Contacts of the strand formed by residues 162 - 167 (chain E) in PDB entry 6XOX
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 162 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E MET* 3.7 17.7 - - + -
153E LEU* 3.8 15.5 - - + -
160E THR 2.8 8.4 + - - +
161E TYR* 1.3 73.1 - - - +
163E TYR* 1.3 65.6 + - - +
164E TRP* 3.4 32.8 + - + +
177E ILE 3.9 1.2 - - - +
179E ARG* 3.3 3.5 + - - +
180E MET* 2.9 38.8 + - + -
200E PHE* 3.5 36.3 - - + -
217E CYS* 3.6 22.7 - - - -
218E MET 3.3 15.0 - - - +
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Residues in contact with TYR 163 (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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15A GLU* 3.2 30.0 + - - -
107E PRO* 3.3 22.0 - - + +
108E PHE* 3.8 18.8 - + + -
161E TYR* 4.5 2.0 - + - -
162E LEU* 1.3 81.9 - - - +
164E TRP* 1.3 63.2 + - - +
165E PHE* 3.7 22.0 - + + -
175E LEU* 4.5 2.0 - - + -
177E ILE 3.2 4.9 - - - +
178E TYR* 3.5 12.1 - - + -
179E ARG* 3.2 39.4 - - + +
216E TYR 3.6 0.2 - - - +
217E CYS* 3.5 4.5 - - - -
218E MET* 2.9 54.7 + - + -
220E HIS* 3.7 29.5 - + + -
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Residues in contact with TRP 164 (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 GLN* 4.5 6.1 - - - -
145E ILE* 3.6 31.0 - - + -
146E SER 4.3 1.3 - - - -
147E CYS* 3.7 22.7 - - + -
162E LEU* 3.4 31.8 - - + +
163E TYR* 1.3 78.7 - - - +
165E PHE* 1.3 55.9 + - - +
175E LEU* 3.5 4.5 - - - +
176E LEU* 2.7 35.7 + - + -
177E ILE* 2.8 49.1 + - + +
180E MET* 4.9 6.8 + - - +
193E GLY* 5.2 0.4 - - - -
194E SER 5.5 0.2 + - - -
201E THR 3.9 14.0 + - - +
202E LEU* 3.5 46.6 - - + +
215E TYR* 4.8 4.5 - - + -
216E TYR 3.4 12.3 - - - -
217E CYS* 4.2 10.8 - - + -
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Residues in contact with PHE 165 (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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45E LEU* 6.4 0.4 - - + -
108E PHE* 3.4 44.4 - - + -
111E TRP* 3.9 16.4 - + - -
163E TYR* 3.7 17.0 - - + -
164E TRP* 1.3 75.7 - - - +
166E LEU* 1.3 61.9 + - - +
173E PRO* 4.4 6.1 - - + -
174E GLN 3.4 17.5 - - - +
175E LEU* 3.6 13.9 - - + -
176E LEU* 4.0 4.0 - - - -
214E VAL 3.3 2.1 - - - +
215E TYR* 3.2 7.4 - - - -
216E TYR* 2.9 58.1 + - + +
218E MET* 3.6 42.2 - - + -
227E PHE* 4.7 7.6 - + + -
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Residues in contact with LEU 166 (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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165E PHE* 1.3 72.5 - - - +
167E GLN* 1.3 79.0 + - - +
168E ARG* 3.5 35.7 - - + +
173E PRO* 3.3 2.9 - - - +
174E GLN* 2.8 62.0 + - + +
176E LEU* 3.5 31.8 - - + +
190E ARG* 6.1 0.2 - - - +
191E PHE* 4.9 9.4 - - + -
210E GLU 5.0 2.5 - - - +
211E ASP* 3.8 15.3 - - - +
213E GLY* 4.1 3.6 - - - -
215E TYR* 3.5 24.2 - - + -
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Residues in contact with GLN 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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39E GLN* 3.9 12.1 + - - +
45E LEU* 3.4 23.7 - - - +
95E TYR* 3.8 15.4 + - - -
166E LEU* 1.3 77.1 - - - +
168E ARG* 1.3 72.1 + - - +
169E PRO* 5.9 0.2 - - - +
170E GLY* 5.2 2.8 - - - +
171E GLN 3.4 23.6 + - - +
172E SER 4.8 0.2 - - - -
173E PRO* 3.6 23.3 - - + -
213E GLY* 3.0 3.1 - - - -
214E VAL* 2.9 47.3 + - + +
216E TYR* 3.5 13.4 + - + -
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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