Contacts of the helix formed by residues 518 - 522 (chain L) in PDB entry 6PSS
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 HIS 518 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1254I VAL* 5.8 3.0 - - - +
325J LYS* 5.5 4.5 + - - -
335J GLN* 5.3 7.8 - - + +
337J ARG* 5.5 6.6 + - - -
340J GLN* 4.1 21.1 - - - -
507L MET 3.1 24.2 - - - +
508L GLU* 3.3 38.1 + - - +
509L THR 3.3 10.8 - - - +
510L PRO* 5.3 0.2 - - + -
511L ILE* 3.9 3.1 - - - -
516L ASP 4.3 6.9 + - - -
517L SER* 1.3 78.4 + - - +
519L LEU* 1.3 61.0 + - - +
520L GLY* 3.1 15.9 - - - -
521L ASP* 2.9 39.2 + - + +
522L PHE* 3.8 6.1 - - - -
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Residues in contact with LEU 519 (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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255J LEU* 4.9 13.9 - - + -
261J ALA* 4.7 10.3 - - + -
505L ILE* 3.7 33.0 - - + -
506L SER 4.0 7.6 - - - +
507L MET* 4.0 8.8 + - + +
509L THR* 3.1 26.2 + - + +
511L ILE* 3.7 18.8 - - + +
518L HIS* 1.3 73.2 - - - +
520L GLY* 1.3 60.7 + - - +
521L ASP 3.2 0.9 + - - -
522L PHE* 3.6 16.7 + - + -
523L ILE* 3.6 13.5 + - - +
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Residues in contact with GLY 520 (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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1252I SER* 4.0 3.3 + - - -
1254I VAL* 3.2 31.0 - - - +
507L MET* 3.3 27.5 + - - +
518L HIS* 3.1 9.8 - - - -
519L LEU* 1.3 78.4 - - - +
521L ASP* 1.3 59.6 + - - +
522L PHE 3.3 0.2 - - - -
523L ILE* 3.4 17.1 + - - +
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Residues in contact with ASP 521 (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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1252I SER* 4.7 9.6 - - - -
1254I VAL* 5.4 0.4 - - - -
1258I PRO 5.4 2.1 - - - +
1259I LEU* 3.4 16.7 - - - +
1260I GLY 4.4 4.8 + - - -
340J GLN* 5.2 7.0 + - - -
346J ARG* 4.9 11.3 + - - -
515L GLU* 3.0 18.7 - - - +
517L SER* 3.0 23.9 + - - +
518L HIS* 2.9 30.5 + - + +
520L GLY* 1.3 76.7 - - - +
522L PHE* 1.3 69.4 + - + +
523L ILE 3.7 0.7 - - - -
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Residues in contact with PHE 522 (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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1259I LEU* 4.0 6.3 - - + -
1260I GLY* 3.8 32.1 - - - -
1261I GLY* 5.7 0.4 - - - -
1264I GLN* 3.6 17.4 + - + +
511L ILE* 3.6 36.8 - - + -
514L ASP* 5.3 5.8 - - + -
515L GLU* 5.2 2.7 - - + -
517L SER* 3.2 31.4 - - - -
518L HIS 3.8 8.3 - - - -
519L LEU* 3.6 11.9 + - + +
520L GLY 3.3 0.4 - - - -
521L ASP* 1.3 87.3 - - + +
523L ILE* 1.3 60.1 + - - +
524L GLU* 3.0 18.9 - - - +
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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