Contacts of the helix formed by residues 196 - 207 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118E VAL* 3.4 38.4 - - + +
119E GLY* 4.0 1.6 - - - +
184E SER* 3.8 12.1 - - - +
185E GLU 4.1 5.6 - - - +
186E TRP* 3.5 31.2 + - + +
192E PHE 4.5 0.6 + - - -
193E TYR 4.3 2.4 + - - -
194E GLU* 3.0 15.5 + - + +
195E SER* 1.3 72.9 - - - +
197E LEU* 1.3 66.2 + - - +
198E ASN 3.1 0.4 - - - -
199E THR* 2.9 19.5 + - + +
200E VAL* 3.2 7.7 + - + +
368E ARG* 6.1 1.8 - - - +
401E SAH 3.4 59.0 - - + +
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Residues in contact with LEU 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E TRP* 3.8 47.2 - - + -
192E PHE* 4.0 18.2 - - + -
195E SER 3.1 1.5 + - - +
196E MET* 1.3 78.5 - - - +
198E ASN* 1.3 52.0 + - - +
200E VAL* 2.9 19.3 + - + +
201E ILE* 2.7 49.7 + - + +
278E VAL* 4.2 14.1 - - + -
280E ILE* 4.7 12.3 - - + -
283E VAL* 4.6 4.9 - - + -
288E LEU* 3.7 38.8 - - + -
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Residues in contact with ASN 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E GLU* 5.1 1.3 - - - +
195E SER* 3.4 29.4 + - - +
196E MET 3.1 0.2 - - - -
197E LEU* 1.3 74.2 - - - +
199E THR* 1.3 63.5 + - - +
201E ILE* 3.3 10.1 + - - +
202E PHE* 3.0 24.0 + - - +
285E THR* 4.1 23.9 - - + +
288E LEU* 3.2 25.8 - - - +
362E PRO* 5.1 6.7 - - - +
367E VAL* 4.4 14.1 - - - +
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Residues in contact with THR 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E VAL* 3.9 10.3 - - + -
169E VAL* 3.5 37.4 - - + +
170E GLU* 3.1 20.8 + - - +
195E SER 4.4 0.4 + - - -
196E MET* 2.9 19.5 + - + +
198E ASN* 1.3 79.4 - - - +
200E VAL* 1.3 62.4 + - - +
202E PHE* 3.2 4.4 + - - +
203E ALA* 3.0 21.3 + - - +
368E ARG* 5.3 4.0 + - - -
401E SAH 3.3 23.3 + - + +
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Residues in contact with VAL 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E VAL* 4.0 14.4 - - + -
182E ILE* 4.8 7.4 - - + -
184E SER* 3.6 26.9 - - - +
186E TRP* 3.7 28.7 - - + -
196E MET* 3.2 4.0 + - + +
197E LEU* 2.9 15.7 + - + +
199E THR* 1.3 76.7 - - - +
201E ILE* 1.3 57.4 + - - +
203E ALA* 3.2 4.6 + - - +
204E ARG* 2.9 27.2 + - - +
214E MET* 3.5 26.8 - - + +
280E ILE* 4.4 12.3 - - + -
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Residues in contact with ILE 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197E LEU* 2.7 37.6 + - + +
198E ASN* 3.3 10.3 - - - +
200E VAL* 1.3 73.3 - - + +
202E PHE* 1.3 63.2 + - - +
204E ARG* 3.3 26.8 + - - +
205E ASP* 3.1 33.2 + - - +
280E ILE 5.6 0.2 - - - +
283E VAL* 3.2 45.3 - - + +
284E LYS* 4.0 11.9 - - - +
285E THR* 4.0 20.9 - - + +
288E LEU* 4.8 2.5 - - + -
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Residues in contact with PHE 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169E VAL* 3.9 17.5 - - + -
170E GLU* 3.7 46.2 - - + +
198E ASN 3.0 13.1 + - - +
199E THR* 3.4 11.4 - - - +
201E ILE* 1.3 78.8 - - - +
203E ALA* 1.3 63.6 - - - +
205E ASP* 3.5 6.5 + - - +
206E LYS* 3.0 61.2 + - + +
207E TRP* 4.5 1.3 - + - -
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Residues in contact with ALA 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E LEU* 4.2 3.1 - - + -
118E VAL* 3.9 27.1 - - + -
169E VAL* 4.1 4.9 - - + -
182E ILE* 3.9 5.5 - - + +
199E THR 3.0 13.2 + - - +
200E VAL 3.2 7.4 + - - +
202E PHE* 1.3 75.3 - - - +
204E ARG* 1.3 59.9 + - - +
207E TRP* 2.8 60.7 + - + +
208E LEU 3.7 0.7 + - - -
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Residues in contact with ARG 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182E ILE* 3.7 12.5 - - - +
200E VAL 2.9 13.2 + - - +
201E ILE* 3.3 28.3 + - - +
203E ALA* 1.3 73.6 - - - +
205E ASP* 1.3 85.1 + - - +
208E LEU* 2.8 55.1 + - + +
214E MET* 3.9 15.7 - - + -
280E ILE 2.8 37.4 + - - -
281E TYR* 3.1 27.3 + - - +
282E THR* 4.5 2.5 + - - -
283E VAL* 2.9 33.5 + - - +
284E LYS* 4.8 5.3 - - - +
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Residues in contact with ASP 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178E LYS* 4.3 6.2 + - - -
201E ILE* 3.1 23.8 + - - +
202E PHE* 3.7 6.0 - - - +
204E ARG* 1.3 109.4 + - - +
206E LYS* 1.3 63.1 + - - +
208E LEU 4.8 1.9 + - - +
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Residues in contact with LYS 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E GLU 5.4 3.4 + - - -
171E GLU* 5.9 0.6 - - - +
172E VAL 4.2 6.7 + - - -
173E GLU* 2.9 34.7 + - - -
177E GLU 4.1 2.8 - - - +
178E LYS* 3.0 26.6 + - - +
202E PHE* 3.0 49.5 + - + +
203E ALA 4.0 2.0 - - - +
205E ASP* 1.3 77.0 - - - +
207E TRP* 1.3 90.4 + - + +
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Residues in contact with TRP 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E LEU* 3.8 15.3 - - + -
140E ILE* 4.1 16.2 - - + -
169E VAL* 3.5 41.1 - - + -
172E VAL 3.5 21.5 - - - -
173E GLU* 4.6 1.6 + - - -
174E LEU* 3.4 41.9 - - + +
176E VAL* 4.5 5.4 + - + -
177E GLU* 3.6 21.3 - - - -
178E LYS* 3.1 7.3 - - - -
179E VAL* 2.8 37.6 + - + -
182E ILE* 5.4 0.2 - - + -
202E PHE* 4.5 1.3 - + - -
203E ALA* 2.8 36.8 + - + +
206E LYS* 1.3 108.7 - - + +
208E LEU* 1.3 63.4 + - - +
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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