Contacts of the helix formed by residues 326 - 332 (chain J) in PDB entry 6ALG
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 SER 326 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265J LEU* 4.4 6.5 - - - -
268J LEU* 4.1 8.7 - - - -
306J LEU 3.3 18.4 - - - -
308J ASP* 3.7 5.5 - - - -
309J ASN* 3.2 32.7 + - - -
325J LYS* 1.3 79.1 - - - +
327J LEU* 1.3 55.7 + - - +
329J ASP* 3.0 17.9 + - - +
330J MET* 2.7 39.4 + - - +
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Residues in contact with LEU 327 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1329I GLU* 4.6 16.4 - - + +
1332I SER* 3.5 39.3 - - - +
1333I LEU* 3.8 27.6 - - + -
245J LEU* 4.6 3.1 - - + -
265J LEU* 3.7 34.5 - - + +
269J TYR* 3.9 15.0 - - - +
306J LEU* 3.7 19.8 + - + +
307J LEU 4.2 2.7 - - - +
326J SER* 1.3 75.8 - - - +
328J ALA* 1.3 59.0 + - - +
330J MET* 2.9 20.7 + - + +
331J ILE* 3.1 19.8 + - - +
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Residues in contact with ALA 328 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1333I LEU* 4.8 1.3 - - - +
115J TRP* 3.7 26.0 - - + +
307J LEU 3.2 19.2 + - - +
308J ASP* 3.5 25.6 - - - +
326J SER* 3.9 0.2 + - - -
327J LEU* 1.3 78.7 - - - +
329J ASP* 1.3 59.0 + - - +
331J ILE* 3.9 4.3 - - - +
332J LYS* 2.9 42.1 + - + +
1329J THR* 4.7 0.2 - - - +
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Residues in contact with ASP 329 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308J ASP* 3.8 10.6 - - - +
309J ASN* 4.3 5.2 - - - +
310J GLY* 4.2 15.7 + - - -
324J LEU 4.4 4.0 - - - +
325J LYS* 3.9 14.2 - - + -
326J SER* 3.0 33.4 + - - +
328J ALA* 1.3 78.2 - - - +
330J MET* 1.3 62.3 + - - +
331J ILE 3.6 0.2 + - - -
332J LYS* 4.0 14.8 + - - +
335J GLN 5.0 1.4 - - - +
336J GLY* 4.5 3.5 - - - -
108N TRP* 3.6 53.7 + - - +
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Residues in contact with MET 330 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1329I GLU* 3.3 30.5 - - - +
263J SER* 3.3 27.6 - - - +
264J ASP 5.2 0.2 - - - +
265J LEU* 4.3 16.6 - - + +
325J LYS* 3.7 39.9 - - + +
326J SER 2.7 22.4 + - - +
327J LEU* 2.9 13.8 + - - +
329J ASP* 1.3 75.8 - - - +
331J ILE* 1.3 57.6 + - - +
335J GLN 5.8 0.2 - - - -
336J GLY* 3.3 21.6 - - - -
337J ARG* 3.5 23.3 + - - +
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Residues in contact with ILE 331 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1326I LEU* 4.4 10.1 - - + -
1329I GLU* 3.3 37.9 - - + +
1330I ILE* 3.7 21.1 - - + -
1333I LEU* 4.1 13.0 - - + -
115J TRP* 5.3 5.4 - - + -
327J LEU 3.1 15.9 + - - +
328J ALA* 4.1 3.8 - - - +
330J MET* 1.3 81.3 - - - +
332J LYS* 1.3 67.6 + - + +
333J GLY 4.7 0.7 - - - +
336J GLY* 3.8 6.4 - - - -
337J ARG* 3.8 7.0 + - - +
338J PHE* 3.7 38.4 + - + +
1328J THR* 3.9 17.8 + - + -
1332J LEU* 5.4 2.0 - - + -
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Residues in contact with LYS 332 (chain J).
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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11B C 3.8 23.8 + - - -
12B G 4.6 11.9 + - - -
308J ASP* 4.5 10.6 + - - +
310J GLY* 6.3 0.8 - - - -
311J ARG* 5.1 1.6 - - - +
328J ALA* 2.9 28.6 + - + +
329J ASP* 4.0 11.1 + - - +
331J ILE* 1.3 82.1 - - + +
333J GLY* 1.3 68.5 + - - +
335J GLN 4.3 0.2 + - - -
336J GLY* 3.3 14.4 + - - -
1327J GLU* 6.0 2.2 - - - +
1328J THR* 4.0 26.2 - - + +
1329J THR* 3.3 28.3 + - - +
108N TRP* 3.7 33.0 - - + +
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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