Contacts of the strand formed by residues 211 - 216 (chain E) in PDB entry 4OA5
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 MET 211 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E LEU* 3.7 34.5 - - + -
44E GLU* 4.6 8.1 - - + -
47E MET* 3.8 33.4 - - + -
48E LEU* 4.5 6.3 - - + -
134E PHE* 3.9 16.4 - - + -
160E VAL* 3.9 16.2 - - + -
161E ALA 3.5 22.4 - - - +
162E ASP* 3.8 13.5 - - + +
204E ILE* 3.9 0.7 - - - -
205E ILE* 2.8 42.6 + - + +
207E THR* 3.5 7.9 + - + +
210E GLY* 1.3 71.1 - - - +
212E MET* 1.3 65.0 + - - +
213E VAL* 3.5 6.5 + - + +
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Residues in contact with MET 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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159E ILE 4.5 5.8 - - - +
160E VAL* 3.2 12.8 - - - +
161E ALA* 2.8 40.5 + - + +
164E THR* 3.5 18.7 + - + +
190E PHE* 4.2 4.9 - - + -
191E ASN* 3.4 30.1 - - - +
194E LEU* 3.7 40.4 - - + -
202E SER* 4.0 19.5 - - - -
203E THR 3.7 11.9 - - - +
204E ILE* 3.6 19.5 - - + +
211E MET* 1.3 70.9 - - - +
213E VAL* 1.3 69.4 + - - +
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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
----------------------------------------------------------
51E LEU* 3.7 36.8 - - + -
158E LEU* 5.0 12.6 - - + -
159E ILE 3.7 3.1 - - - -
160E VAL* 4.4 10.3 - - + -
201E LEU 4.0 0.9 - - - +
202E SER* 3.4 2.1 - - - -
203E THR* 2.9 38.8 + - - +
205E ILE* 3.6 32.8 - - + -
211E MET* 3.9 4.5 - - + +
212E MET* 1.3 80.8 - - - +
214E SER* 1.3 62.7 + - - +
215E ILE* 6.2 1.3 - - + -
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Residues in contact with SER 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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158E LEU* 3.3 8.6 - - - +
159E ILE* 2.8 48.8 + - - -
194E LEU* 3.7 21.6 - - - +
200E TYR* 3.3 17.5 - - - +
201E LEU 3.4 3.8 - - - -
202E SER* 2.7 26.2 + - - -
212E MET* 4.5 1.1 - - - -
213E VAL* 1.3 77.4 - - - +
215E ILE* 1.3 64.3 + - - +
216E LYS 3.8 0.2 + - - -
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Residues in contact with ILE 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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156E GLY* 3.9 21.5 - - - +
157E GLY 3.5 2.9 - - - -
158E LEU* 3.8 18.2 - - + -
200E TYR* 3.2 5.7 - - - -
201E LEU* 2.9 54.6 + - + +
213E VAL* 6.2 1.3 - - + -
214E SER* 1.3 73.7 - - - +
216E LYS* 1.3 74.2 + - - +
217E LEU* 3.4 12.0 + - + +
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Residues in contact with LYS 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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123D THR* 6.1 1.8 - - - +
149E ALA 3.4 12.8 - - - +
150E LYS* 3.3 33.1 + - - +
153E ILE* 2.8 37.0 + - + +
154E ARG 3.7 11.4 + - - +
155E LYS 4.0 0.8 - - - +
156E GLY* 2.7 34.3 + - - -
157E GLY 2.9 16.2 + - - +
159E ILE* 4.3 19.7 - - + -
199E LYS 4.0 4.0 - - - +
200E TYR* 4.0 11.4 - - + -
214E SER 3.8 1.2 + - - -
215E ILE* 1.3 71.7 - - - +
217E LEU* 1.3 57.5 + - - +
218E THR* 2.7 36.8 + - - +
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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