Contacts of the strand formed by residues 165 - 169 (chain E) in PDB entry 1M54
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 CYS 165 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E ILE* 3.8 7.9 - - - -
144E GLU* 5.6 0.2 - - - -
154E LEU* 4.1 9.6 - - - -
155E ALA* 3.9 25.4 - - - +
158E ALA* 4.0 15.9 - - + -
163E TYR 3.3 2.1 + - - +
164E ARG* 1.3 75.6 - - - +
166E ILE* 1.3 73.8 + - - +
167E ILE* 3.4 26.0 - - - -
184E LEU 5.8 1.3 - - - +
185E GLY 4.8 6.1 + - - +
186E ALA* 3.7 14.7 - - + +
187E GLU* 3.0 27.3 + - - +
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Residues in contact with ILE 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141E THR* 4.6 8.5 - - + -
142E ILE 3.4 8.2 + - - +
143E ILE* 3.7 9.5 - - + +
144E GLU 3.1 23.4 + - - -
164E ARG* 4.1 14.1 - - + +
165E CYS* 1.3 75.4 - - - +
167E ILE* 1.3 80.3 + - - +
168E VAL* 4.9 3.8 - - + +
187E GLU* 3.2 38.4 - - + +
189E VAL* 4.4 18.6 - - + -
210E LEU* 4.5 14.4 - - + -
214E ILE* 3.4 33.4 - - + -
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Residues in contact with ILE 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144E GLU* 3.6 29.4 - - + -
146E THR 4.1 1.3 - - - +
147E SER* 3.5 33.2 - - - -
151E GLY* 3.9 23.3 - - - +
155E ALA* 4.8 0.4 - - + -
165E CYS* 3.4 24.0 - - - -
166E ILE* 1.3 95.7 - - - +
168E VAL* 1.3 67.9 + - - +
169E MET* 4.2 4.0 - - + +
181E LEU* 4.5 12.1 - - + -
186E ALA* 4.7 8.3 - - + -
187E GLU 3.1 8.4 + - - +
188E ILE* 3.4 11.2 - - + +
189E VAL 3.2 24.1 + - - +
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Residues in contact with VAL 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E ILE* 5.1 4.9 - - + +
144E GLU 3.3 4.4 + - - +
145E PRO* 2.6 48.2 - - + +
146E THR* 4.2 0.3 - - - -
166E ILE* 4.9 8.1 - - + -
167E ILE* 1.3 77.7 - - - +
169E MET* 1.3 50.9 + - - +
189E VAL* 3.4 18.8 - - + -
191E THR* 3.8 19.7 - - - +
203E HIS* 2.4 43.0 + - - +
206E VAL* 5.5 2.0 - - + -
207E ALA* 4.8 20.4 - - + +
210E LEU* 4.9 13.5 - - + -
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Residues in contact with MET 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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147E SER* 3.2 42.2 - - - +
167E ILE* 4.3 0.2 - - + -
168E VAL* 1.3 72.9 - - - +
170E PRO* 1.4 63.8 - - - +
173E MET* 4.4 14.8 - - + -
177E LYS* 5.2 4.7 - - + -
178E VAL* 3.6 28.9 - - + +
181E LEU* 4.5 5.8 - - + -
188E ILE* 3.4 31.4 - - + -
189E VAL 2.8 8.9 + - - -
190E ARG* 2.6 77.6 - - - -
191E THR 2.8 3.2 + - - -
203E HIS* 3.1 1.3 - - - -
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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