Contacts of the helix formed by residues 3066 - 3070 (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 ALA3066 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3036B ALA* 4.2 15.5 - - + -
3037B ALA* 4.4 0.8 - - - +
3065B ILE* 1.3 77.9 - - - +
3067B SER* 1.3 65.0 + - - +
3068B GLU* 3.1 28.3 - - - +
3069B SER* 3.0 23.3 + - - +
4000B CAB 3.2 11.7 - - - +
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Residues in contact with SER3067 (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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3065B ILE* 3.7 14.1 + - - -
3066B ALA* 1.3 69.7 - - - +
3068B GLU* 1.3 60.5 + - - +
3069B SER 3.0 2.4 + - - -
3070B ILE* 3.2 16.1 + - - +
3098B HIS* 3.4 21.5 - - - -
3099B GLY* 3.2 11.3 + - - -
3101B ASP 3.4 0.9 + - - -
3102B THR* 2.9 47.5 + - - +
4000B CAB 2.9 26.0 + - - -
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Residues in contact with GLU3068 (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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1229A SER* 5.6 1.2 + - - -
1230A TYR 4.7 9.2 - - - +
1231A GLY* 5.4 0.5 - - - -
1232A ASN 5.6 0.3 + - - -
1233A VAL* 5.5 0.3 - - - +
1254A THR* 3.7 19.9 - - - +
1258A SER* 3.8 14.6 - - - -
1259A VAL 3.7 21.2 + - - +
1260A SER* 3.4 17.1 - - - +
1294A GLU* 3.8 10.9 - - - +
1295A GLN* 5.3 3.6 + - - -
3066B ALA* 3.1 26.4 - - - +
3067B SER* 1.3 73.9 + - - +
3069B SER* 1.3 65.6 + - - +
3070B ILE* 3.4 3.5 + - - +
3101B ASP* 4.1 1.8 - - - +
3102B THR* 4.1 11.9 - - - +
4000B CAB 2.9 29.4 + - - -
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Residues in contact with SER3069 (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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1259A VAL 4.4 0.2 + - - -
1260A SER* 3.6 10.3 - - - -
1261A SER* 3.0 42.5 + - - -
1262A ARG* 5.7 3.1 + - - +
3065B ILE* 4.5 6.5 - - - +
3066B ALA* 3.0 15.0 + - - +
3067B SER 3.0 1.0 - - - -
3068B GLU* 1.3 87.2 - - - +
3070B ILE* 1.3 63.2 + - - +
3071B THR* 3.9 10.0 + - - +
3074B ASP* 4.4 2.3 - - - +
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Residues in contact with ILE3070 (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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1231A GLY* 4.0 18.8 - - - -
1232A ASN* 3.1 19.5 + - - +
1262A ARG* 5.4 0.5 + - - -
3063B MET* 5.5 2.9 - - - -
3065B ILE* 3.8 16.4 - - + -
3067B SER 3.2 18.9 + - - +
3068B GLU 3.4 0.9 - - - +
3069B SER* 1.3 80.8 - - - +
3071B THR* 1.3 68.2 + - - +
3074B ASP* 3.6 26.2 - - + +
3075B LEU* 4.0 17.0 - - + +
3078B LEU* 5.9 4.0 - - + -
3098B HIS* 3.8 14.1 - - + +
3102B THR* 3.8 8.7 - - - +
3105B GLU* 5.5 0.2 - - - +
3106B THR* 3.8 22.9 - - - +
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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