Contacts of the strand formed by residues 213 - 221 (chain E) in PDB entry 4DOH
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 213 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188E THR* 2.9 53.2 + - + +
189E LYS* 5.8 0.6 - - - +
212E THR* 1.3 79.0 - - - +
214E TYR* 1.3 62.6 + - - +
215E CYS* 4.9 0.2 - - - -
236E CYS* 4.2 18.6 - - + -
237E ALA* 3.6 13.2 - - - +
238E ARG* 3.6 54.0 - - + +
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Residues in contact with TYR 214 (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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148D ASP* 4.1 8.2 + - - -
151D HIS* 5.5 1.4 - - - -
144E LEU* 4.8 0.9 - - - +
151E ILE* 3.6 28.6 - - + +
185E VAL* 3.9 20.9 - - + -
186E LEU 3.3 13.9 - - - -
187E ASN* 3.6 35.8 + - + -
194E TRP* 5.3 3.8 - + - -
205E LEU* 6.1 0.9 - - + -
208E LEU* 3.4 37.0 - - + +
209E GLU* 3.1 24.7 + - - +
212E THR* 3.4 35.2 + - + -
213E LEU* 1.3 74.0 - - - +
215E CYS* 1.3 63.3 + - - +
216E VAL* 4.8 5.3 - - + +
235E GLN 4.1 0.5 - - - +
236E CYS* 3.4 1.6 - - - -
237E ALA* 3.0 32.1 + - - +
239E THR* 4.0 4.0 - - + -
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Residues in contact with CYS 215 (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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184E SER 3.5 1.6 - - - +
185E VAL* 3.4 4.3 - - - -
186E LEU* 2.7 55.0 + - + +
188E THR* 3.8 21.3 - - - -
213E LEU* 4.9 2.2 - - - -
214E TYR* 1.3 73.2 - - - +
216E VAL* 1.3 63.9 + - - +
217E HIS* 4.3 2.8 - - + -
235E GLN 3.6 2.9 - - - +
236E CYS* 2.0 42.4 - - - -
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Residues in contact with VAL 216 (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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142E VAL* 4.8 3.2 - - + +
144E LEU* 4.2 30.5 - - + -
151E ILE* 5.5 2.9 - - + -
153E VAL* 4.5 7.2 - - + -
183E VAL* 4.2 15.7 - - + -
184E SER 3.4 3.4 - - - +
185E VAL* 4.2 21.3 - - + -
205E LEU* 4.5 12.3 - - + -
214E TYR* 4.8 5.4 - - + +
215E CYS* 1.3 82.6 - - - +
217E HIS* 1.3 63.4 + - - +
218E VAL* 4.0 19.5 - - + -
233E GLU 3.4 2.4 - - - +
235E GLN* 2.8 40.8 + - - +
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Residues in contact with HIS 217 (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 ASN 3.7 0.5 + - - +
184E SER* 3.0 46.0 + - - -
215E CYS* 5.7 3.1 - - + -
216E VAL* 1.3 74.6 - - - +
218E VAL* 1.3 67.2 + - - +
219E GLU* 4.0 7.9 + - - +
232E SER* 3.0 25.8 + - - -
233E GLU 3.0 21.3 - - - +
234E LYS* 3.9 12.3 - - + -
301E NAG 3.5 23.6 + - - -
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Residues in contact with VAL 218 (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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139E PRO* 3.7 2.6 - - - +
140E PRO* 3.5 25.5 - - + +
142E VAL* 3.9 26.7 - - + -
153E VAL* 5.2 0.7 - - + -
155E LEU* 3.7 24.0 - - + -
181E TYR* 4.0 10.5 - - + -
182E ASN 3.2 12.3 - - - +
183E VAL* 3.9 18.6 - - + -
216E VAL* 4.0 16.8 - - + -
217E HIS* 1.3 85.6 - - - +
219E GLU* 1.3 58.5 + - - +
232E SER* 3.5 18.3 - - - -
233E GLU* 3.6 7.8 + - - +
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Residues in contact with GLU 219 (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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139E PRO* 5.2 0.9 - - - -
140E PRO* 4.7 0.9 - - - -
181E TYR* 3.5 2.9 - - - -
182E ASN* 2.8 43.1 + - + +
217E HIS* 4.0 9.7 - - - +
218E VAL* 1.3 73.8 - - - +
220E SER* 1.3 65.7 + - - +
221E PHE* 5.7 1.8 - - + -
229E ALA* 5.7 5.0 - - - +
230E GLN 4.3 12.7 - - - +
232E SER* 3.5 25.6 + - - +
301E NAG 3.2 49.6 + - - +
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Residues in contact with SER 220 (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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137E ILE* 3.9 24.4 + - - +
138E GLY 3.2 27.1 + - - -
139E PRO* 4.4 2.6 - - - +
140E PRO* 3.8 4.5 - - - +
158E PRO* 3.6 6.6 - - - +
179E LEU* 4.2 3.7 - - - +
180E LYS 3.9 3.4 - - - -
181E TYR* 3.1 29.8 - - - -
218E VAL 4.1 1.8 + - - -
219E GLU* 1.3 77.2 - - - +
221E PHE* 1.3 63.5 + - - +
230E GLN* 5.4 6.0 + - - +
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Residues in contact with PHE 221 (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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184D ARG* 6.6 0.2 - - + -
137E ILE* 5.8 1.3 - - - -
179E LEU* 3.7 2.5 - - - +
180E LYS* 2.7 87.4 + - + +
182E ASN* 5.1 4.9 - - + +
197E CYS* 3.7 18.4 - - - -
219E GLU* 3.8 4.2 + - + +
220E SER* 1.3 78.6 - - - +
222E VAL* 1.3 70.4 + - - +
223E PRO* 3.7 26.1 - - + +
301E NAG 3.9 32.8 - - + +
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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