Contacts of the helix formed by residues 2321 - 2325 (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 TYR2321 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2086K THR* 5.4 2.7 - - + +
2116K PHE* 3.9 29.5 - + + +
2284L SER 3.0 9.7 + - - +
2285L HIS 3.4 31.0 - - - -
2286L THR* 4.0 18.8 - - - -
2287L SER 3.9 16.8 - - - +
2288L VAL* 3.7 26.8 - - + +
2291L LEU* 3.4 25.7 - - + +
2320L SER* 1.3 69.3 - - - +
2322L VAL* 1.3 64.9 + - + +
2324L GLN* 3.1 36.0 + - - +
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Residues in contact with VAL2322 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2278L ILE* 4.3 4.5 - - + -
2280L PRO* 3.7 26.7 - - + -
2283L TYR 5.0 2.7 - - - +
2284L SER* 4.2 6.3 + - - -
2287L SER 5.3 0.9 - - - +
2290L ILE* 4.0 24.0 - - + -
2291L LEU* 4.8 9.2 - - - +
2294L LEU* 3.9 20.0 - - + -
2304L GLU* 3.4 30.5 - - + +
2320L SER* 3.1 9.3 + - - +
2321L TYR* 1.3 78.4 - - + +
2323L SER* 1.3 64.0 + - - +
2324L GLN 3.0 1.2 + - - -
2325L ARG* 3.0 5.5 + - - +
2326L ALA* 3.0 23.2 + - + -
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Residues in contact with SER2323 (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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909E ASN* 3.1 25.5 + - - -
911E HIS* 3.8 29.5 + - - +
912E GLN* 3.5 4.0 + - - +
2422E GOL 4.1 2.7 + - - -
2304L GLU* 2.5 26.9 + - - -
2320L SER* 3.2 21.4 + - - -
2321L TYR 3.2 0.6 - - - -
2322L VAL* 1.3 76.1 - - - +
2324L GLN* 1.3 60.0 + - - +
2325L ARG 3.2 0.9 + - - -
2326L ALA* 3.9 1.7 - - - +
2329L VAL* 3.8 18.2 - - - +
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Residues in contact with GLN2324 (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* 4.6 12.8 - - + +
912E GLN* 3.2 24.3 + - - +
918E HIS* 6.4 1.3 - - + -
2422E GOL 5.1 8.9 - - - -
2114K GLU* 5.2 4.0 - - - +
2116K PHE* 3.3 34.3 - - - -
2291L LEU* 4.1 10.4 - - + +
2295L ASN* 5.3 0.7 - - - +
2320L SER 4.0 8.3 - - - +
2321L TYR* 3.3 35.1 - - - +
2322L VAL 3.0 0.6 + - - -
2323L SER* 1.3 79.1 - - - +
2325L ARG* 1.3 55.7 + - - +
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Residues in contact with ARG2325 (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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912E GLN* 3.5 5.3 + - - +
2291L LEU* 3.7 13.4 - - + +
2294L LEU* 3.3 36.2 + - + -
2295L ASN* 3.5 30.0 + - - +
2297L CYS 3.0 22.6 + - - -
2298L ASP* 5.0 0.8 - - - +
2299L GLY 4.6 2.8 - - - +
2300L LEU 2.8 25.7 + - - +
2302L VAL* 3.6 16.8 - - + +
2322L VAL 3.0 4.8 + - - +
2324L GLN* 1.3 79.8 - - - +
2326L ALA* 1.3 69.7 + - - +
2327L ASP* 3.2 27.2 + - - +
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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
------------------------------------------------------------
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