Contacts of the helix formed by residues 2321 - 2340 (chain B) in PDB entry 4D0N
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 SER2321 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2300B LYS* 3.9 13.7 - - - -
2319B ALA* 3.4 3.3 - - - +
2320B SER* 1.3 79.8 - - - +
2322B LYS* 1.3 60.8 + - - +
2323B GLU* 3.4 17.7 + - - +
2324B GLU* 3.2 23.5 + - - +
2325B ARG* 2.9 27.5 + - - +
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Residues in contact with LYS2322 (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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2299B GLU* 3.5 65.8 + - + +
2300B LYS* 4.1 4.1 - - + +
2321B SER* 1.3 72.7 - - - +
2323B GLU* 1.3 80.0 + - + +
2325B ARG* 3.4 4.1 + - - +
2326B ASN* 3.0 47.0 + - - +
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Residues in contact with GLU2323 (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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2321B SER* 3.3 17.9 + - - +
2322B LYS* 1.3 97.7 + - + +
2324B GLU* 1.3 57.9 + - - +
2326B ASN* 3.2 9.1 + - - +
2327B SER* 3.0 27.3 + - - -
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Residues in contact with GLU2324 (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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2240B GLY* 5.6 1.4 - - - -
2241B SER 3.8 18.0 + - - +
2242B VAL* 4.6 0.9 - - - +
2319B ALA* 4.1 4.0 - - + -
2320B SER* 3.2 30.1 + - - -
2321B SER* 3.2 17.7 + - - +
2323B GLU* 1.3 76.2 - - - +
2325B ARG* 1.3 65.5 + - - +
2327B SER* 3.0 22.3 + - - +
2328B TRP* 3.1 37.1 + - + +
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Residues in contact with ARG2325 (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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2294B GLU* 3.0 45.5 + - - +
2295B VAL 4.9 2.0 + - - -
2298B GLU 4.3 3.0 + - - -
2299B GLU* 2.7 45.0 + - - +
2300B LYS 3.5 15.7 - - - +
2301B GLY 3.0 27.8 + - - +
2302B LEU* 4.2 7.2 - - + +
2319B ALA* 3.6 9.3 - - + +
2321B SER 2.9 18.9 + - - +
2322B LYS* 3.5 7.7 - - - +
2323B GLU 3.2 0.2 - - - -
2324B GLU* 1.3 77.2 - - - +
2326B ASN* 1.3 87.4 + - - +
2328B TRP* 3.4 5.6 + - - +
2329B ILE* 3.2 32.5 + - - +
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Residues in contact with ASN2326 (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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2294B GLU* 5.1 1.8 + - - -
2322B LYS* 3.0 33.2 + - - +
2323B GLU* 3.2 10.1 + - - +
2325B ARG* 1.3 110.8 + - - +
2327B SER* 1.3 64.8 + - - +
2329B ILE* 3.1 7.5 + - - +
2330B GLN* 3.1 22.2 + - - +
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Residues in contact with SER2327 (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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2238B ARG* 3.5 19.1 + - - -
2323B GLU 3.0 11.8 + - - -
2324B GLU* 3.0 22.7 + - - +
2326B ASN* 1.3 76.2 - - - +
2328B TRP* 1.3 65.9 + - - +
2330B GLN* 3.3 6.6 + - - +
2331B ILE* 3.2 25.5 + - - +
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Residues in contact with TRP2328 (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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2238B ARG* 3.7 44.0 - - + -
2239B ASP 4.2 2.7 - - - -
2240B GLY* 4.0 17.6 - - - -
2242B VAL* 3.7 20.7 - - + +
2256B ALA* 3.6 34.1 - - + -
2258B LEU* 4.1 22.4 - - + -
2263B LEU* 5.3 2.0 - - + -
2302B LEU* 4.2 14.8 - - + -
2319B ALA* 4.8 4.5 - - + -
2324B GLU* 3.1 41.7 + - + +
2325B ARG* 3.6 6.1 - - - +
2327B SER* 1.3 84.7 + - - +
2329B ILE* 1.3 60.0 + - - +
2331B ILE* 3.5 10.3 - - + +
2332B ILE* 3.0 44.7 + - + +
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Residues in contact with ILE2329 (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 VAL* 4.0 21.7 - - + +
2293B ARG* 4.4 1.1 - - - -
2294B GLU* 3.7 36.3 - - + +
2302B LEU* 3.5 30.5 - - + -
2325B ARG* 3.2 29.8 + - - +
2326B ASN* 3.1 10.7 + - - +
2328B TRP* 1.3 77.9 - - - +
2330B GLN* 1.3 57.6 + - - +
2332B ILE* 3.9 1.7 - - - +
2333B GLN* 3.0 32.2 + - + +
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Residues in contact with GLN2330 (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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2326B ASN 3.1 12.5 + - - +
2327B SER* 3.3 9.6 + - - +
2329B ILE* 1.3 78.6 - - - +
2331B ILE* 1.3 58.6 + - - +
2333B GLN* 3.3 5.6 + - - +
2334B ASP* 2.8 49.3 + - - +
