Contacts of the strand formed by residues 3224 - 3228 (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 VAL3224 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3222B PRO* 3.5 9.7 + - + +
3223B GLN* 1.3 82.4 - - - +
3225B ASP* 1.3 67.5 + - - +
3246B ALA* 4.8 0.2 - - - -
3248B ALA* 3.4 33.9 - - + +
3250B ILE* 4.0 20.6 - - + -
3314B ARG* 2.7 52.6 + - + +
3317B ALA* 4.5 2.9 - - + -
3318B MET* 3.7 38.1 - - + +
3321B MET* 4.8 2.5 - - - -
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Residues in contact with ASP3225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1230A TYR* 2.5 25.6 + - - +
1232A ASN 4.8 6.4 - - - +
1233A VAL* 5.0 1.4 - - - -
1234A THR* 5.0 8.4 + - - +
3223B GLN* 3.0 30.9 + - - +
3224B VAL* 1.3 78.4 - - - +
3226B ILE* 1.3 59.9 + - - +
3241B LEU* 3.5 31.3 - - + +
3246B ALA* 3.6 10.6 - - + +
3248B ALA 3.2 7.3 + - - -
3249B LEU* 3.4 11.5 - - + -
3250B ILE* 2.8 33.4 + - - +
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Residues in contact with ILE3226 (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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1228A TYR* 3.8 34.1 + - + +
1230A TYR* 3.3 43.7 + - + -
1237A ALA* 5.6 2.8 - - - +
3225B ASP* 1.3 82.1 - - - +
3227B ALA* 1.3 68.0 + - - +
3241B LEU* 3.8 12.5 - - - +
3250B ILE* 3.4 24.0 - - + +
3252B ALA* 4.3 4.3 - - + -
3310B PRO* 3.6 41.1 - - + +
3311B GLU* 3.9 9.0 - - - +
3314B ARG* 4.1 9.4 - - + -
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Residues in contact with ALA3227 (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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1228A TYR 6.0 0.2 - - - +
3226B ILE* 1.3 77.2 - - - +
3228B TYR* 1.3 61.4 + - - +
3237B ALA* 4.4 16.6 - - + -
3238B TYR* 3.5 45.2 + - + +
3241B LEU* 4.5 8.5 - - + +
3249B LEU* 5.4 3.1 - - + +
3250B ILE 3.0 8.2 + - - +
3251B HIS* 3.9 1.4 - - - -
3252B ALA* 3.0 26.2 + - - +
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Residues in contact with TYR3228 (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* 3.7 41.4 + - + +
1228A TYR* 3.3 47.8 - + + +
1282A HIS* 5.8 0.7 - - + -
1284A ASN* 5.0 3.6 + - - -
1309A ASN* 5.5 0.2 - - - +
1310A PRO* 3.8 27.0 - - + +
1311A GLU* 2.7 31.1 + - + -
3226B ILE 4.3 0.2 + - - -
3227B ALA* 1.3 75.3 - - - +
3229B SER* 1.3 73.0 + - - +
3230B TYR* 3.6 20.0 - + - -
3233B VAL* 3.8 9.2 - - - +
3237B ALA* 5.7 2.6 - - - +
3238B TYR* 3.9 6.2 + - - -
3252B ALA* 4.1 9.4 - - + -
3282B HIS* 3.3 39.5 + + + +
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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
------------------------------------------------------------
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