Contacts of the helix formed by residues 1142 - 1155 (chain C) 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 THR1142 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1021C THR* 4.0 30.7 - - + +
1138C TRP* 3.1 25.5 + - - +
1139C TYR 3.4 3.5 - - - +
1141C GLN* 1.3 86.9 - - + +
1143C PRO* 1.3 62.7 - - - +
1144C ASN* 3.4 4.3 - - - +
1145C ARG* 4.3 19.8 - - + +
1146C ALA* 3.1 24.6 + - - +
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Residues in contact with PRO1143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1139C TYR* 3.4 18.8 - - + +
1140C ASN 4.1 7.0 - - - +
1141C GLN 3.4 12.1 - - - +
1142C THR* 1.3 82.2 - - - +
1144C ASN* 1.3 75.0 + - - +
1146C ALA* 4.3 2.2 - - + -
1147C LYS* 2.9 41.0 + - + +
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Residues in contact with ASN1144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1142C THR* 3.4 3.0 - - - +
1143C PRO* 1.3 91.1 - - - +
1145C ARG* 1.3 59.3 + - + +
1147C LYS* 3.6 4.2 - - - +
1148C ARG* 3.0 59.2 + - - +
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Residues in contact with ARG1145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007C LEU* 3.2 24.0 - - - +
1010C ASP* 3.2 50.5 + - + +
1011C GLU* 3.3 36.2 + - - +
1101C ASN* 2.9 32.7 + - - -
1102C MET* 5.9 0.2 - - - +
1104C PHE* 4.2 5.3 - - - -
1105C GLN* 4.0 20.1 - - - +
1138C TRP* 4.4 8.2 - - + +
1142C THR* 3.8 21.9 + - - +
1143C PRO 3.5 0.2 - - - -
1144C ASN* 1.3 80.5 - - + +
1146C ALA* 1.3 57.4 + - - +
1148C ARG* 3.9 2.1 - - - +
1149C VAL* 2.9 41.1 + - + +
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Residues in contact with ALA1146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1138C TRP* 3.2 25.7 - - + -
1139C TYR* 3.3 35.4 - - + -
1142C THR 3.1 21.2 + - - +
1143C PRO 3.8 2.5 - - - +
1145C ARG* 1.3 74.6 - - - +
1147C LYS* 1.3 65.5 + - - +
1150C ILE* 2.9 32.4 + - - +
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Residues in contact with LYS1147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2001B PO4 4.9 13.7 + - - +
1139C TYR* 3.4 28.3 - - + +
1143C PRO* 2.9 28.5 + - + +
1144C ASN* 3.6 5.8 - - - +
1146C ALA* 1.3 76.0 - - - +
1148C ARG* 1.3 65.7 + - + +
1150C ILE* 3.9 2.5 - - - +
1151C THR* 2.9 31.7 + - - +
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Residues in contact with ARG1148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009C ILE* 4.7 18.6 + - - +
1010C ASP* 2.9 31.6 + - - +
1144C ASN* 3.0 49.3 + - - +
1145C ARG* 3.9 2.7 - - - +
1147C LYS* 1.3 78.5 - - + +
1149C VAL* 1.3 56.6 + - - +
1151C THR* 3.4 2.6 + - - -
1152C THR* 2.9 31.4 + - - -
1160C ALA* 3.9 23.1 - - + +
1161C TYR* 3.3 30.7 - - + +
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Residues in contact with VAL1149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006C MET* 4.1 2.5 - - + -
1010C ASP* 4.0 1.8 - - - +
1098C ALA* 4.3 5.6 - - + +
1101C ASN* 3.8 29.6 - - - +
1102C MET* 4.2 11.7 - - + -
1133C LEU* 5.9 0.4 - - + -
1138C TRP* 4.1 18.6 - - + -
1145C ARG* 2.9 28.7 + - + +
1146C ALA 3.9 2.2 - - - +
1148C ARG* 1.3 75.9 - - - +
