Contacts of the helix formed by residues 3235 - 3244 (chain B) 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 ASP3235 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3234B THR* 1.3 72.7 - - - +
3236B THR* 1.3 75.5 + - - +
3237B ALA 3.5 1.1 - - - -
3238B TYR* 3.1 21.4 + - + +
3239B LYS* 3.1 44.7 + - - +
3262B ARG 4.6 8.4 + - - +
3263B VAL* 3.9 15.8 - - + +
3266B ALA* 3.4 25.7 + - + +
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Residues in contact with THR3236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1240A ALA* 3.8 14.6 - - + +
1241A LEU* 3.7 22.4 - - + -
1244A ASN* 3.6 44.4 + - + +
3234B THR* 3.1 19.9 + - - -
3235B ASP* 1.3 86.2 + - - +
3237B ALA* 1.3 64.7 + - - +
3239B LYS* 3.9 3.7 - - - +
3240B ALA* 3.0 22.2 + - + +
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Residues in contact with ALA3237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1226A ILE 5.6 3.1 - - - +
1237A ALA* 4.7 14.8 - - + +
1240A ALA* 5.4 0.2 - - - -
1241A LEU* 4.0 23.2 - - + +
3227B ALA* 4.4 16.2 - - + -
3228B TYR 5.7 2.7 - - - +
3234B THR 4.5 3.1 + - - +
3235B ASP 3.5 0.2 - - - -
3236B THR* 1.3 81.6 - - - +
3238B TYR* 1.3 66.7 + - + +
3240B ALA* 3.9 5.3 - - - +
3241B LEU* 3.1 32.0 + - + +
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Residues in contact with TYR3238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3227B ALA* 3.5 29.8 + - + -
3228B TYR 3.9 4.6 + - - -
3229B SER* 3.9 12.0 + - - -
3233B VAL* 4.6 8.5 - - + +
3234B THR 4.0 15.9 - - - -
3235B ASP* 3.1 19.1 + - + +
3237B ALA* 1.3 80.7 - - + +
3239B LYS* 1.3 62.4 + - + +
3241B LEU* 3.8 1.0 - - - +
3242B ALA* 3.2 18.9 + - - +
3249B LEU* 3.4 28.4 - - + +
3250B ILE 5.2 0.2 - - - -
3251B HIS* 2.6 48.3 + - + -
3263B VAL* 3.8 19.8 - - + +
3266B ALA* 5.4 0.7 - - + -
3267B LEU* 3.7 23.1 - - + -
3270B LEU* 4.2 14.6 - - + -
3277B ILE* 6.0 0.2 - - + -
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Residues in contact with LYS3239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3235B ASP* 3.1 45.2 + - - +
3236B THR* 3.9 3.8 - - - +
3238B TYR* 1.3 74.0 - - - +
3240B ALA* 1.3 60.1 + - - +
3242B ALA* 3.2 5.5 + - - +
3243B GLN* 2.8 49.9 + - + +
3266B ALA* 3.6 21.0 - - + +
3269B GLN* 4.1 17.8 + - - -
3270B LEU* 4.8 11.7 - - + -
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Residues in contact with ALA3240 (chain B).
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* 4.0 10.8 - - + -
1237A ALA* 5.3 0.4 - - - -
1240A ALA* 3.4 33.4 - - + -
3236B THR* 3.0 15.2 + - + +
3237B ALA* 3.9 4.5 - - - +
3239B LYS* 1.3 77.5 - - - +
3241B LEU* 1.3 63.6 + - + +
3243B GLN* 3.5 8.4 + - - +
3244B ASN* 2.6 34.7 + - - +
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Residues in contact with LEU3241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1230A TYR* 5.1 1.8 - - - +
1234A THR* 5.4 0.9 - - - +
1236A THR* 3.7 24.9 - - + -
1237A ALA* 3.9 26.2 - - + +
3223B GLN* 4.7 0.5 + - - -
3225B ASP* 3.5 31.8 - - + +
3226B ILE 3.8 24.9 - - - +
3227B ALA* 4.5 4.5 - - + -
3237B ALA* 3.1 23.6 + - + +
3238B TYR 3.8 0.2 - - - +
3240B ALA* 1.3 75.8 - - - +
3242B ALA* 1.3 63.9 + - - +
3244B ASN* 3.2 12.4 + - - +
3245B GLY 3.6 0.9 + - - -
3246B ALA* 3.3 18.9 + - - +
3249B LEU* 3.5 21.3 - - + -
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Residues in contact with ALA3242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3238B TYR 3.2 12.2 + - - +
3239B LYS 3.7 2.7 - - - +
3241B LEU* 1.3 78.4 - - - +
3243B GLN* 1.3 64.8 + - + +
3244B ASN 3.2 0.9 + - - -
3245B GLY* 3.2 11.3 + - - -
3246B ALA* 3.9 16.7 + - - +
3249B LEU* 4.4 8.2 - - + +
3270B LEU* 3.5 31.4 - - + -
3275B THR* 4.4 12.3 - - + +
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Residues in contact with GLN3243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3239B LYS* 2.8 35.7 + - + +
3240B ALA* 3.9 8.8 + - - +
3242B ALA* 1.3 76.7 - - + +
3244B ASN* 1.3 64.9 + - - +
3245B GLY 3.3 1.6 + - - -
3270B LEU* 6.4 0.7 - - + -
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Residues in contact with ASN3244 (chain B).
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* 3.7 29.4 + - + +
3223B GLN* 3.5 17.1 + - - +
3240B ALA* 2.6 27.6 + - - +
3241B LEU 3.7 6.3 - - - +
3242B ALA 3.1 1.4 - - - -
3243B GLN* 1.3 85.5 - - - +
3245B GLY* 1.3 55.1 + - - +
3246B ALA 3.8 0.2 - - - -
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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