Contacts of the helix formed by residues 196 - 207 (chain N) in PDB entry 5DST
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 MET 196 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80N TYR* 6.1 0.4 - - - -
118N VAL* 3.4 38.4 - - + +
119N GLY* 4.0 1.1 - - - +
184N SER* 3.8 11.7 - - - +
185N GLU 4.1 5.4 - - - +
186N TRP* 3.4 32.3 + - + +
192N PHE 4.6 0.4 + - - -
193N TYR 4.5 1.4 + - - -
194N GLU* 3.0 15.2 + - + +
195N SER* 1.3 75.6 - - - +
197N LEU* 1.3 66.2 + - - +
199N THR* 2.9 19.8 + - + +
200N VAL* 3.2 7.4 + - - +
368N ARG* 6.1 2.0 - - - +
401N SAH 3.6 58.6 - - + +
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Residues in contact with LEU 197 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186N TRP* 3.8 47.4 - - + -
192N PHE* 3.9 20.2 - - + -
195N SER* 3.1 2.5 + - - -
196N MET* 1.3 78.4 - - - +
198N ASN* 1.3 52.0 + - - +
200N VAL* 2.9 19.7 + - + +
201N ILE* 2.8 47.7 + - + +
278N VAL* 4.2 13.2 - - + -
280N ILE* 4.7 12.3 - - + -
283N VAL* 4.6 4.0 - - + -
288N LEU* 3.7 39.0 - - + -
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Residues in contact with ASN 198 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170N GLU* 5.1 1.1 - - - +
195N SER* 3.4 28.9 + - - +
196N MET 3.1 0.2 - - - -
197N LEU* 1.3 74.2 - - - +
199N THR* 1.3 58.4 + - - +
201N ILE* 3.4 11.4 - - - +
202N PHE* 3.0 26.5 + - - +
285N THR* 4.1 23.9 - - + +
288N LEU* 3.3 23.6 - - - +
362N PRO* 5.1 6.7 - - - +
367N VAL* 4.5 12.9 - - - +
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Residues in contact with THR 199 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118N VAL* 3.9 10.1 - - + -
169N VAL* 3.5 27.5 - - + +
170N GLU* 3.3 19.4 + - - +
195N SER 5.1 0.5 + - - -
196N MET* 2.9 20.6 + - + -
198N ASN* 1.3 75.2 - - - +
200N VAL* 1.3 67.4 + - - +
202N PHE* 3.3 4.3 + - - +
203N ALA* 3.0 22.0 + - - +
368N ARG* 5.3 4.3 + - - -
401N SAH 3.5 33.5 + - + +
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Residues in contact with VAL 200 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118N VAL* 4.1 10.1 - - + -
182N ILE* 4.8 6.5 - - + -
184N SER* 3.5 27.4 - - - +
186N TRP* 3.7 28.9 - - + -
196N MET* 3.2 4.4 + - + +
197N LEU* 2.9 16.2 + - + +
199N THR* 1.3 77.5 - - - +
201N ILE* 1.3 53.3 + - - +
203N ALA* 3.0 9.0 + - - +
204N ARG* 2.7 33.0 + - - +
214N MET* 3.5 27.8 - - + +
280N ILE* 4.4 11.9 - - + -
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Residues in contact with ILE 201 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197N LEU* 2.8 38.0 + - + +
198N ASN* 3.4 10.3 - - - +
200N VAL* 1.3 71.8 - - - +
202N PHE* 1.3 65.1 + - - +
204N ARG* 3.0 29.9 + - - +
205N ASP* 2.9 32.6 + - - +
283N VAL* 3.2 44.9 - - + +
284N LYS* 4.0 11.9 - - - +
285N THR* 4.0 20.0 - - + +
288N LEU* 4.7 2.9 - - + -
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Residues in contact with PHE 202 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169N VAL* 3.9 17.7 - - + -
170N GLU* 3.7 46.0 - - + +
198N ASN 3.0 11.1 + - - +
199N THR* 3.4 11.7 - - - +
201N ILE* 1.3 80.3 - - - +
203N ALA* 1.3 62.7 + - - +
205N ASP* 3.3 6.9 + - - +
206N LYS* 2.9 61.5 + - + +
207N TRP* 4.6 0.9 - + - -
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Residues in contact with ALA 203 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116N LEU* 4.2 2.9 - - + -
118N VAL* 3.8 28.0 - - + -
169N VAL* 4.2 5.4 - - + -
182N ILE* 3.9 4.7 - - + +
199N THR 3.0 14.1 + - - +
200N VAL 3.4 7.2 - - - +
202N PHE* 1.3 80.0 - - - +
204N ARG* 1.3 56.8 + - - +
207N TRP* 2.8 59.2 + - + +
208N LEU 3.8 0.5 + - - -
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Residues in contact with ARG 204 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182N ILE* 3.6 11.8 - - - +
200N VAL 2.7 15.8 + - - +
201N ILE* 3.4 27.9 - - - +
203N ALA* 1.3 72.0 - - - +
205N ASP* 1.3 88.6 + - - +
208N LEU* 2.9 49.9 + - + +
214N MET* 3.8 16.6 - - + -
280N ILE 2.9 27.3 + - - -
281N TYR* 3.1 28.9 + - - +
282N THR* 4.5 2.3 + - - -
283N VAL* 2.9 34.5 + - - +
284N LYS* 4.9 5.1 - - - +
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Residues in contact with ASP 205 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178N LYS* 4.4 6.1 + - - -
201N ILE* 2.9 29.7 + - - +
202N PHE* 3.5 6.5 + - - +
204N ARG* 1.3 105.2 + - - +
206N LYS* 1.3 65.9 + - - +
208N LEU 4.5 2.9 + - - +
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Residues in contact with LYS 206 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169N VAL 5.5 0.2 + - - -
170N GLU 5.5 3.4 + - - -
171N GLU 5.7 0.8 + - - -
172N VAL 4.2 4.2 + - - -
173N GLU* 3.1 33.5 + - - -
177N GLU 4.1 2.6 - - - +
178N LYS* 3.1 26.7 + - - +
202N PHE* 2.9 44.4 + - + +
203N ALA 4.0 1.3 - - - +
205N ASP* 1.3 75.4 - - - +
207N TRP* 1.3 95.6 + - + +
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Residues in contact with TRP 207 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116N LEU* 3.7 17.9 - - + -
140N ILE* 4.1 16.6 - - + -
169N VAL* 3.6 41.3 - - + -
172N VAL 3.6 20.0 - - - -
173N GLU* 4.6 2.4 + - - -
174N LEU* 3.4 41.2 - - + +
176N VAL 4.3 7.0 + - - -
177N GLU 3.6 20.0 - - - -
178N LYS* 3.2 5.5 - - - -
179N VAL* 2.7 43.9 + - + +
182N ILE* 5.5 0.4 - - + -
202N PHE* 4.6 1.8 - + - -
203N ALA* 2.8 31.2 + - + +
206N LYS* 1.3 107.6 - - + +
208N LEU* 1.3 63.9 + - - +
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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