1150C ILE* 1.3 60.4 + - + +
1152C THR* 3.2 7.6 + - - -
1153C PHE* 2.9 56.3 + - + -
1161C TYR* 3.6 14.4 - - - +
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Residues in contact with ILE1150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1130C ALA* 3.3 33.4 - - + +
1133C LEU* 3.6 35.4 - - + -
1134C ALA* 3.9 6.7 - - + +
1138C TRP* 4.4 10.3 - - + -
1139C TYR* 3.7 30.1 - - + -
1146C ALA 2.9 21.0 + - - +
1147C LYS* 3.9 3.4 - - - +
1149C VAL* 1.3 73.5 - - + +
1151C THR* 1.3 61.5 + - - +
1153C PHE* 2.9 7.8 + - + +
1154C ARG* 2.9 37.9 + - - +
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Residues in contact with THR1151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015B LEU* 6.1 2.9 - - + +
1147C LYS* 2.9 21.9 + - - +
1148C ARG* 3.7 3.4 - - - -
1150C ILE* 1.3 76.9 - - - +
1152C THR* 1.3 54.6 + - - +
1154C ARG* 4.7 12.2 + - - +
1155C THR* 2.5 52.6 + - + +
1157C THR 5.6 0.2 - - - +
1159C ASP* 5.4 2.7 - - + -
1160C ALA* 3.8 26.7 - - + +
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Residues in contact with THR1152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006C MET* 4.8 0.7 - - + -
1094C VAL* 3.6 28.2 - - + +
1095C ARG* 3.9 5.0 - - - +
1098C ALA* 3.9 20.2 - - + -
1148C ARG 2.9 9.3 + - - -
1149C VAL* 3.3 12.1 - - - -
1150C ILE 3.1 0.2 - - - -
1151C THR* 1.3 77.2 - - - +
1153C PHE* 1.3 56.6 + - - +
1156C GLY* 3.3 23.0 + - - -
1157C THR 3.7 11.8 + - - +
1158C TRP* 4.7 7.2 - - + -
1160C ALA* 4.3 1.7 - - - +
1161C TYR* 2.8 37.2 - - + -
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Residues in contact with PHE1153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091C LEU* 4.7 5.8 - - + -
1095C ARG* 2.7 49.2 + - + -
1098C ALA* 3.5 12.1 - - + -
1099C LEU* 4.0 25.1 - - + -
1102C MET* 4.0 17.5 - - - -
1121C LEU* 3.7 42.4 - - + -
1126C TRP* 3.6 8.9 - - + -
1130C ALA* 5.8 1.3 - - + -
1133C LEU* 4.5 16.6 - - + -
1149C VAL* 2.9 44.5 + - + -
1150C ILE* 2.9 14.5 + - + +
1152C THR* 1.3 77.9 - - - +
1154C ARG* 1.3 60.1 + - + +
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Residues in contact with ARG1154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008B ARG* 3.0 20.8 + - - +
1013B LEU* 4.5 9.9 - - + +
1015B LEU* 5.7 5.4 - - - +
1060B LYS* 2.9 44.9 - - - +
2001B PO4 4.1 12.3 + - - -
1095C ARG* 2.9 23.0 + - - -
1126C TRP* 3.8 18.8 - - - +
1127C ASP* 3.5 36.0 + - - +
1130C ALA* 3.6 30.4 - - + +
1131C VAL* 5.6 3.4 - - - +
1150C ILE* 2.9 18.7 + - - +
1151C THR* 4.5 11.7 + - - +
1153C PHE* 1.3 73.4 - - + +
1155C THR* 1.3 62.6 + - + +
1156C GLY 3.0 3.8 - - - -
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Residues in contact with THR1155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1013B LEU* 2.9 39.8 + - + +
1014B ARG* 4.1 14.2 - - + +
1015B LEU* 4.6 7.6 - - + +
1095C ARG* 3.9 3.8 + - - -
1151C THR* 2.5 34.9 + - + +
1154C ARG* 1.3 76.0 - - + +
1156C GLY* 1.3 63.6 + - - +
1157C THR* 3.1 37.5 + - - +
1159C ASP* 4.9 5.0 + - + +
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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