Contacts of the strand formed by residues 210 - 217 (chain E) in PDB entry 1J8H
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 HIS 210 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163E TRP* 3.7 1.0 + - - +
164E VAL* 3.3 6.6 - - - +
165E ASN* 2.9 42.3 + - - +
166E GLY 5.1 4.9 + - - -
208E ARG 3.6 0.9 + - - +
209E ASN* 1.3 72.1 - - - +
211E PHE* 1.3 66.0 + - - +
212E ARG* 3.8 40.6 + - + +
241E GLU* 2.6 30.0 + - - +
242E ALA 3.9 4.3 - - - -
243E TRP* 3.4 51.4 - + + -
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Residues in contact with PHE 211 (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 VAL* 6.0 1.6 - - + -
146E LEU* 3.7 29.6 - - + -
162E TRP* 4.8 6.1 - - + -
163E TRP 3.6 3.1 - - - +
164E VAL* 3.8 23.6 - - + -
197E LEU* 3.9 6.7 - - + -
199E VAL* 4.3 16.8 - - + -
203E PHE* 3.8 34.8 - + - -
204E TRP* 3.7 32.1 - + - -
209E ASN* 3.5 27.4 - - + -
210E HIS* 1.3 75.3 - - - +
212E ARG* 1.3 59.5 + - - +
241E GLU* 3.2 6.1 - - - +
242E ALA* 2.8 45.5 + - + +
244E GLY* 3.9 5.2 - - - -
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Residues in contact with ARG 212 (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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161E SER 3.7 0.7 - - - +
162E TRP* 3.4 10.7 - - - -
163E TRP* 2.8 55.4 + - + +
210E HIS* 3.8 24.8 + - + -
211E PHE* 1.3 76.5 - - - +
213E CYS* 1.3 71.1 + - - +
214E GLN* 3.6 25.7 + - + +
239E SER* 4.2 13.2 + - - -
240E ALA 3.5 12.5 - - - +
241E GLU* 3.4 25.0 + - + +
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Residues in contact with CYS 213 (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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128E VAL* 4.0 4.2 - - + +
130E VAL* 3.8 16.6 - - + +
148E CYS* 2.0 53.6 - - + -
160E LEU* 3.9 22.2 - - - -
161E SER 3.6 2.7 - - - -
162E TRP* 4.2 11.6 - - + -
212E ARG* 1.3 72.7 - - - +
214E GLN* 1.3 63.3 + - - +
215E VAL* 4.6 1.1 - - - -
239E SER* 3.1 5.0 - - - -
240E ALA 2.9 31.0 + - - -
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Residues in contact with GLN 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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159E GLU 3.6 1.3 - - - +
160E LEU* 3.2 2.6 - - - +
161E SER* 2.7 53.2 + - - +
163E TRP* 3.8 31.7 - - + +
212E ARG* 3.6 23.7 + - + -
213E CYS* 1.3 74.4 - - - +
215E VAL* 1.3 63.5 + - - +
216E GLN* 5.3 1.1 - - + +
237E ILE* 3.5 39.8 - - + +
238E VAL 3.6 2.5 - - - -
239E SER* 3.8 7.0 + - - -
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Residues in contact with VAL 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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126E PRO* 3.9 14.8 - - + -
128E VAL* 4.0 25.1 - - + -
150E ALA* 4.0 15.9 - - + -
158E VAL* 3.8 33.0 - - + -
159E GLU 3.3 4.5 - - - +
160E LEU* 3.7 24.5 - - + -
213E CYS* 4.6 0.4 - - - -
214E GLN* 1.3 80.3 - - - +
216E GLN* 1.3 64.4 + - - +
217E PHE 3.8 1.0 + - - -
236E GLN 3.8 0.2 - - - +
237E ILE* 4.5 2.5 - - - -
238E VAL* 2.6 43.1 + - - +
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Residues in contact with GLN 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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9E ARG* 5.7 1.4 + - - -
157E HIS 3.7 0.5 - - - +
158E VAL* 3.3 5.2 - - - -
159E GLU* 2.8 41.8 + - + +
214E GLN* 4.2 1.4 - - + +
215E VAL* 1.3 73.0 - - - +
217E PHE* 1.3 64.8 + - - +
218E TYR* 3.5 36.4 + - + +
235E THR* 4.1 12.8 - - - +
236E GLN* 3.5 10.4 - - - +
237E ILE* 3.8 30.4 - - + +
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Residues in contact with PHE 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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123E VAL* 3.8 4.7 - - + -
124E PHE 3.3 23.1 - - - -
125E PRO* 3.8 17.9 - - + -
126E PRO* 3.5 31.4 - - + -
153E PHE* 4.4 1.1 - - + -
154E PHE 3.5 18.6 - - - -
155E PRO* 4.0 13.9 - - + -
157E HIS* 3.3 10.3 - - + -
158E VAL* 4.1 8.7 - - + -
215E VAL 3.8 0.8 + - - +
216E GLN* 1.3 74.5 - - - +
218E TYR* 1.3 70.3 + - - +
219E GLY* 3.5 30.7 - - - -
233E PRO 3.8 11.7 - - - -
234E VAL 3.8 11.2 - - - -
235E THR* 3.0 7.3 - - - +
236E GLN* 2.7 40.6 + - + +
238E VAL* 5.4 0.4 - - + -
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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