Contacts of the helix formed by residues 1235 - 1244 (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 ASP1235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1234A THR* 1.3 74.9 - - - +
1236A THR* 1.3 71.4 + - - +
1237A ALA 3.5 0.9 - - - -
1238A TYR* 3.2 13.3 + - + +
1239A LYS* 3.1 44.9 + - - +
1262A ARG 4.4 8.5 + - - +
1263A VAL* 4.0 15.0 - - + +
1266A ALA* 3.5 34.1 - - + +
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Residues in contact with THR1236 (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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1234A THR* 2.8 24.4 + - - +
1235A ASP* 1.3 84.1 + - - +
1237A ALA* 1.3 64.5 + - - +
1239A LYS* 3.4 3.6 + - - +
1240A ALA* 3.0 22.4 + - + +
3240B ALA* 3.7 30.1 - - + +
3241B LEU* 3.7 17.0 - - + -
3244B ASN* 3.7 29.1 + - + +
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Residues in contact with ALA1237 (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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1227A ALA* 4.7 14.6 - - + -
1228A TYR 5.7 3.1 - - - +
1234A THR 4.5 3.1 + - - +
1235A ASP 3.5 0.6 - - - -
1236A THR* 1.3 79.8 - - - +
1238A TYR* 1.3 67.3 - - + +
1240A ALA* 3.5 5.2 + - - +
1241A LEU* 3.0 32.9 + - + +
3226B ILE 5.6 2.7 - - - +
3237B ALA* 4.7 13.9 - - + -
3240B ALA* 5.3 1.1 - - - -
3241B LEU* 3.9 25.1 - - + +
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Residues in contact with TYR1238 (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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1227A ALA* 3.5 29.4 + - + +
1228A TYR 4.1 4.2 + - - -
1229A SER* 3.8 12.3 + - - -
1233A VAL* 4.4 11.8 - - + +
1234A THR 3.8 21.3 - - - -
1235A ASP* 3.2 9.4 + - + +
1237A ALA* 1.3 81.7 - - + +
1239A LYS* 1.3 63.3 + - + +
1241A LEU* 3.5 2.0 + - - +
1242A ALA* 3.1 17.8 + - - +
1249A LEU* 3.5 27.7 - - + +
1250A ILE 5.3 0.4 - - - -
1251A HIS* 2.8 46.0 + - + -
1263A VAL* 3.9 19.8 - - + +
1266A ALA* 5.6 0.2 - - + -
1267A LEU* 3.5 26.9 - - + -
1270A LEU* 4.2 13.0 - - + -
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Residues in contact with LYS1239 (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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1235A ASP* 3.1 33.3 + - - +
1236A THR* 3.9 3.6 - - - +
1238A TYR* 1.3 76.4 - - - +
1240A ALA* 1.3 55.3 - - - +
1242A ALA* 3.2 6.7 + - - +
1243A GLN* 2.7 51.7 + - + +
1266A ALA* 3.8 29.1 - - + +
1269A GLN* 4.3 16.5 + - - -
1270A LEU* 4.5 14.8 - - + -
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Residues in contact with ALA1240 (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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1236A THR* 3.0 14.1 + - + +
1237A ALA* 3.9 4.3 - - - +
1239A LYS* 1.3 77.2 - - - +
1241A LEU* 1.3 62.4 + - + +
1243A GLN* 3.3 13.6 + - - +
1244A ASN* 2.8 32.2 + - - +
3236B THR* 4.0 11.0 - - + -
3237B ALA* 5.4 0.4 - - - -
3240B ALA* 3.4 33.2 - - + -
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Residues in contact with LEU1241 (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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1223A GLN* 4.5 2.1 + - - -
1225A ASP* 3.5 28.9 - - + +
1226A ILE 3.8 24.7 - - - +
1227A ALA* 4.4 5.4 - - + -
1237A ALA* 3.0 26.7 + - + +
1238A TYR 3.6 0.7 - - - +
1240A ALA* 1.3 77.8 - - - +
1242A ALA* 1.3 61.5 + - - +
1244A ASN* 3.2 11.9 + - + +
1245A GLY 3.6 0.7 + - - -
1246A ALA* 3.2 19.0 + - - +
1249A LEU* 3.6 24.2 - - + -
3230B TYR* 5.3 2.0 - - - +
3234B THR* 5.6 0.9 - - - +
3236B THR* 3.7 24.9 - - + -
3237B ALA* 4.0 23.1 - - + +
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Residues in contact with ALA1242 (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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1238A TYR 3.1 9.0 + - - +
1239A LYS 3.7 5.2 - - - +
1241A LEU* 1.3 78.8 - - - +
1243A GLN* 1.3 63.9 + - + +
1245A GLY* 3.2 12.1 + - - -
1246A ALA* 3.9 16.7 + - - +
1249A LEU* 4.5 4.9 - - + +
1270A LEU* 3.6 33.4 - - + -
1275A THR* 4.3 13.2 - - + +
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Residues in contact with GLN1243 (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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1239A LYS* 2.7 34.1 + - + +
1240A ALA* 3.5 16.6 + - - +
1242A ALA* 1.3 77.1 - - + +
1244A ASN* 1.3 62.2 + - - +
1245A GLY 3.3 2.9 + - - -
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Residues in contact with ASN1244 (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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1223A GLN* 3.2 18.0 + - - +
1240A ALA* 2.8 27.9 + - - +
1241A LEU* 3.2 5.4 + - - +
1242A ALA 3.1 1.0 - - - -
1243A GLN* 1.3 83.7 - - - +
1245A GLY* 1.3 55.3 + - - +
1246A ALA 3.7 2.2 - - - -
3236B THR* 3.6 32.2 + - + +
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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
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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