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Residues in contact with ILE2331 (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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2237B VAL* 3.5 32.5 - - + +
2238B ARG* 3.2 48.5 - - + +
2258B LEU* 4.0 11.4 - - + -
2327B SER 3.2 16.0 + - - +
2328B TRP* 3.5 16.8 - - + +
2330B GLN* 1.3 76.0 - - - +
2332B ILE* 1.3 61.0 + - - +
2334B ASP* 3.6 10.4 - - + +
2335B THR* 2.6 39.6 + - - +
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Residues in contact with ILE2332 (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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2258B LEU* 3.9 25.1 - - + -
2263B LEU* 4.3 17.0 - - + -
2287B LEU* 4.9 7.1 - - + +
2290B LEU* 4.6 5.6 - - + -
2292B VAL* 3.5 26.0 - - + -
2302B LEU* 4.6 12.1 - - + -
2304B LEU* 4.3 16.8 - - + -
2328B TRP* 3.0 40.9 + - + +
2329B ILE* 3.9 4.5 - - - +
2331B ILE* 1.3 78.1 - - - +
2333B GLN* 1.3 61.3 + - - +
2335B THR* 3.2 2.3 + - - -
2336B ILE* 2.8 37.1 + - + +
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Residues in contact with GLN2333 (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 LEU 5.7 0.4 + - - -
2292B VAL* 4.3 22.9 + - + +
2329B ILE* 3.0 23.2 + - + +
2330B GLN* 3.5 6.3 - - - +
2332B ILE* 1.3 78.1 - - - +
2334B ASP* 1.3 59.1 + - - +
2336B ILE* 3.3 19.0 + - - +
2337B ASN* 2.8 68.1 + - - +
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Residues in contact with ASP2334 (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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2330B GLN* 2.8 43.4 + - - +
2331B ILE* 3.6 11.9 - - + +
2332B ILE 3.3 0.2 - - - -
2333B GLN* 1.3 74.3 - - - +
2335B THR* 1.3 59.4 + - - +
2337B ASN* 3.4 10.3 + - - +
2338B THR* 2.9 34.3 + - - +
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Residues in contact with THR2335 (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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2237B VAL* 3.7 17.9 - - + +
2258B LEU* 3.5 15.0 - - + +
2259B LEU 3.5 17.3 - - - +
2260B THR* 3.4 27.5 - - + +
2287B LEU* 3.6 9.6 - - + -
2331B ILE* 2.6 25.5 + - - +
2332B ILE 3.7 3.8 - - - -
2334B ASP* 1.3 73.8 - - - +
2336B ILE* 1.3 64.7 + - - +
2338B THR* 3.7 6.1 + - - -
2339B LEU* 3.2 22.5 + - - +
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Residues in contact with ILE2336 (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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2287B LEU* 3.7 30.5 - - + +
2288B LYS 4.5 2.0 - - - +
2290B LEU* 3.5 32.8 - - + +
2291B ILE* 5.2 0.2 - - - -
2292B VAL* 3.7 25.1 - - + -
2332B ILE* 2.8 27.6 + - + +
2333B GLN* 3.6 19.3 - - - +
2335B THR* 1.3 76.7 - - - +
2337B ASN* 1.3 64.6 + - - +
2339B LEU* 3.0 9.3 + - - +
2340B ASN* 2.4 40.3 + - - +
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Residues in contact with ASN2337 (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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2333B GLN* 2.8 54.1 + - - +
2334B ASP* 3.8 10.7 + - - +
2336B ILE* 1.3 77.8 - - - +
2338B THR* 1.3 64.4 + - - +
2340B ASN* 3.4 16.1 + - - +
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Residues in contact with THR2338 (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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2334B ASP* 2.9 22.0 + - - +
2335B THR* 3.8 7.4 - - - -
2337B ASN* 1.3 76.9 - - - +
2339B LEU* 1.3 64.8 + - - +
2340B ASN 3.4 4.0 + - - +
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Residues in contact with LEU2339 (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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2260B THR* 3.9 15.3 - - - +
2261B ASP* 4.1 26.0 - - + +
2286B SER* 5.6 0.7 - - - +
2287B LEU* 4.0 26.2 - - + -
2288B LYS* 4.2 21.1 - - + +
2335B THR 3.2 10.6 + - - +
2336B ILE 3.0 10.1 + - - +
2338B THR* 1.3 83.3 - - - +
2340B ASN* 1.3 62.9 + - - +
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Residues in contact with ASN2340 (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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2287B LEU 4.6 0.2 + - - -
2288B LYS* 2.7 36.4 + - - +
2336B ILE* 2.4 50.7 + - - +
2337B ASN* 3.4 12.6 + - - +
2338B THR 3.4 4.5 - - - +
2339B LEU* 1.3 90.2 - - - +
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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