Contacts of the helix formed by residues 185 - 201 (chain G) in PDB entry 5NSS
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 185 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10G GLY* 4.3 9.6 - - - +
11G GLU* 4.1 24.4 - - + +
182G ARG* 3.0 11.0 + - + +
184G SER* 1.3 76.3 - - - +
186G ILE* 1.3 63.4 + - - +
187G MET 3.1 3.7 + - - -
188G LEU* 3.3 12.0 + - + +
189G MET* 3.2 20.0 + - - +
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Residues in contact with ILE 186 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182G ARG 3.1 6.1 + - - +
183G GLU* 3.3 25.8 + - - +
185G ASP* 1.3 78.2 - - - +
187G MET* 1.3 57.4 + - - +
189G MET* 3.7 8.2 - - - +
190G ALA* 2.9 31.2 + - - +
217G LEU 4.1 7.2 - - - +
218G LEU* 3.9 19.1 - - - +
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Residues in contact with MET 187 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183G GLU 4.4 1.2 + - - -
184G SER 4.4 8.2 + - - +
185G ASP* 3.1 1.0 - - - +
186G ILE* 1.3 78.4 - - - +
188G LEU* 1.3 58.0 + - - +
190G ALA* 4.0 3.6 - - - +
191G GLU* 2.9 32.2 + - - +
214G ARG* 5.8 5.2 - - + +
217G LEU* 6.2 0.9 - - - -
218G LEU* 4.7 13.3 - - + +
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Residues in contact with LEU 188 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185G ASP* 3.3 13.4 + - + +
187G MET* 1.3 78.6 - - - +
189G MET* 1.3 58.2 + - - +
191G GLU* 4.6 4.5 - - - -
192G TYR* 2.9 33.6 + - - +
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Residues in contact with MET 189 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185G ASP 3.2 14.8 + - - +
186G ILE* 3.9 8.7 - - - +
187G MET 3.3 0.4 - - - -
188G LEU* 1.3 78.3 - - - +
190G ALA* 1.3 57.9 + - - +
192G TYR* 4.3 3.0 - - - +
193G PHE* 2.9 31.7 + - - +
229G LEU* 5.6 10.8 - - + -
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Residues in contact with ALA 190 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186G ILE 2.9 17.7 + - - +
187G MET* 4.0 3.8 - - - +
189G MET* 1.3 75.7 - - - +
191G GLU* 1.3 59.8 + - - +
193G PHE* 3.8 3.8 - - - +
194G ALA* 2.9 30.8 + - - +
217G LEU* 4.2 24.5 - - + +
233G VAL* 4.4 14.3 - - + +
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Residues in contact with GLU 191 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187G MET 2.9 18.6 + - - +
188G LEU* 4.3 4.0 - - - +
190G ALA* 1.3 75.0 - - - +
192G TYR* 1.3 60.4 + - - +
194G ALA* 3.4 4.6 + - - +
195G ILE* 2.9 31.6 + - - +
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Residues in contact with TYR 192 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188G LEU 2.9 22.2 + - - +
189G MET* 4.3 2.5 - - - +
191G GLU* 1.3 77.8 - - - +
193G PHE* 1.3 57.4 + - - +
195G ILE* 4.1 4.8 - - - +
196G GLN* 2.9 31.0 + - - +
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Residues in contact with PHE 193 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189G MET 2.9 22.2 + - - +
190G ALA 3.9 0.4 - - - +
192G TYR* 1.3 77.2 - - - +
194G ALA* 1.3 58.2 + - - +
196G GLN* 4.0 4.5 - - - +
197G MET* 2.9 29.5 + - - +
229G LEU 5.8 0.2 - - - -
230G LYS* 4.9 15.0 - - + +
233G VAL* 3.8 23.8 - - + -
234G GLU* 5.1 5.1 - - + +
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Residues in contact with ALA 194 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190G ALA 2.9 18.8 + - - +
191G GLU* 3.9 5.6 - - - +
193G PHE* 1.3 75.7 - - - +
195G ILE* 1.3 59.1 + - - +
197G MET* 3.8 1.4 - - - +
198G CYS* 2.9 29.8 + - - +
206G PHE* 4.6 5.2 - - + +
207G PRO* 5.7 1.9 - - + -
208G GLY* 5.4 13.2 - - - +
233G VAL* 4.8 4.2 - - + +
237G VAL* 4.3 23.7 - - + +
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Residues in contact with ILE 195 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191G GLU 2.9 17.9 + - - +
192G TYR* 4.1 4.7 - - - +
194G ALA* 1.3 76.5 - - - +
196G GLN* 1.3 57.9 + - - +
198G CYS* 3.8 1.6 - - - +
199G ARG* 2.9 29.1 + - - +
206G PHE* 4.3 19.9 - - + +
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Residues in contact with GLN 196 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192G TYR 2.9 20.8 + - - +
193G PHE* 4.0 4.9 - - - +
195G ILE* 1.3 75.6 - - - +
197G MET* 1.3 60.0 + - - +
199G ARG* 3.7 6.4 - - - +
200G GLU* 2.9 30.1 + - - +
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Residues in contact with MET 197 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193G PHE 2.9 19.0 + - - +
194G ALA 3.8 4.7 - - - +
195G ILE 3.3 0.2 - - - -
196G GLN* 1.3 77.7 - - - +
198G CYS* 1.3 60.9 + - - +
200G GLU* 3.6 5.7 + - - +
201G ILE* 3.2 23.4 + - - +
234G GLU* 4.4 17.5 - - + -
237G VAL* 4.1 20.0 - - + -
238G TYR* 4.6 13.8 - - + +
29J ASP* 5.7 4.5 - - + +
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Residues in contact with CYS 198 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194G ALA 2.9 18.1 + - - +
195G ILE 3.9 3.6 - - - +
196G GLN 3.3 0.2 - - - -
197G MET* 1.3 75.5 - - - +
199G ARG* 1.3 60.8 + - - +
201G ILE* 3.5 6.2 + - - -
203G LEU* 3.1 44.3 + - + +
205G LEU 4.3 1.6 - - - +
206G PHE* 3.9 27.8 - - + +
207G PRO 4.9 2.2 - - - -
237G VAL* 5.6 1.3 - - + +
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Residues in contact with ARG 199 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195G ILE 2.9 19.0 + - - +
196G GLN* 3.7 7.2 - - - +
197G MET 3.3 0.2 - - - -
198G CYS* 1.3 76.4 - - - +
200G GLU* 1.3 62.4 + - - +
202G LYS* 3.3 12.9 + - - +
203G LEU 5.1 2.7 - - - +
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Residues in contact with GLU 200 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196G GLN 2.9 17.0 + - - +
197G MET* 3.6 6.0 + - - +
198G CYS 3.4 0.2 - - - -
199G ARG* 1.3 76.5 - - - +
201G ILE* 1.3 59.1 + - - +
202G LYS* 3.3 2.1 + - - +
29J ASP* 5.1 16.0 - - + +
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Residues in contact with ILE 201 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197G MET 3.2 16.8 + - - +
198G CYS* 4.0 7.2 - - - +
199G ARG 3.2 1.0 - - - -
200G GLU* 1.3 75.4 - - - +
202G LYS* 1.3 70.2 + - - +
203G LEU* 3.3 6.0 + - + +
238G TYR* 6.0 5.4 - - + -
27J PRO* 4.3 25.3 - - + +
28J LEU* 5.9 0.9 - - - -
29J ASP* 5.9 4.0 - - + +
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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