Contacts of the helix formed by residues 2282 - 2287 (chain L) in PDB entry 2BT4
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 ALA2282 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1888J VAL* 3.6 7.6 - - + +
1889J ALA* 3.4 36.3 - - + +
1892J ASP* 3.2 20.8 + - + +
2215L PRO* 4.2 4.3 - - + +
2216L ASN* 5.3 0.2 - - - +
2281L ALA* 1.3 79.6 - - - +
2283L TYR* 1.3 61.6 + - - +
2285L HIS* 3.1 22.6 + - - +
2286L THR* 3.6 12.2 + - - +
2360L CA2 3.3 10.7 + - - -
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Residues in contact with TYR2283 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1859J GLU* 3.4 43.2 + - - +
1860J GLY* 4.4 1.9 + - - -
1863J VAL* 5.2 0.3 - - - +
1889J ALA* 3.8 10.5 - - + +
2215L PRO* 3.3 33.0 - - + -
2257L ASN 2.7 25.1 + - - -
2258L HIS* 4.1 0.3 - - - -
2259L GLU* 3.6 28.5 + - + -
2262L LEU* 3.7 17.0 - - + -
2280L PRO* 3.0 9.3 + - + +
2281L ALA 3.0 1.6 + - - -
2282L ALA* 1.3 75.3 - - - +
2284L SER* 1.3 65.7 + - - +
2285L HIS 3.1 0.4 - - - -
2286L THR* 3.6 17.5 - - - -
2287L SER* 3.0 26.7 + - - +
2290L ILE* 3.8 20.8 - - + +
2322L VAL* 5.0 2.9 - - - +
2408L TRS 3.9 6.7 - - - -
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Residues in contact with SER2284 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2280L PRO* 3.2 23.8 - - - +
2281L ALA 2.6 21.4 + - - -
2283L TYR* 1.3 80.1 - - - +
2285L HIS* 1.3 69.0 + - - +
2304L GLU* 4.2 0.2 - - - -
2306L HIS* 2.8 33.2 - - - -
2320L SER* 3.3 13.0 - - - -
2321L TYR* 3.0 31.5 + - - +
2322L VAL* 4.2 3.3 + - - -
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Residues in contact with HIS2285 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1888J VAL* 4.4 10.1 - - + -
2281L ALA 4.2 1.0 + - - -
2282L ALA* 3.1 21.5 + - - +
2283L TYR 3.1 0.2 - - - -
2284L SER* 1.3 91.7 - - - +
2286L THR* 1.3 64.4 + - + +
2306L HIS* 5.0 0.2 - + - -
2310L ILE* 4.4 10.8 - - + -
2316L PHE* 4.0 13.5 - + + +
2317L ARG* 3.1 43.5 + - + -
2319L HIS* 2.8 27.9 + - - +
2320L SER* 5.4 0.2 - - - -
2321L TYR* 3.4 16.7 - - - -
2360L CA2 2.7 31.5 + - - -
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Residues in contact with THR2286 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1886J THR 3.5 20.2 - - - +
1888J VAL* 3.6 28.9 - - + +
1889J ALA 5.8 0.3 + - - -
1921J TYR* 5.5 2.7 - - + +
2086K THR* 3.6 13.0 - - - +
2282L ALA 3.7 5.1 + - - +
2283L TYR* 3.4 18.7 + - - -
2285L HIS* 1.3 85.3 - - - +
2287L SER* 1.3 59.9 + - - +
2288L VAL 3.5 5.3 + - - -
2321L TYR* 4.0 8.0 - - - -
2408L TRS 2.8 39.2 + - - -
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Residues in contact with SER2287 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2259L GLU* 2.6 27.1 + - - -
2283L TYR* 3.0 25.8 + - - +
2285L HIS 3.9 0.4 - - - -
2286L THR* 1.3 74.1 + - - +
2288L VAL* 1.3 62.4 + - - +
2289L ALA 3.5 0.2 + - - -
2290L ILE* 2.9 42.6 + - - +
2291L LEU 3.4 11.8 + - - -
2321L TYR* 3.9 14.6 - - - +
2322L VAL* 5.3 1.4 - - - +
2408L TRS 3.6 2.2 - - - -
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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