Contacts of the strand formed by residues 166 - 173 (chain E) in PDB entry 4QOZ
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 ILE 166 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157E VAL* 3.8 29.8 - - + -
158E LEU 3.4 10.3 - - - +
159E LEU* 4.5 4.9 - - + +
165E GLU* 1.3 74.6 - - - +
167E GLU* 1.3 62.1 + - - +
168E ASP* 4.0 5.2 - - - +
169E THR* 4.0 19.3 - - + -
300E LYS* 4.0 27.8 - - + +
303E ALA* 4.1 17.9 - - + -
304E ARG* 5.9 3.1 - - + -
307E VAL* 6.4 0.2 - - + -
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Residues in contact with GLU 167 (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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129E TYR* 2.6 43.6 + - + -
158E LEU* 2.8 22.0 + - + +
160E ASN* 3.1 25.4 + - + -
165E GLU* 3.3 2.9 + - - +
166E ILE* 1.3 74.0 - - - +
168E ASP* 1.3 63.4 + - + +
217E LYS* 5.1 8.5 + - - +
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Residues in contact with ASP 168 (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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158E LEU* 2.9 32.5 + - + +
166E ILE* 3.6 3.1 - - - +
167E GLU* 1.3 83.5 - - + +
169E THR* 1.3 79.9 + - - +
213E TRP* 3.2 17.1 + - + -
217E LYS* 2.5 42.8 + - - +
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Residues in contact with THR 169 (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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156E VAL 3.3 7.2 - - - -
157E VAL* 3.9 23.3 - - + -
166E ILE* 4.0 13.5 - - + -
168E ASP* 1.3 92.1 + - - +
170E PHE* 1.3 62.8 + - - +
171E GLN* 6.0 0.2 - - - +
213E TRP* 3.8 10.3 + - - -
296E LEU* 4.0 18.2 - - - +
300E LYS* 3.9 20.5 + - - -
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Residues in contact with PHE 170 (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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154E PHE 3.7 13.9 - - - -
155E PRO* 3.3 3.3 - - - +
156E VAL* 2.9 40.0 + - + +
169E THR* 1.3 76.2 - - - +
171E GLN* 1.3 64.7 + - - +
172E GLN* 3.3 38.1 - - + -
206E VAL* 4.5 1.3 - - + -
209E LYS* 3.8 26.0 - - + -
210E VAL* 3.4 38.8 - - + -
213E TRP* 3.7 44.2 - + + -
296E LEU* 4.3 3.1 - - - +
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Residues in contact with GLN 171 (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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153E GLU* 2.7 36.1 + - + +
154E PHE 3.5 5.2 - - - +
155E PRO* 4.8 1.8 - - + -
170E PHE* 1.3 80.1 - - - +
172E GLN* 1.3 77.7 + - - +
173E TYR* 4.1 20.6 + - + -
294E CYS* 4.5 6.1 - - - -
296E LEU* 3.3 39.1 - - + +
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Residues in contact with GLN 172 (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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153E GLU* 3.7 0.3 - - - -
154E PHE* 2.9 34.7 + - - +
170E PHE* 3.3 31.9 - - + -
171E GLN* 1.3 81.7 + - - +
173E TYR* 1.3 70.2 + - - +
201E ASP* 5.6 3.5 + - - +
206E VAL* 3.7 27.5 - - + +
209E LYS* 3.9 25.6 + - - +
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Residues in contact with TYR 173 (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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152E ILE 3.4 13.2 - - - +
153E GLU* 3.9 23.0 + - + -
171E GLN* 4.1 21.4 + - + -
172E GLN* 1.3 80.0 - - - +
174E VAL* 1.3 62.4 + - - +
192E ILE* 3.8 30.0 - - + +
196E GLN* 3.5 61.1 + - + +
197E VAL* 4.9 2.9 - - + -
199E ARG* 6.1 1.6 - - - -
200E ALA* 3.4 15.5 - - + +
201E ASP 4.5 0.7 + - - -
206E VAL* 3.7 12.3 - - - +
294E CYS* 6.0 1.0 - - - -
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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