Contacts of the helix formed by residues 2290 - 2302 (chain B) in PDB entry 2DQZ
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 THR2290 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385B SO4 3.3 19.5 - - - +
2064B ARG* 4.4 1.3 - - - -
2288B GLN 4.8 4.5 - - - +
2289B LYS* 1.3 79.2 - - - +
2291B GLU* 1.3 64.1 + - - +
2292B GLU* 3.6 7.7 + - - +
2293B GLU* 2.8 43.7 + - - +
2294B LEU* 3.0 22.5 + - - +
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Residues in contact with GLU2291 (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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385B SO4 3.1 13.9 + - - +
2064B ARG* 4.7 0.2 - - - +
2088B THR* 2.7 41.6 + - + +
2112B LEU* 4.2 6.3 - - - +
2113B SER* 3.3 25.0 + - - -
2114B GLU* 3.4 31.7 + - - +
2175B TRP* 3.9 4.3 - - + -
2290B THR* 1.3 72.2 - - - +
2292B GLU* 1.3 66.5 + - - +
2294B LEU* 3.0 5.8 + - - +
2295B LEU* 2.9 23.6 + - + +
3275C LYS* 3.1 28.7 + - - +
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Residues in contact with GLU2292 (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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2290B THR* 3.3 7.0 + - - +
2291B GLU* 1.3 80.1 - - - +
2293B GLU* 1.3 63.1 + - + +
2295B LEU* 3.3 23.3 + - - +
2296B GLU* 3.0 58.5 + - - +
2299B LEU* 6.0 1.0 - - - +
3275C LYS* 5.6 3.2 - - - +
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Residues in contact with GLU2293 (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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2272B ALA* 5.7 0.2 - - - -
2288B GLN 4.4 0.7 - - - +
2289B LYS* 3.2 35.2 + - + +
2290B THR* 2.8 53.9 + - - +
2291B GLU 3.1 0.4 - - - -
2292B GLU* 1.3 78.6 - - + +
2294B LEU* 1.3 57.8 + - - +
2296B GLU* 3.7 12.9 + - - +
2297B THR* 2.8 28.4 + - - -
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Residues in contact with LEU2294 (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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2064B ARG* 3.4 33.0 - - - +
2065B PHE* 4.5 2.7 - - + -
2174B ILE* 4.0 27.6 - - + +
2175B TRP* 3.5 34.7 - - + +
2272B ALA* 4.7 1.3 - - + -
2286B LEU* 4.0 24.7 - - + +
2289B LYS* 3.8 20.6 - - + -
2290B THR 3.0 13.2 + - - +
2291B GLU 3.0 4.0 + - - +
2293B GLU* 1.3 76.4 - - - +
2295B LEU* 1.3 56.7 + - - +
2297B THR* 3.6 11.2 + - - +
2298B THR* 2.6 33.3 + - - -
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Residues in contact with LEU2295 (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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2088B THR* 4.1 21.8 - - + -
2089B GLN* 3.4 28.3 - - - +
2090B ASP* 4.3 6.5 - - - +
2091B PRO* 4.5 7.4 - - + -
2112B LEU* 4.2 18.2 - - + -
2175B TRP* 4.0 3.4 - - + -
2291B GLU* 2.9 17.4 + - + +
2292B GLU* 3.3 26.4 + - - +
2294B LEU* 1.3 74.7 - - - +
2296B GLU* 1.3 61.0 + - - +
2298B THR* 3.1 13.5 - - + +
2299B LEU* 2.9 44.3 + - + +
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Residues in contact with GLU2296 (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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2292B GLU* 3.0 44.5 + - - +
2293B GLU* 3.8 12.3 - - - +
2295B LEU* 1.3 73.6 - - - +
2297B THR* 1.3 65.8 + - - +
2299B LEU* 3.2 12.9 + - + +
2300B LYS* 2.9 42.0 + - - +
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Residues in contact with THR2297 (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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2174B ILE* 4.3 6.1 - - + -
2268B ILE* 3.9 26.2 - - + +
2271B THR* 3.6 33.1 + - + +
2272B ALA* 3.8 22.0 - - + +
2293B GLU 2.8 15.3 + - - -
2294B LEU* 3.6 12.7 - - + -
2295B LEU 3.3 0.2 - - - -
2296B GLU* 1.3 77.0 - - - +
2298B THR* 1.3 64.8 + - - +
2300B LYS* 3.1 8.1 + - - +
2301B MET* 3.0 29.7 + - + +
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Residues in contact with THR2298 (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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2089B GLN* 5.9 1.8 - - - -
2090B ASP* 5.5 8.3 - - + +
2145B MET* 4.0 15.3 - - + -
2173B GLY* 6.2 0.2 - - - -
2174B ILE* 3.8 13.9 - - + +
2175B TRP* 4.1 11.8 - - + -
2294B LEU 2.6 19.8 + - - -
2295B LEU* 3.1 16.9 - - + -
2297B THR* 1.3 78.8 - - - +
2299B LEU* 1.3 70.5 + - + +
2301B MET* 3.0 14.7 + - - +
2302B LYS* 3.4 7.8 + - - -
2303B PHE* 3.9 28.6 + - + -
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Residues in contact with LEU2299 (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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2090B ASP* 3.4 44.0 - - + +
2091B PRO* 5.1 4.5 - - + -
2292B GLU* 6.0 0.7 - - - +
2295B LEU* 2.9 30.0 + - + +
2296B GLU* 3.6 13.9 - - + +
2298B THR* 1.3 79.9 - - + +
2300B LYS* 1.3 63.4 + - - +
2302B LYS* 3.2 23.5 + - - +
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Residues in contact with LYS2300 (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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2271B THR* 3.8 35.5 + - + -
2296B GLU* 2.9 32.9 + - - +
2297B THR* 3.4 8.8 + - - +
2299B LEU* 1.3 77.1 - - + +
2301B MET* 1.3 62.8 + - - +
2302B LYS* 3.1 11.8 + - - +
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Residues in contact with MET2301 (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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2174B ILE* 5.7 0.7 - - + -
2264B LEU* 4.4 5.4 - - + -
2267B GLN* 3.7 29.6 - - - +
2268B ILE* 3.9 30.1 - - + -
2271B THR* 3.8 24.7 - - - -
2297B THR* 3.0 26.5 + - + +
2298B THR 3.0 1.7 + - - +
2300B LYS* 1.3 74.8 - - - +
2302B LYS* 1.3 70.5 + - - +
2303B PHE* 3.3 47.1 - - + -
2316B GLN* 4.7 8.0 - - + +
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Residues in contact with LYS2302 (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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2298B THR 3.4 3.8 + - - -
2299B LEU* 3.2 19.3 + - - +
2300B LYS* 3.1 10.9 - - - +
2301B MET* 1.3 80.9 - - - +
2303B PHE* 1.3 62.1 + - - +
2304B LEU 3.7 1.3 - - - -
2305B SER* 4.2 22.9 - - - +
2316B GLN 4.5 3.5 - - - +
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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