Contacts of the helix formed by residues 2232 - 2247 (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 THR2232 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2220L LEU* 3.4 18.2 - - - +
2221L GLY* 4.9 3.4 - - - -
2222L GLN* 5.9 3.1 - - + -
2230L SER 4.8 4.7 - - - +
2231L ASP* 1.3 77.9 - - - +
2233L LEU* 1.3 66.6 + - - +
2234L ALA* 3.6 9.6 + - - +
2235L ASP* 2.9 31.4 + - - +
2236L VAL* 3.0 21.1 + - - +
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Residues in contact with LEU2233 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2213L ASN* 4.2 14.1 - - + +
2217L LEU* 3.7 29.2 - - + +
2218L ASN* 4.2 12.4 + - - +
2220L LEU* 4.0 16.5 + - + +
2232L THR* 1.3 74.2 - - - +
2234L ALA* 1.3 57.2 + - - +
2236L VAL* 3.0 13.8 + - + +
2237L GLU* 2.9 27.6 + - - +
2253L PHE* 3.8 27.3 - - + -
2255L GLN* 3.8 36.1 - - + -
2338L TYR* 4.8 2.9 - - - +
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Residues in contact with ALA2234 (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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2232L THR* 3.6 8.9 + - - +
2233L LEU* 1.3 78.9 - - - +
2235L ASP* 1.3 62.3 + - - +
2237L GLU* 3.3 15.3 + - - +
2238L ALA* 3.0 21.5 + - - +
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Residues in contact with ASP2235 (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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2230L SER 4.5 0.9 - - - +
2231L ASP* 3.3 27.7 - - + +
2232L THR* 2.9 39.8 + - - +
2234L ALA* 1.3 79.0 - - - +
2236L VAL* 1.3 60.8 + - - +
2238L ALA* 3.3 8.9 + - - +
2239L LEU* 3.1 26.3 + - + +
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Residues in contact with VAL2236 (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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2220L LEU* 3.7 14.8 - - + -
2231L ASP* 5.0 1.6 - - + -
2232L THR 3.0 13.2 + - - +
2233L LEU* 3.0 11.7 + - + +
2235L ASP* 1.3 73.0 - - - +
2237L GLU* 1.3 66.6 + - - +
2239L LEU* 3.1 11.0 + - + +
2240L CYS* 3.0 20.4 + - - -
2253L PHE* 3.8 13.7 - - + -
2335L VAL* 3.7 32.1 - - + -
2338L TYR* 3.7 44.9 - - + -
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Residues in contact with GLU2237 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2233L LEU 2.9 10.1 + - - +
2234L ALA* 3.5 15.8 - - - +
2236L VAL* 1.3 75.1 - - - +
2238L ALA* 1.3 64.2 + - - +
2240L CYS* 3.1 3.5 + - - +
2241L VAL* 2.9 34.1 + - + +
2251L VAL* 5.6 0.3 - - - +
2253L PHE* 3.6 54.3 + - + +
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Residues in contact with ALA2238 (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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2234L ALA 3.0 12.0 + - - +
2235L ASP* 3.4 12.1 - - - +
2236L VAL 3.1 0.2 - - - -
2237L GLU* 1.3 80.4 - - - +
2239L LEU* 1.3 61.9 + - - +
2241L VAL* 3.4 7.9 + - - +
2242L LYS* 3.1 23.7 + - - +
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Residues in contact with LEU2239 (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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2231L ASP* 5.0 3.6 - - - +
2235L ASP* 3.1 17.8 + - + +
2236L VAL* 3.1 13.0 + - + +
2238L ALA* 1.3 76.7 - - - +
2240L CYS* 1.3 59.9 + - - +
2242L LYS* 3.5 14.6 + - + +
2243L ALA* 3.0 28.4 + - - +
2335L VAL* 3.5 48.0 - - + +
2336L GLN* 4.7 1.3 - - - +
2338L TYR* 5.7 0.7 - - + -
2339L VAL* 4.3 19.9 - - + +
