Contacts of the strand formed by residues 3276 - 3281 (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 GLN3276 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3247B LYS 3.1 6.3 + - - -
3248B ALA* 3.3 15.2 - - + -
3249B LEU 2.9 27.5 + - - -
3271B ARG* 3.3 25.4 + - - +
3274B GLY 3.7 4.8 + - - +
3275B THR* 1.3 76.1 - - - +
3277B ILE* 1.3 60.1 + - - +
3278B ILE* 4.0 6.1 - - + -
3301B ASP 5.1 0.7 - - - +
3303B VAL* 4.4 4.9 - - - +
3321B MET* 3.4 28.1 - - + +
3325B GLN* 3.3 25.9 + - - +
3327B SER* 2.8 23.5 + - - -
3330B LEU* 3.5 27.0 - - + +
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Residues in contact with ILE3277 (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* 6.0 0.2 - - + -
3249B LEU* 3.9 22.4 - - + +
3251B HIS* 5.1 5.4 - - + -
3267B LEU* 3.8 42.4 - - + +
3270B LEU* 4.3 14.6 - - + -
3271B ARG* 4.4 6.2 - - + +
3275B THR* 3.5 11.8 + - + +
3276B GLN* 1.3 81.0 + - - +
3278B ILE* 1.3 67.2 + - - +
3279B ARG* 4.8 6.3 - - + -
3301B ASP 5.6 0.2 + - - -
3302B TRP* 3.3 42.1 - - + +
3303B VAL* 2.9 26.5 + - - +
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Residues in contact with ILE3278 (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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3248B ALA* 4.7 10.1 - - + -
3249B LEU 3.0 8.8 + - - +
3250B ILE* 3.5 20.5 - - + +
3251B HIS* 2.8 32.4 + - - -
3276B GLN* 4.7 4.7 - - + +
3277B ILE* 1.3 81.5 - - - +
3279B ARG* 1.3 60.2 + - - +
3280B SER 3.5 0.7 + - - -
3303B VAL* 3.1 17.5 - - + +
3304B VAL 4.4 1.1 - - - -
3305B ALA* 4.0 26.2 - - + +
3313B ALA* 4.8 0.2 - - + -
3317B ALA* 3.6 31.6 - - + -
3330B LEU* 4.8 11.0 - - + -
3334B PHE* 3.8 24.9 - - + -
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Residues in contact with ARG3279 (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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3251B HIS* 3.8 13.5 - - + -
3256B ASN 3.3 17.6 + - - -
3257B GLY* 2.9 35.1 + - - +
3259B VAL* 4.0 14.8 - - + -
3267B LEU* 6.0 0.2 - - + -
3277B ILE* 4.8 7.9 - - + -
3278B ILE* 1.3 71.6 - - - +
3280B SER* 1.3 60.6 + - - +
3289B VAL* 3.9 6.7 - - + +
3290B LEU 3.7 11.3 + - - -
3292B ASN 4.0 0.2 - - - +
3294B GLU* 4.0 8.5 - - - +
3295B GLN* 3.8 23.2 + - - +
3297B ASP* 2.6 43.7 + - - +
3302B TRP* 4.2 15.3 - - + -
3303B VAL 2.7 15.8 + - - +
3304B VAL* 3.5 19.5 - - + +
3305B ALA* 2.9 25.4 + - - +
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Residues in contact with SER3280 (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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3250B ILE* 3.7 22.9 - - - -
3251B HIS 2.7 20.5 + - - +
3253B GLY 3.3 1.4 + - - -
3257B GLY* 3.2 19.2 - - - -
3278B ILE 3.5 1.0 + - - -
3279B ARG* 1.3 73.8 - - - +
3281B SER* 1.3 69.5 + - - +
3284B ASN* 5.0 0.2 + - - -
3289B VAL* 4.1 7.6 - - - -
3305B ALA* 4.1 10.5 - - - -
3308B LEU 2.9 24.5 + - - -
3309B ASN* 3.3 0.7 - - - -
3310B PRO* 3.1 18.6 - - - +
3313B ALA* 4.5 0.4 - - - -
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Residues in contact with SER3281 (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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1176A ASN* 3.4 16.0 + - - -
3252B ALA* 3.9 2.0 - - - +
3253B GLY 3.1 13.7 - - - +
3255B GLY 3.1 23.8 - - - -
3257B GLY 3.9 4.5 - - - -
3280B SER* 1.3 82.9 + - - +
3282B HIS* 1.3 55.9 + - - +
3283B VAL 3.2 15.9 + - - -
3284B ASN* 2.7 26.7 + - - +
3289B VAL* 4.2 6.0 - - - +
3310B PRO* 3.1 15.9 - - - +
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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