157A VAL* 3.7 10.9 - - + +
1159A VAL* 5.3 2.0 - - + -
1168A GLY* 3.9 24.6 - - - +
1171A VAL* 5.1 1.8 - - + -
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Residues in contact with TYR1108 (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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1104A GLU 3.5 16.4 + - - +
1105A GLU* 3.3 5.2 + - - +
1106A THR 3.3 0.2 - - - -
1107A ALA* 1.3 76.6 - - - +
1109A PHE* 1.3 67.5 + - - +
1111A ASN* 3.2 8.2 + - + +
1112A LEU* 3.2 40.1 + - + +
1168A GLY 3.5 7.6 + - - +
1169A ARG* 3.6 32.3 - - + -
1308A LEU* 3.4 34.9 - - + +
1312A LYS* 3.5 38.6 - - + +
1315A ILE* 4.1 11.4 - - + -
1316A LEU* 3.6 15.6 - - + +
1337A TYR* 2.8 27.1 + - - +
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Residues in contact with PHE1109 (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* 3.7 55.6 - - + -
1076A LEU* 4.8 7.9 - - + -
1079A GLY* 4.5 4.5 - - - -
1105A GLU 3.0 14.1 + - - +
1106A THR* 3.3 10.5 + - - +
1108A TYR* 1.3 75.8 - - - +
1110A LEU* 1.3 66.8 + - + +
1112A LEU* 3.0 20.2 + - - +
1113A VAL* 3.1 34.7 + - + +
1215A ILE* 3.9 23.1 - - + -
1218A ILE* 5.7 0.9 - - + -
1221A LEU* 4.4 18.4 - - + -
1315A ILE* 3.6 16.7 - - + +
1318A MET* 5.6 1.8 - - + -
1319A VAL* 3.8 27.8 - - + -
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Residues in contact with LEU1110 (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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1078A LEU* 4.9 3.1 - - + -
1079A GLY* 3.9 16.8 - - - +
1082A VAL* 4.2 8.3 - - + -
1096A ILE* 3.7 29.4 - - + -
1106A THR* 3.1 33.0 + - + +
1107A ALA 4.0 1.1 - - - +
1109A PHE* 1.3 84.9 - - + +
1111A ASN* 1.3 65.1 + - - +
1113A VAL* 4.1 3.8 - - - -
1114A GLN* 3.0 62.3 + - + +
1120A ILE* 4.6 7.0 - - + -
1122A VAL* 4.6 8.3 - - + -
1157A VAL* 3.7 14.7 - - + +
1208A THR* 4.6 0.2 - - - +
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Residues in contact with ASN1111 (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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1107A ALA 3.2 15.7 + - - +
1108A TYR* 3.2 20.5 + - + +
1110A LEU* 1.3 76.4 - - - +
1112A LEU* 1.3 58.3 + - - +
1156A GLY* 3.4 9.5 - - - -
1157A VAL* 2.8 39.6 + - + +
1167A SER* 5.4 1.9 + - - -
1169A ARG* 4.0 28.9 - - - +
1206A ARG 4.3 4.9 + - - -
1207A HIS* 3.4 24.1 - - - +
1208A THR* 2.8 31.5 + - - +
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Residues in contact with LEU1112 (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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1108A TYR* 3.2 40.1 + - + +
1109A PHE 3.0 7.2 + - - +
1111A ASN* 1.3 82.4 - - - +
1113A VAL* 1.3 64.4 + - + +
1114A GLN 3.8 0.4 - - - -
1206A ARG 4.9 3.1 - - - +
1207A HIS* 5.5 0.2 - - - +
1208A THR* 5.4 0.2 - - - -
1211A SER* 2.6 29.8 + - - -
1213A PHE* 3.6 8.3 - - + +
1315A ILE* 4.2 8.1 - - + -
1316A LEU* 3.6 36.1 - - + -
1319A VAL* 4.1 20.2 - - + -
1337A TYR* 3.5 37.9 - - + +
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Residues in contact with VAL1113 (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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1109A PHE* 3.1 41.0 + - + +
1110A LEU* 4.1 6.1 - - - -
1112A LEU* 1.3 83.9 - - - +
1114A GLN* 1.3 69.1 + - - +
1115A LYS 3.3 4.0 + - - -
1213A PHE* 4.1 9.0 - - + -
1214A ASP* 3.7 4.9 - - - +
1215A ILE* 3.1 44.0 + - + +
1218A ILE* 4.1 17.5 - - + -
1319A VAL* 4.0 29.2 - - + -
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Residues in contact with GLN1114 (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* 2.6 29.7 + - - -
1082A VAL* 3.4 13.3 - - + +
1083A ALA* 3.3 28.1 + - - +
1110A LEU* 3.0 46.7 + - + +
1112A LEU 3.8 0.2 - - - -
1113A VAL* 1.3 80.1 - - - +
1115A LYS* 1.3 60.2 + - - +
1116A THR* 3.0 8.8 + - + +
1120A ILE* 3.6 29.2 - - + -
1208A THR* 3.0 31.6 - - + -
1215A ILE* 4.1 7.4 - - - +
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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