Contacts of the helix formed by residues 3263 - 3273 (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 VAL3263 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3233B VAL* 4.0 23.6 - - + +
3234B THR* 3.7 29.8 - - - +
3235B ASP* 3.9 7.2 - - + +
3238B TYR* 3.8 23.6 - - + +
3251B HIS* 5.6 0.4 - - + -
3259B VAL* 4.1 12.1 - - + -
3260B SER* 3.0 12.8 + - - +
3262B ARG* 1.3 81.9 - - - +
3264B VAL* 1.3 67.5 + - - +
3265B PRO* 3.3 3.8 - - - -
3266B ALA* 3.2 4.9 + - - +
3267B LEU* 3.2 34.9 + - + +
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Residues in contact with VAL3264 (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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3259B VAL* 4.1 14.1 - - + +
3260B SER 3.2 16.4 + - - +
3261B SER* 4.0 11.2 - - - +
3263B VAL* 1.3 75.5 - - - +
3265B PRO* 1.3 70.9 - - + +
3267B LEU* 3.0 9.1 + - - +
3268B GLN* 2.9 45.7 + - + +
3295B GLN* 3.9 25.6 - - - +
3300B ASN* 5.2 1.3 - - - +
3302B TRP* 4.3 9.6 - - + -
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Residues in contact with PRO3265 (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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3261B SER 3.4 15.3 - - - +
3262B ARG 4.0 7.9 - - - +
3263B VAL 3.4 3.8 - - - -
3264B VAL* 1.3 95.2 - - + +
3266B ALA* 1.3 56.3 + - - +
3268B GLN* 3.1 15.9 + - - +
3269B GLN* 2.9 30.6 + - - +
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Residues in contact with ALA3266 (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* 3.4 35.6 + - + +
3238B TYR* 5.4 0.9 - - + -
3239B LYS* 3.6 25.8 - - + +
3262B ARG 5.3 0.2 + - - -
3263B VAL* 3.2 7.1 + - - +
3265B PRO* 1.3 78.7 - - - +
3267B LEU* 1.3 61.2 + - + +
3269B GLN* 3.6 7.9 - - - +
3270B LEU* 2.8 39.8 + - + +
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Residues in contact with LEU3267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3238B TYR* 3.7 35.0 - - + -
3251B HIS* 5.0 9.0 - - + -
3259B VAL* 3.7 35.9 - - + -
3263B VAL* 3.2 15.9 + - + +
3264B VAL 3.0 8.8 + - - +
3266B ALA* 1.3 78.9 - - + +
3268B GLN* 1.3 60.5 + - - +
3270B LEU* 3.5 10.9 + - + +
3271B ARG* 3.0 27.7 + - - +
3277B ILE* 3.8 28.5 - - + +
3279B ARG* 6.0 0.7 - - - -
3302B TRP* 3.4 26.6 + - + -
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Residues in contact with GLN3268 (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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3264B VAL* 2.9 34.5 + - + +
3265B PRO* 3.1 16.0 + - - +
3267B LEU* 1.3 72.1 - - - +
3269B GLN* 1.3 66.5 + - - +
3271B ARG* 3.2 8.1 + - - +
3272B LYS* 3.1 28.8 + - + +
3299B LYS* 4.5 10.7 - - - +
3300B ASN* 2.9 31.9 + - + +
3302B TRP* 4.0 12.6 - - + +
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Residues in contact with GLN3269 (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* 4.1 23.4 + - - -
3265B PRO 2.9 16.7 + - - +
3266B ALA* 3.6 6.5 - - - +
3268B GLN* 1.3 76.0 - - - +
3270B LEU* 1.3 64.4 - - + +
3272B LYS* 3.1 12.9 + - - +
3273B ASN* 3.0 35.4 + - - +
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Residues in contact with LEU3270 (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* 4.1 19.7 - - + +
3239B LYS* 4.6 11.7 - - + +
3242B ALA* 3.5 26.5 - - + -
3243B GLN* 6.4 0.4 - - + -
3249B LEU* 3.8 26.0 - - + -
3266B ALA* 2.8 32.4 + - + +
3267B LEU* 3.7 10.5 - - + +
3269B GLN* 1.3 78.4 - - + +
3271B ARG* 1.3 62.6 + - - +
3273B ASN* 3.0 22.7 + - + +
3274B GLY 3.3 0.3 + - - -
3275B THR* 3.1 28.7 + - - +
3277B ILE* 4.3 9.0 - - + -
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Residues in contact with ARG3271 (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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3267B LEU 3.0 15.3 + - - +
3268B GLN* 3.4 10.1 - - - +
3269B GLN 3.2 0.2 - - - -
3270B LEU* 1.3 75.1 - - - +
3272B LYS* 1.3 66.5 + - + +
3274B GLY* 2.9 24.2 + - - -
3275B THR 3.2 24.4 + - - -
3276B GLN* 3.3 23.9 - - - +
3277B ILE* 4.4 6.0 - - + +
3300B ASN 3.4 18.6 - - - +
3301B ASP* 2.5 48.8 + - + +
3302B TRP* 3.9 15.3 - - + +
3325B GLN 5.3 0.8 + - - -
3327B SER* 3.5 9.0 + - - -
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Residues in contact with LYS3272 (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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3268B GLN* 3.1 16.5 + - + +
3269B GLN* 3.1 11.9 + - - +
3271B ARG* 1.3 80.9 - - + +
3273B ASN* 1.3 62.5 + - - +
3274B GLY* 3.1 4.6 + - - -
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Residues in contact with ASN3273 (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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3269B GLN* 3.0 27.8 + - - +
3270B LEU* 3.0 21.3 + - + +
3272B LYS* 1.3 79.9 - - - +
3274B GLY* 1.3 58.1 + - - +
3275B THR* 3.6 5.1 + - - +
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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