Contacts of the helix formed by residues 1142 - 1156 (chain A) in PDB entry 5NDD
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1021A THR* 4.1 19.5 - - + +
1022A GLU* 5.8 2.5 - - + +
1105A GLN* 3.4 27.0 + - - +
1138A TRP* 3.1 18.1 + - - +
1139A TYR 3.6 2.9 - - - -
1141A GLN* 1.3 88.0 - - + +
1143A PRO* 1.3 58.0 - - - +
1145A ARG* 3.7 12.3 - - + +
1146A ALA* 2.9 25.8 + - - +
2203A PO4 3.1 24.7 - - - +
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Residues in contact with PRO1143 (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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1139A TYR* 3.1 32.7 - - + +
1140A ASN 3.9 5.4 - - - +
1141A GLN 3.5 8.3 - - - +
1142A THR* 1.3 84.7 - - - +
1144A ASN* 1.3 72.1 + - - +
1146A ALA* 3.2 1.7 + - - +
1147A LYS* 2.8 50.1 + - - +
2203A PO4 3.5 10.5 - - - +
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Residues in contact with ASN1144 (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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1143A PRO* 1.3 79.1 - - - +
1145A ARG* 1.3 62.2 + - - +
1147A LYS* 3.6 22.2 + - - +
1148A ARG* 3.4 41.2 + - - +
2203A PO4 2.9 29.7 + - - +
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Residues in contact with ARG1145 (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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1007A LEU* 4.5 3.0 - - - +
1010A ASP* 3.3 39.9 + - - +
1011A GLU* 2.7 34.8 + - - -
1101A ASN* 2.5 41.7 + - - -
1105A GLN* 3.4 44.0 + - - +
1138A TRP* 4.7 0.9 - - - +
1142A THR* 3.7 11.0 - - + +
1144A ASN* 1.3 79.7 - - - +
1146A ALA* 1.3 64.5 + - - +
1148A ARG* 3.4 15.4 + - - +
1149A VAL* 3.4 24.4 + - + +
2203A PO4 2.8 20.4 + - - +
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Residues in contact with ALA1146 (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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1138A TRP* 3.7 39.0 - - + +
1139A TYR* 4.0 22.9 - - + -
1142A THR 2.9 20.5 + - - +
1143A PRO 3.2 2.7 + - - +
1145A ARG* 1.3 72.8 - - - +
1147A LYS* 1.3 55.1 + - - +
1149A VAL* 3.3 1.7 + - - +
1150A ILE* 2.8 42.1 + - + +
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Residues in contact with LYS1147 (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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231A PRO* 4.4 13.9 + - - +
232A GLU* 3.2 25.5 + - - +
234A LEU* 6.6 0.2 - - + -
1139A TYR* 3.3 24.3 + - + -
1143A PRO* 2.8 37.1 + - - +
1144A ASN* 3.8 19.0 + - - +
1146A ALA* 1.3 73.6 - - - +
1148A ARG* 1.3 54.5 + - + +
1150A ILE* 3.7 7.4 - - - +
1151A THR* 2.7 40.9 + - - +
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Residues in contact with ARG1148 (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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1009A ILE* 4.8 8.6 + - - +
1010A ASP* 2.7 38.8 + - - +
1144A ASN* 3.4 33.5 + - - +
1145A ARG* 3.4 22.2 + - - +
1146A ALA 3.3 0.4 - - - -
1147A LYS* 1.3 78.5 - - + +
1149A VAL* 1.3 54.7 + - - +
1151A THR* 4.5 0.4 - - - -
1152A THR* 2.7 32.7 + - - -
1160A ALA* 3.3 35.8 - - + +
1161A TYR* 3.7 26.3 - - + +
1164A GLU* 6.0 0.2 + - - -
2203A PO4 5.3 3.2 + - - -
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Residues in contact with VAL1149 (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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1006A MET* 5.7 0.2 - - - -
1098A ALA* 3.5 27.6 - - + +
1101A ASN* 3.9 21.8 - - + +
1102A MET* 3.8 4.0 - - + -
1105A GLN* 5.8 0.2 - - - +
1138A TRP* 3.8 21.8 - - + -
1145A ARG* 3.4 17.2 + - - +
1146A ALA 3.3 6.0 + - - +
