Contacts of the strand formed by residues 198 - 205 (chain E) in PDB entry 3STJ
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 LEU 198 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E VAL* 4.1 16.2 - - + -
70E ILE* 5.3 0.7 - - + -
78E LEU* 4.7 10.5 - - + -
127E ILE* 3.8 17.4 - - + +
128E ALA 2.8 16.6 + - - +
129E ILE* 4.3 15.0 - - + -
130E ALA* 3.0 23.9 + - - +
190E ALA* 3.7 27.6 - - + -
191E LEU 3.6 3.4 - - - +
192E LEU* 4.1 6.2 - - + +
196E GLY 4.1 0.2 + - - -
197E GLU* 1.4 68.1 - - - +
199E ILE* 1.3 59.8 + - - +
200E GLY 3.5 24.2 - - - +
201E ILE* 4.0 20.6 - - + -
221E SER* 3.3 19.6 + - - +
224E ALA* 5.5 0.7 - - + -
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Residues in contact with ILE 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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130E ALA* 3.9 8.3 - - + -
131E ASP 5.6 0.2 - - - +
132E SER* 3.7 5.1 - - - -
135E LEU* 3.9 40.8 - - + -
140E PHE 4.9 1.6 - - - +
141E ALA* 4.1 16.8 - - + -
159E VAL* 4.3 6.7 - - + -
176E ILE* 3.2 16.1 - - - +
191E LEU* 2.8 46.5 + - + +
192E LEU 3.9 7.2 - - - +
193E ASN* 3.9 29.2 - - + +
197E GLU 3.4 2.4 + - - +
198E LEU* 1.3 76.7 - - - +
200E GLY* 1.3 58.3 + - - +
221E SER* 3.0 25.0 + - - +
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Residues in contact with GLY 200 (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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176E ILE* 4.4 0.9 - - - -
191E LEU* 2.8 42.1 + - - +
198E LEU* 3.5 10.4 - - - +
199E ILE* 1.3 80.8 - - - +
201E ILE* 1.4 62.3 + - - -
218E ALA* 4.2 5.6 - - - -
219E ILE 3.1 14.1 - - - -
220E PRO* 4.3 0.2 - - - -
221E SER* 3.7 6.8 - - - -
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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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68E VAL* 3.6 31.0 - - + -
78E LEU* 4.0 23.6 - - + -
79E THR 4.5 10.1 - - - +
80E ASN* 4.0 15.0 - - - +
113E ILE* 5.2 2.2 - - + -
188E GLY* 3.9 28.5 - - - +
189E GLY 3.4 2.5 - - - +
198E LEU* 4.0 17.9 - - + -
200E GLY* 1.4 71.6 - - - -
202E ASN* 1.4 51.5 + - - +
203E THR* 2.9 23.5 + - - +
218E ALA* 3.9 1.1 - - - -
219E ILE* 2.9 37.4 + - + +
224E ALA* 4.0 23.1 - - + -
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Residues in contact with ASN 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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80E ASN* 3.1 1.6 - - - +
143E ALA* 3.9 9.5 - - - +
144E VAL 4.2 3.3 - - - +
182E ILE* 3.7 35.6 - - + +
186E ASN* 4.2 13.7 - - - +
187E SER* 3.4 3.0 - - - -
188E GLY 2.9 29.3 + - - -
189E GLY* 3.0 13.2 + - - +
190E ALA 3.2 20.9 - - - +
191E LEU* 3.3 34.6 - - - +
201E ILE* 1.4 67.0 - - - +
203E THR* 1.3 58.4 + - - +
217E PHE 3.7 5.8 - - - +
218E ALA* 3.9 7.0 - - - +
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Residues in contact with THR 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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80E ASN* 3.0 22.2 + - - +
82E HIS* 3.3 20.3 + - + -
112E ASP* 3.6 23.6 - - - +
170E GLU* 3.6 15.0 - - - +
175E PHE* 4.1 19.1 - - + -
182E ILE* 5.6 1.8 - - - +
187E SER* 4.1 6.9 + - - -
201E ILE 2.9 16.2 + - - -
202E ASN* 1.3 70.3 - - - +
204E ALA* 1.3 61.4 + - + +
217E PHE 2.8 13.6 + - - -
219E ILE* 3.1 14.1 - - + +
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Residues in contact with ALA 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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169E LEU* 3.9 37.7 - - + -
170E GLU* 5.2 1.1 - - - +
175E PHE* 5.0 1.1 - - + -
182E ILE* 4.7 2.2 - - - +
203E THR* 1.3 87.9 - - + +
205E ILE* 1.3 65.6 + - - +
217E PHE* 2.7 38.1 + - + +
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Residues in contact with ILE 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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169E LEU* 5.0 6.5 - - - +
182E ILE* 3.4 48.9 - - + +
183E ASN* 4.5 10.5 - - - -
184E ARG* 5.2 3.6 - - + +
204E ALA* 1.3 83.8 - - - +
206E LEU* 1.3 68.2 + - - +
207E ALA* 3.8 26.4 + - + -
210E GLY 4.6 7.9 - - - +
211E GLY 4.3 1.1 - - - -
212E SER* 4.1 14.8 - - - +
215E ILE 3.4 13.2 - - - +
216E GLY* 4.1 2.2 - - - -
217E PHE* 4.2 4.7 - - - -
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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