Contacts of the strand formed by residues 208 - 215 (chain E) in PDB entry 5U17
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 208 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A LEU* 6.0 2.0 - - + -
161E TRP 3.5 1.9 + - - +
162E VAL* 3.3 8.0 - - - +
163E ASN* 2.7 47.6 + - - +
164E GLY 4.9 4.4 + - - -
207E ASN* 1.3 75.1 - - - +
209E PHE* 1.3 74.3 + - - +
210E ARG* 3.8 31.3 + - + +
239E GLU* 2.9 27.0 + - - +
240E ALA 3.8 6.1 - - - -
241E TRP* 3.4 50.0 - + + -
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Residues in contact with PHE 209 (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* 5.9 1.1 - - + -
144E LEU* 3.7 25.6 - - + -
160E TRP* 4.9 5.8 - - + -
161E TRP 3.5 3.1 - - - -
162E VAL* 3.9 11.7 - - + -
195E LEU* 3.8 20.6 - - + -
197E VAL* 4.3 13.5 - - + -
201E PHE* 3.8 37.5 - + - -
202E TRP* 3.6 40.2 - + - -
207E ASN* 3.8 24.5 - - + -
208E HIS* 1.3 77.0 - - - +
210E ARG* 1.3 60.4 + - - +
239E GLU* 3.2 6.5 - - - +
240E ALA 2.8 43.7 + - - +
242E GLY* 3.9 3.4 - - - -
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Residues in contact with ARG 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 3.6 32.2 - - - +
103A ASP* 3.2 32.3 + - - -
105A SER* 4.4 1.2 + - - -
107A THR* 5.8 1.3 - - - -
159E SER 3.8 0.3 - - - +
160E TRP* 3.3 10.0 - - - -
161E TRP* 2.8 73.0 + - + +
164E GLY* 4.6 11.3 - - - -
208E HIS* 3.8 21.0 - - + -
209E PHE* 1.3 76.8 - - - +
211E CYS* 1.3 71.0 + - - +
212E GLN* 3.6 16.5 + - + +
237E SER* 3.9 15.5 + - - +
238E ALA 3.4 14.4 - - - +
239E GLU* 4.2 4.9 - - + +
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Residues in contact with CYS 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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126E VAL* 4.0 4.6 - - - +
128E VAL* 3.5 14.8 - - + +
146E CYS* 2.0 54.3 - - + -
158E LEU* 3.7 24.7 - - - -
159E SER 3.5 2.9 - - - -
160E TRP* 4.0 10.5 - - + -
210E ARG* 1.3 73.5 - - - +
212E GLN* 1.3 61.1 + - - +
213E VAL* 4.6 1.1 - - - -
237E SER* 3.2 4.5 - - - -
238E ALA 2.8 31.8 + - - +
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Residues in contact with GLN 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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103A ASP* 3.5 20.9 + - - +
105A SER* 4.4 3.1 + - - -
157E GLU 3.6 1.8 + - - +
158E LEU* 3.2 3.1 - - - +
159E SER* 2.8 55.4 + - - +
161E TRP* 3.8 20.8 + - + +
210E ARG* 3.6 16.0 + - - +
211E CYS* 1.3 74.9 - - - +
213E VAL* 1.3 65.6 + - - +
214E GLN* 5.1 7.3 + - - +
235E ILE* 3.6 41.7 - - + +
236E VAL 3.8 2.9 - - - -
237E SER* 3.9 7.2 - - - -
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Residues in contact with VAL 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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124E PRO* 3.9 17.9 - - + -
126E VAL* 3.7 28.7 - - + -
148E ALA* 3.9 17.0 - - + -
156E VAL* 3.7 22.4 - - + -
157E GLU 3.3 6.7 - - - +
158E LEU* 4.1 19.5 - - + +
191E LEU* 6.1 0.2 - - + -
211E CYS* 4.6 0.2 - - - -
212E GLN* 1.3 80.6 - - - +
214E GLN* 1.3 72.2 + - - +
215E PHE* 3.7 1.6 + - - +
234E GLN 3.9 0.2 - - - +
235E ILE* 3.5 1.4 - - - -
236E VAL* 2.9 40.0 + - - +
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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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155E HIS 3.8 0.2 - - - +
156E VAL* 3.1 7.6 - - - +
157E GLU* 2.7 47.3 + - + +
212E GLN* 4.1 8.0 - - - +
213E VAL* 1.3 72.1 - - - +
215E PHE* 1.3 69.4 + - - +
216E TYR* 3.4 35.4 + - + +
233E THR* 3.7 15.2 - - - +
234E GLN* 3.3 29.0 + - - +
235E ILE* 3.3 25.9 - - + +
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Residues in contact with PHE 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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121E VAL* 3.9 9.4 - - + -
122E PHE 3.3 24.0 - - - -
123E PRO* 3.8 17.7 - - + -
124E PRO* 3.6 30.1 - - + -
151E PHE* 4.6 0.7 - - + -
152E TYR 3.7 17.0 - - - -
153E PRO* 4.0 14.8 - - + -
155E HIS* 3.6 8.7 - - + -
156E VAL* 3.9 8.5 - - + -
213E VAL 3.7 0.4 + - - +
214E GLN* 1.3 79.1 + - - +
216E TYR* 1.3 69.9 + - - +
217E GLY* 3.5 22.0 - - - -
231E PRO 3.7 12.8 - - - -
232E VAL 3.8 12.6 - - - -
233E THR* 3.3 3.5 - - - +
234E GLN* 2.8 39.7 + - + +
236E VAL* 5.6 0.2 - - + -
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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