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Residues in contact with CYS2240 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2211L ILE* 3.8 31.6 - - + -
2236L VAL 3.0 14.8 + - - -
2237L GLU 3.1 7.8 + - - +
2239L LEU* 1.3 78.6 - - - +
2241L VAL* 1.3 66.0 + - - +
2243L ALA* 4.0 5.0 - - - +
2244L ALA* 2.9 26.2 + - - +
2251L VAL* 3.6 10.2 - - + +
2253L PHE* 4.1 15.0 - - + -
2338L TYR* 3.8 34.1 - - - -
2339L VAL* 5.7 0.9 - - - -
2342L VAL* 4.5 4.7 - - + +
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Residues in contact with VAL2241 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2237L GLU* 2.9 31.1 + - + +
2238L ALA* 3.8 10.8 - - - +
2240L CYS* 1.3 75.4 - - - +
2242L LYS* 1.3 59.3 + - - +
2244L ALA* 3.8 2.1 - - - +
2245L ALA* 2.9 31.5 + - + +
2249L GLY 5.0 0.3 - - - +
2250L THR* 5.8 1.0 - - - +
2251L VAL* 3.8 23.3 - - + +
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Residues in contact with LYS2242 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2238L ALA 3.1 15.4 + - - +
2239L LEU* 3.6 15.8 - - + +
2241L VAL* 1.3 82.1 - - - +
2243L ALA* 1.3 64.6 + - - +
2245L ALA* 3.1 6.3 + - - +
2246L ALA* 2.9 25.3 + - + +
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Residues in contact with ALA2243 (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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2239L LEU 3.0 18.4 + - - +
2240L CYS* 4.0 3.8 - - - +
2242L LYS* 1.3 77.8 - - - +
2244L ALA* 1.3 60.8 + - - +
2246L ALA* 3.3 8.5 + - - +
2247L HIS* 3.1 28.3 - - + -
2339L VAL* 4.1 29.4 - - + +
2342L VAL* 3.9 19.2 - - + +
2343L GLU* 5.4 2.0 - - + +
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Residues in contact with ALA2244 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2204L LEU* 4.6 1.7 - - + +
2209L ILE* 4.7 3.6 - - + -
2240L CYS 2.9 17.9 + - - +
2241L VAL 3.8 2.7 - - - +
2243L ALA* 1.3 73.6 - - - +
2245L ALA* 1.3 65.7 + - - +
2247L HIS* 2.9 12.3 + - - +
2248L GLY 3.1 0.2 + - - -
2249L GLY* 2.8 40.5 + - - +
2250L THR* 3.9 4.0 - - - +
2251L VAL* 3.6 21.1 - - + -
2342L VAL* 3.8 15.1 - - + +
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Residues in contact with ALA2245 (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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2241L VAL* 2.9 21.2 + - + +
2242L LYS* 3.1 6.7 + - - +
2244L ALA* 1.3 79.0 - - - +
2246L ALA* 1.3 61.7 + - - +
2247L HIS 2.9 1.5 + - - -
2248L GLY* 3.1 12.3 + - - +
2249L GLY 3.6 11.0 - - - +
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Residues in contact with ALA2246 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2242L LYS* 2.9 13.6 + - + +
2243L ALA* 3.4 15.3 - - - +
2244L ALA 3.1 0.2 - - - -
2245L ALA* 1.3 78.8 - - - +
2247L HIS* 1.3 70.4 + - + +
2248L GLY 3.5 0.4 + - - -
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Residues in contact with HIS2247 (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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2204L LEU* 3.9 12.1 - - + +
2243L ALA* 3.1 24.0 - - - +
2244L ALA* 2.9 7.3 + - - +
2245L ALA 2.9 0.4 - - - -
2246L ALA* 1.3 90.7 + - + +
2248L GLY* 1.3 58.9 + - - +
2249L GLY 3.4 1.5 + - - -
2342L VAL* 5.2 1.8 - - + -
2343L GLU* 4.0 32.6 + - + +
2346L ALA* 3.8 31.5 - - + +
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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