Contacts of the helix formed by residues 2309 - 2313 (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 ASN2309 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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923E SER 3.1 17.8 + - - -
926E ALA 2.8 28.1 + - - -
927E ASP 3.6 17.5 + - - +
929E VAL* 3.9 14.8 - - - +
2308L SER* 1.3 73.0 - - - +
2310L ILE* 1.3 61.5 + - - +
2311L HIS* 2.9 32.4 + - - +
2312L GLN* 2.9 33.8 + - - +
2313L ARG* 3.5 7.7 - - - +
2331L ALA* 4.3 2.5 - - - -
2332L GLY* 3.4 9.5 - - - +
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Residues in contact with ILE2310 (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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2285L HIS* 4.4 6.3 - - + -
2306L HIS* 4.1 28.3 - - + +
2308L SER* 3.1 11.3 + - - +
2309L ASN* 1.3 72.0 + - - +
2311L HIS* 1.3 81.8 + - + +
2312L GLN 3.1 0.9 - - - -
2313L ARG* 3.2 22.7 + - - +
2317L ARG* 3.3 27.1 - - + +
2318L HIS* 3.2 26.5 - - - +
2320L SER* 5.0 8.7 - - - -
2331L ALA* 4.5 7.4 - - + +
2360L CA2 3.7 35.4 - - + +
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Residues in contact with HIS2311 (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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911E HIS* 4.1 26.5 + + - -
918E HIS 5.6 0.2 - - - -
923E SER* 3.9 31.0 - - - +
924E GLN* 4.6 11.6 - - - +
929E VAL* 4.5 11.2 - - + +
2419E GOL 2.8 34.4 + - - +
2309L ASN* 2.9 21.7 + - - +
2310L ILE* 1.3 94.5 - - + +
2312L GLN* 1.3 59.1 + - - +
2313L ARG 3.4 0.2 - - - -
2318L HIS* 3.3 39.8 + - - -
2329L VAL* 6.2 1.6 - - - +
2331L ALA* 4.4 13.1 - - + +
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Residues in contact with GLN2312 (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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923E SER 3.4 13.6 + - - +
924E GLN* 3.3 18.0 + - - +
925E ARG* 3.3 20.2 + - - +
926E ALA 2.9 27.1 + - - -
927E ASP* 4.7 3.1 - - - +
2309L ASN* 2.9 25.0 + - - +
2311L HIS* 1.3 78.8 - - - +
2313L ARG* 1.3 62.6 + - + +
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Residues in contact with ARG2313 (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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2224L GLN* 4.7 6.3 + - - +
2227L ILE* 4.5 18.3 - - - +
2228L TYR* 2.4 36.4 + - - -
2308L SER* 2.8 42.4 + - - -
2309L ASN 3.5 14.1 - - - +
2310L ILE* 3.2 14.1 + - - +
2311L HIS 3.4 0.2 - - - -
2312L GLN* 1.3 83.7 - - + +
2314L GLU* 1.3 81.8 + - - +
2315L PRO* 3.5 1.9 - - - +
2317L ARG* 3.9 29.9 - - - +
2318L HIS* 2.9 12.7 + - - -
2360L CA2 4.0 11.9 + - - +
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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