1147A LYS 3.3 0.4 - - - -
1148A ARG* 1.3 74.3 - - - +
1150A ILE* 1.3 64.3 + - - +
1152A THR* 3.1 10.1 + - - -
1153A PHE* 3.1 36.8 + - + -
1161A TYR* 3.4 17.3 - - - +
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Residues in contact with ILE1150 (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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234A LEU* 4.0 13.2 - - + -
1130A ALA* 3.6 32.9 - - + +
1133A LEU* 3.6 41.5 - - + +
1134A ALA* 3.8 11.0 - - + +
1138A TRP* 3.9 18.4 - - + -
1139A TYR* 4.5 8.3 - - + -
1146A ALA* 2.8 28.6 + - + +
1147A LYS* 3.7 5.8 - - - +
1149A VAL* 1.3 70.8 - - - +
1151A THR* 1.3 60.9 + - - +
1153A PHE* 3.1 11.7 + - - +
1154A ARG* 2.9 27.1 + - + +
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Residues in contact with THR1151 (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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234A LEU* 6.2 0.3 - - - +
1147A LYS* 2.7 26.1 + - - +
1148A ARG* 3.7 5.7 - - - -
1150A ILE* 1.3 77.8 - - - +
1152A THR* 1.3 52.2 + - - +
1154A ARG* 4.3 17.9 + - - +
1155A THR* 2.7 62.3 + - + +
1159A ASP* 5.9 2.9 - - + -
1160A ALA* 4.0 19.7 - - + +
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Residues in contact with THR1152 (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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1006A MET* 4.0 10.2 - - + +
1094A VAL* 3.7 30.1 - - + +
1095A ARG* 3.7 3.2 - - - +
1098A ALA* 3.7 14.4 - - + -
1148A ARG 2.7 21.4 + - - -
1149A VAL* 3.1 10.2 + - - -
1151A THR* 1.3 77.2 - - - +
1153A PHE* 1.3 54.6 + - - +
1156A GLY* 2.8 31.5 + - - -
1157A THR 3.7 22.2 + - - +
1158A TRP* 5.4 0.9 - - + -
1160A ALA* 4.1 4.6 - - - +
1161A TYR* 3.7 16.1 - - - -
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Residues in contact with PHE1153 (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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1091A LEU* 4.3 8.3 - - + -
1095A ARG* 2.5 61.0 + - + +
1098A ALA* 3.5 7.2 - - + -
1099A LEU* 3.5 28.5 - - + -
1102A MET* 3.5 25.4 - - - -
1121A LEU* 3.9 36.8 - - + -
1126A TRP* 3.7 9.9 - - - +
1129A ALA* 6.0 0.7 - - + -
1130A ALA* 6.0 1.8 - - + -
1133A LEU* 4.0 23.1 - - + -
1149A VAL* 3.1 29.0 + - + -
1150A ILE* 3.1 11.7 + - + +
1152A THR* 1.3 76.3 - - - +
1154A ARG* 1.3 62.2 + - - +
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Residues in contact with ARG1154 (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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234A LEU* 4.6 20.0 - - - +
1095A ARG* 3.5 7.4 + - - -
1126A TRP* 3.7 28.8 - - + +
1127A ASP* 3.4 29.0 + - - +
1130A ALA* 3.9 18.4 - - + -
1150A ILE* 2.9 16.9 + - - +
1151A THR* 3.7 18.0 + - - +
1153A PHE* 1.3 78.6 - - - +
1155A THR* 1.3 76.7 + - - +
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Residues in contact with THR1155 (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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1095A ARG* 3.8 5.6 + - - -
1151A THR* 2.7 47.2 + - + +
1154A ARG* 1.3 95.3 - - - +
1156A GLY* 1.3 61.1 + - - +
1157A THR* 3.2 34.6 + - - +
1159A ASP* 5.3 2.9 - - + +
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Residues in contact with GLY1156 (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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1092A ASP* 4.2 2.1 - - - +
1094A VAL* 3.3 26.3 - - - +
1095A ARG* 3.6 29.3 - - - +
1152A THR 2.8 23.6 + - - -
1155A THR* 1.3 72.5 - - - +
1157A THR* 1.3 60.8 + - - +
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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