Contacts of the helix formed by residues 318 - 327 (chain I) in PDB entry 6PST
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 318 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293I ALA* 4.6 7.2 - - - +
316I GLU* 3.8 8.2 + - - -
317I LEU* 1.3 74.3 - - - +
319I LEU* 1.3 68.5 + - - +
320I ASP* 2.1 34.6 + - - -
321I LEU* 3.0 14.8 + - - +
322I LEU* 2.9 24.9 + - - +
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Residues in contact with LEU 319 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289I VAL* 3.0 38.8 - - + +
290I GLU* 4.3 13.0 - - + -
293I ALA* 3.3 30.3 - - + +
318I SER* 1.3 75.5 - - - +
320I ASP* 1.3 62.4 + - - +
322I LEU* 3.2 10.2 + - + +
323I ALA* 2.9 23.4 + - - +
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Residues in contact with ASP 320 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318I SER* 2.1 32.5 + - - -
319I LEU* 1.3 75.4 - - - +
321I LEU* 1.3 77.7 + - - +
323I ALA* 3.2 8.0 + - - +
324I LYS* 2.9 57.9 + - - +
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Residues in contact with LEU 321 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310I ILE* 4.0 22.9 - - + +
311I CYS* 5.1 2.2 - - + -
315I MET* 4.0 17.3 - - + -
316I GLU 3.6 22.4 - - - +
317I LEU* 4.3 10.8 - - + -
318I SER* 3.0 22.8 + - - +
320I ASP* 1.3 90.2 + - - +
322I LEU* 1.3 61.5 + - - +
324I LYS* 3.9 27.6 - - + +
325I LEU* 2.9 41.2 + - + +
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Residues in contact with LEU 322 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237I LEU* 4.9 1.8 - - + -
289I VAL* 3.9 31.0 - - + +
292I ILE* 3.5 40.2 - - + +
317I LEU* 3.3 41.1 - - + -
318I SER 2.9 17.2 + - - +
319I LEU* 3.2 12.3 + - + +
321I LEU* 1.3 78.2 - - - +
323I ALA* 1.3 53.1 + - - +
325I LEU* 3.9 6.3 - - + +
326I SER* 2.4 39.4 + - - +
333I ILE* 4.8 4.9 - - + -
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Residues in contact with ALA 323 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319I LEU 2.9 12.8 + - - +
320I ASP* 3.6 10.1 - - - +
322I LEU* 1.3 75.7 - - - +
324I LYS* 1.3 59.0 + - + +
326I SER* 3.2 6.5 + - - -
327I GLN* 2.9 41.3 + - - +
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Residues in contact with LYS 324 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310I ILE* 4.1 20.0 - - + +
320I ASP* 2.9 57.8 + - - +
321I LEU* 3.7 22.3 - - + +
322I LEU 3.2 0.2 - - - -
323I ALA* 1.3 78.1 - - + +
325I LEU* 1.3 61.2 + - - +
327I GLN* 3.0 36.0 + - - +
328I SER* 3.4 10.2 + - - -
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Residues in contact with LEU 325 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297I VAL* 5.7 1.1 - - + -
301I TYR* 4.4 24.0 - - + -
310I ILE* 3.2 43.1 - - + -
311I CYS* 4.3 18.8 - - - -
317I LEU* 4.5 14.4 - - + -
321I LEU* 2.9 22.3 + - + +
322I LEU* 3.9 6.1 - - + +
324I LYS* 1.3 73.3 - - - +
326I SER* 1.3 61.6 + - - +
328I SER* 2.8 17.8 + - - -
330I HIS* 3.0 40.2 + - + +
332I ARG 5.8 0.4 - - - +
333I ILE* 5.4 10.8 - - + -
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Residues in contact with SER 326 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232I ILE* 3.9 21.6 - - - +
322I LEU* 2.4 26.5 + - - +
323I ALA* 3.2 7.9 + - - -
325I LEU* 1.3 75.5 - - - +
327I GLN* 1.3 61.6 + - - +
329I GLY* 3.2 14.2 + - - -
330I HIS 4.0 12.4 + - - +
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Residues in contact with GLN 327 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323I ALA* 2.9 25.3 + - - +
324I LYS* 3.0 37.1 + - - +
326I SER* 1.3 71.8 - - - +
328I SER* 1.3 55.6 + - - +
329I GLY 3.1 8.1 + - - -
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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