Contacts of the helix formed by residues 193 - 204 (chain B) in PDB entry 1SXP
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 GLY 193 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192B SER* 1.3 74.6 + - - +
194B GLN* 1.3 61.8 + - - -
195B ARG 3.0 2.7 - - - -
196B GLU* 2.8 23.4 + - - +
197B SER 3.2 7.6 + - - -
223B ASN* 5.7 1.6 + - - -
226B TYR* 3.9 16.2 - - - -
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Residues in contact with GLN 194 (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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192B SER 4.0 0.4 + - - -
193B GLY* 1.3 70.8 - - - -
195B ARG* 1.3 58.1 + - + +
197B SER* 3.2 9.8 + - - -
198B LYS* 2.9 38.9 + - + +
226B TYR* 5.1 3.3 + - - +
259B LYS* 4.4 33.4 - - - +
285B GLU* 5.8 1.6 + - - -
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Residues in contact with ARG 195 (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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186B TYR* 2.8 26.1 + - - -
188B GLY* 5.7 1.0 - - - -
189B SER 4.7 4.6 + - - +
191B ARG* 3.1 45.5 - - + +
192B SER 4.1 2.4 + - - +
193B GLY 3.0 0.6 - - - -
194B GLN* 1.3 80.1 - - + +
196B GLU* 1.3 58.3 + - - +
198B LYS* 3.7 2.8 + - - +
199B MET* 3.0 56.2 + - - +
256B ILE* 3.6 22.4 + - - +
257B GLY 3.4 22.3 + - - -
258B ASP* 4.0 33.2 + - - +
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Residues in contact with GLU 196 (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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190B PHE* 3.5 22.8 - - + -
191B ARG 3.1 14.7 + - - +
192B SER* 4.6 3.8 - - - -
193B GLY 2.8 15.0 + - - +
195B ARG* 1.3 73.8 - - - +
197B SER* 1.3 67.1 + - - +
199B MET* 3.2 3.0 + - - +
200B VAL* 2.9 25.6 + - + +
220B GLN 4.0 1.9 - - - +
221B PHE* 3.6 34.0 - - + +
222B LYS 4.1 1.7 + - - -
223B ASN* 3.1 47.0 + - - +
226B TYR* 3.7 15.8 - - + +
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Residues in contact with SER 197 (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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193B GLY 3.2 2.4 + - - -
194B GLN* 3.4 14.1 - - - -
196B GLU* 1.3 80.4 - - - +
198B LYS* 1.3 63.9 + - - +
200B VAL* 3.3 1.9 + - - +
201B GLU* 3.0 24.8 + - - +
226B TYR* 3.6 45.0 - - - -
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Residues in contact with LYS 198 (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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194B GLN* 2.9 29.1 + - + +
195B ARG* 3.9 6.5 - - - +
197B SER* 1.3 73.4 - - - +
199B MET* 1.3 63.8 + - - +
201B GLU* 3.3 8.6 + - + +
202B PHE* 3.2 38.4 + - + -
256B ILE* 3.5 21.8 - - + -
257B GLY* 4.3 12.8 - - - +
283B ASP* 2.7 34.1 + - - +
285B GLU* 2.7 42.6 + - - +
301B ASN 5.4 3.2 + - - -
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Residues in contact with MET 199 (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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186B TYR* 3.4 23.3 - - + -
189B SER 3.4 21.8 - - - +
190B PHE* 5.0 2.7 - - - -
191B ARG 5.0 3.4 - - - +
195B ARG* 3.0 57.4 + - - +
196B GLU 3.2 4.2 + - - +
198B LYS* 1.3 76.6 - - + +
200B VAL* 1.3 60.3 + - - +
202B PHE* 5.3 0.2 - - - -
203B LEU* 2.8 50.4 + - + +
204B PHE* 3.4 2.4 - - + -
212B PHE* 3.9 17.5 - - + -
221B PHE* 4.0 21.8 - - + -
256B ILE* 5.1 6.1 - - + -
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Residues in contact with VAL 200 (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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196B GLU* 2.9 20.3 + - + +
197B SER 3.9 3.8 - - - +
199B MET* 1.3 76.1 - - - +
201B GLU* 1.3 61.2 + - - +
204B PHE* 3.2 33.7 + - + +
221B PHE* 3.8 23.1 - - + -
226B TYR* 3.7 25.6 - - + +
227B PRO 3.7 23.3 - - - +
228B TRP* 4.0 11.2 - - + -
303B ARG* 2.8 26.9 + - - +
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Residues in contact with GLU 201 (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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197B SER* 3.0 15.1 + - - +
198B LYS* 3.3 14.4 - - + +
199B MET 3.1 0.2 - - - -
200B VAL* 1.3 79.1 - - - +
202B PHE* 1.3 71.9 + - + +
301B ASN 5.5 0.9 - - - +
302B ASN* 3.6 13.3 - - - +
303B ARG* 2.9 74.0 + - - +
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Residues in contact with PHE 202 (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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184B VAL* 5.6 0.2 - - - +
198B LYS* 3.2 36.0 + - + +
201B GLU* 1.3 84.1 - - + +
203B LEU* 1.3 66.1 + - + +
204B PHE 3.8 0.2 - - - -
206B THR* 3.2 18.7 - - - +
210B ILE* 3.7 6.9 - - - +
254B LEU* 3.2 24.9 - - + +
256B ILE* 4.3 13.2 - - + -
283B ASP* 3.7 33.9 - - + -
300B VAL* 3.7 20.6 - - + -
301B ASN 4.0 19.5 - - - -
302B ASN* 3.5 31.6 - - - -
303B ARG* 4.7 1.1 - - - +
306B LEU* 3.9 25.9 - - + +
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Residues in contact with LEU 203 (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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184B VAL* 4.8 3.1 - - + -
186B TYR* 3.5 47.1 - - + -
199B MET* 2.8 31.1 + - + +
202B PHE* 1.3 85.2 - - + +
204B PHE* 1.3 66.2 + - + +
205B ASP 4.2 0.2 + - - -
206B THR* 3.9 4.7 + - - +
210B ILE* 3.7 29.9 - - + +
212B PHE* 3.6 26.7 - - + -
231B ALA 4.9 0.3 - - - -
232B PRO* 3.6 27.6 - - + +
254B LEU* 4.3 13.7 - - + -
256B ILE* 5.4 1.8 - - + -
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Residues in contact with PHE 204 (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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199B MET* 3.4 10.8 - - + -
200B VAL* 3.2 34.0 + - + +
203B LEU* 1.3 81.4 - - + +
205B ASP* 1.3 73.5 + - - +
206B THR* 3.1 5.9 + - - +
212B PHE* 5.1 1.8 - + - -
218B GLU* 5.3 0.2 - - + -
221B PHE* 3.7 38.6 - + - -
228B TRP* 3.5 52.0 - + + -
230B LYS 3.6 4.7 - - - +
231B ALA* 3.5 29.6 - - + -
232B PRO* 3.7 15.5 - - + -
234B PHE* 4.1 9.4 - + - -
303B ARG* 3.2 20.6 + - - -
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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