Contacts of the helix formed by residues 193 - 206 (chain J) 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 ASP 193 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191J SER 3.3 6.9 + - - +
192J MET* 1.3 73.6 - - - +
194J LEU* 1.3 64.7 + - - +
195J GLU* 3.1 23.1 - - - +
196J GLN* 3.4 39.1 + - + +
197J GLU* 3.3 23.2 + - - +
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Residues in contact with LEU 194 (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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127J LEU* 4.3 8.5 - - + -
192J MET* 3.6 25.1 + - + +
193J ASP* 1.3 77.2 + - - +
195J GLU* 1.3 74.4 + - + +
197J GLU* 3.4 4.8 + - - +
198J CYS* 2.8 32.5 + - - -
224J LEU* 3.7 29.3 - - + +
227J PHE* 4.1 35.4 - - + +
228J VAL* 4.7 1.8 - - + +
232J ASN 5.0 2.0 - - - +
234J PRO* 3.7 37.0 - - + -
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Residues in contact with GLU 195 (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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193J ASP* 3.1 16.2 - - - +
194J LEU* 1.3 88.2 + - - +
196J GLN* 1.3 60.3 + - - +
198J CYS* 3.2 9.5 + - + +
199J GLU* 2.9 40.4 + - + +
228J VAL* 3.3 42.6 - - + +
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Residues in contact with GLN 196 (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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193J ASP* 3.4 34.8 - - + +
195J GLU* 1.3 78.1 - - - +
197J GLU* 1.3 58.3 + - - +
199J GLU* 3.3 5.7 + - - -
200J GLN* 3.0 61.5 + - - +
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Residues in contact with GLU 197 (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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192J MET* 4.5 9.0 - - + +
193J ASP 3.3 18.9 + - - +
194J LEU* 3.7 4.9 - - - +
195J GLU 3.3 0.4 - - - -
196J GLN* 1.3 77.1 - - - +
198J CYS* 1.3 61.0 + - - +
200J GLN* 4.5 10.5 - - - +
201J LEU* 2.8 50.9 + - + +
220J ARG* 3.8 25.2 + - - +
224J LEU* 4.6 5.4 - - + -
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Residues in contact with CYS 198 (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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194J LEU 2.8 23.2 + - - +
195J GLU* 3.2 13.4 + - + +
197J GLU* 1.3 76.6 - - - +
199J GLU* 1.3 57.4 + - + +
201J LEU* 3.4 1.0 + - - +
202J ARG* 2.9 43.9 + - - +
221J ILE* 3.8 16.5 - - + +
224J LEU* 3.6 39.3 - - - -
225J GLU* 4.5 4.3 - - - -
228J VAL* 4.9 6.7 - - - -
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Residues in contact with GLU 199 (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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195J GLU* 2.9 26.2 + - + +
196J GLN* 3.3 3.3 + - - +
198J CYS* 1.3 78.8 - - + +
200J GLN* 1.3 70.4 + - - +
202J ARG* 3.5 6.2 + - - +
203J GLU* 2.9 32.3 + - - +
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Residues in contact with GLN 200 (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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196J GLN* 3.0 61.9 + - - +
197J GLU* 4.2 13.6 - - - +
199J GLU* 1.3 87.9 + - - +
201J LEU* 1.3 63.1 + - + +
203J GLU* 3.4 21.9 + - - +
204J GLU* 2.9 28.2 + - - +
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Residues in contact with LEU 201 (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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197J GLU* 2.8 49.1 + - + +
198J CYS 3.8 0.2 - - - +
200J GLN* 1.3 79.3 - - - +
202J ARG* 1.3 56.7 + - - +
204J GLU* 3.4 6.6 + - + +
205J LEU* 2.8 32.8 + - - +
217J LEU* 3.7 47.5 - - + +
220J ARG* 4.8 17.9 - - + +
221J ILE* 3.7 21.5 - - + -
224J LEU* 5.1 0.2 - - + -
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Residues in contact with ARG 202 (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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198J CYS* 2.9 27.6 + - - +
199J GLU* 3.9 5.8 - - - +
201J LEU* 1.3 72.8 - - - +
203J GLU* 1.3 59.9 + - - +
205J LEU* 3.2 18.7 + - + +
206J ASN* 2.9 41.7 + - - +
221J ILE* 3.4 41.0 - - - +
225J GLU* 3.8 17.0 + - - +
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Residues in contact with GLU 203 (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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199J GLU* 2.9 17.8 + - + +
200J GLN* 3.4 35.1 + - - +
201J LEU 3.2 0.2 - - - -
202J ARG* 1.3 77.4 - - - +
204J GLU* 1.3 60.6 + - - +
206J ASN* 3.2 27.2 + - - +
207J GLU* 3.8 9.8 - - - +
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Residues in contact with GLU 204 (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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200J GLN 2.9 15.4 + - - +
201J LEU* 4.1 7.3 - - + +
203J GLU* 1.3 75.9 - - - +
205J LEU* 1.3 52.2 + - - +
206J ASN 3.1 0.7 - - - -
207J GLU* 3.1 35.9 + - - +
208J THR* 2.3 51.5 + - + +
213J LYS* 3.7 22.0 + - - -
217J LEU* 3.9 10.1 - - + +
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Residues in contact with LEU 205 (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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201J LEU* 2.8 21.7 + - + +
202J ARG* 3.2 27.3 + - + +
204J GLU* 1.3 74.4 - - - +
206J ASN* 1.3 58.4 + - - +
207J GLU 3.1 3.1 - - - -
208J THR* 3.5 1.8 - - - +
214J ARG* 2.8 75.5 + - + +
217J LEU* 3.7 31.6 - - + +
218J THR* 3.8 24.7 - - + +
221J ILE* 4.9 9.9 - - + -
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Residues in contact with ASN 206 (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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202J ARG* 2.9 30.7 + - - +
203J GLU* 3.3 19.3 - - - +
204J GLU 3.1 1.0 - - - -
205J LEU* 1.3 79.8 - - - +
207J GLU* 1.3 57.4 + - + +
208J THR 3.9 0.4 - - - -
214J ARG* 5.0 1.6 - - - +
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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