Contacts of the strand formed by residues 3248 - 3253 (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 ALA3248 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3223B GLN 3.6 2.0 + - - -
3224B VAL* 3.4 21.5 - - + -
3225B ASP 3.2 21.7 + - - -
3246B ALA* 3.3 6.3 - - - +
3247B LYS* 1.3 81.8 - - - +
3249B LEU* 1.3 63.6 + - - +
3275B THR* 4.0 1.3 - - - -
3276B GLN* 3.3 18.6 - - + +
3278B ILE* 4.7 11.4 - - + -
3317B ALA* 4.9 0.9 - - + -
3321B MET* 3.7 22.0 - - - -
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Residues in contact with LEU3249 (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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3225B ASP* 3.4 9.0 - - + +
3226B ILE 5.0 0.2 - - - +
3227B ALA* 5.4 3.4 - - + -
3238B TYR* 3.4 37.0 - - + +
3241B LEU* 3.5 40.4 - - + -
3242B ALA* 4.4 3.1 - - + -
3246B ALA* 4.2 9.0 - - + -
3248B ALA* 1.3 79.8 - - - +
3250B ILE* 1.3 66.9 + - - +
3251B HIS* 3.6 0.9 + - + -
3270B LEU* 3.8 22.7 - - + -
3275B THR* 4.2 12.6 - - + -
3276B GLN 2.9 10.6 + - - +
3277B ILE* 3.9 11.6 - - + +
3278B ILE* 3.0 26.2 + - - +
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Residues in contact with ILE3250 (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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3224B VAL* 4.0 9.2 - - + -
3225B ASP 2.8 19.0 + - - +
3226B ILE* 3.4 16.7 - - + +
3227B ALA* 3.0 27.5 + - - +
3238B TYR* 5.6 0.2 - - - -
3249B LEU* 1.3 74.5 - - - +
3251B HIS* 1.3 61.4 + - - +
3278B ILE* 3.5 32.3 - - + +
3280B SER* 3.7 26.7 - - - -
3310B PRO* 3.7 19.1 - - + +
3313B ALA* 3.9 10.8 - - + +
3314B ARG* 3.8 33.9 - - + +
3317B ALA* 4.4 0.2 - - + -
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Residues in contact with HIS3251 (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 4.0 2.2 - - - -
3229B SER* 3.5 24.2 - - - -
3238B TYR* 2.6 42.6 + + + -
3249B LEU* 3.6 3.2 + - + +
3250B ILE* 1.3 71.4 - - - +
3252B ALA* 1.3 56.2 + - - +
3253B GLY* 3.2 7.0 + - - -
3257B GLY 3.6 16.8 - - - -
3258B SER 2.7 23.6 + - - -
3259B VAL* 3.3 26.8 - - + +
3263B VAL* 5.6 0.2 - - + -
3267B LEU* 5.0 3.1 - - + +
3277B ILE* 5.1 8.5 - - + -
3278B ILE 2.8 16.6 + - - +
3279B ARG* 4.3 12.1 - - + -
3280B SER* 2.7 36.7 + - - +
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Residues in contact with ALA3252 (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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3226B ILE* 4.3 4.7 - - + -
3227B ALA 3.0 18.1 + - - +
3228B TYR* 4.1 19.5 - - + -
3229B SER* 3.1 21.8 + - - -
3250B ILE 3.6 0.6 + - - -
3251B HIS* 1.3 70.2 - - - +
3253B GLY* 1.3 64.5 + - - +
3281B SER* 3.9 11.0 - - - +
3282B HIS* 3.4 7.7 - - - +
3310B PRO* 3.4 31.4 - - + -
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Residues in contact with GLY3253 (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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3229B SER* 3.5 7.0 - - - -
3251B HIS* 3.2 30.9 + - - -
3252B ALA* 1.3 75.3 - - - +
3254B THR* 1.3 67.0 + - - -
3257B GLY* 4.5 0.9 - - - -
3258B SER 3.7 2.9 - - - -
3280B SER 3.3 7.6 + - - -
3281B SER* 3.1 6.0 - - - -
3282B HIS* 2.9 27.3 + - - -
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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