Contacts of the strand formed by residues 203 - 208 (chain E) in PDB entry 1AXC
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 VAL 203 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E SER* 3.3 35.7 - - - +
135E CYS* 3.8 12.3 - - + -
160E ILE 4.2 0.9 - - - -
161E SER* 3.5 1.2 - - - -
162E CYS* 2.8 33.8 + - + +
201E GLU 3.4 1.8 - - - +
202E PRO* 1.3 79.3 - - - +
204E GLN* 1.3 72.3 + - - +
205E LEU* 3.7 32.8 - - + +
229E MET* 4.3 12.6 - - + +
230E SER* 4.0 14.4 - - - +
231E ALA* 4.0 7.6 - - + +
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Residues in contact with GLN 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159E VAL* 3.6 21.3 - - + +
160E ILE 3.1 5.8 - - - -
161E SER* 3.3 26.6 + - - +
203E VAL* 1.3 80.1 - - - +
205E LEU* 1.3 66.8 + - - +
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Residues in contact with LEU 205 (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 VAL 3.5 0.7 - - - +
159E VAL* 3.1 5.2 - - - +
160E ILE* 2.7 35.3 + - - +
203E VAL* 3.7 8.3 - - + +
204E GLN* 1.3 80.2 - - - +
206E THR* 1.3 63.6 + - - +
207E PHE* 3.3 31.8 - - + -
229E MET* 3.6 28.9 - - + -
230E SER 3.3 28.5 - - - +
231E ALA* 4.2 4.3 - - + -
232E ASP* 4.0 15.9 - - - +
233E VAL 4.4 4.9 - - - +
235E LEU* 5.7 0.4 - - + -
253E PRO* 4.4 15.0 - - + -
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Residues in contact with THR 206 (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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157E ALA* 3.6 26.2 - - + -
158E VAL 3.2 8.5 - - - +
159E VAL* 3.9 18.1 - - + +
205E LEU* 1.3 76.8 + - - +
207E PHE* 1.3 75.2 + - - +
253E PRO* 3.5 1.8 - - - +
254E LYS* 3.0 51.6 + - + +
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Residues in contact with PHE 207 (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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157E ALA* 3.0 6.2 - - - -
158E VAL* 2.9 32.8 + - + +
160E ILE* 4.0 21.8 - - + -
205E LEU* 3.3 45.3 - - + -
206E THR* 1.3 81.8 - - - +
208E ALA* 1.3 62.3 + - - +
212E LEU* 4.2 10.5 - - + -
229E MET* 4.8 1.6 - - - -
233E VAL 4.8 0.2 - - - -
235E LEU* 3.5 36.8 - - + -
251E LEU* 3.4 44.4 - - + -
252E ALA 3.8 4.5 - - - -
253E PRO* 3.4 26.0 - - + -
254E LYS* 3.9 9.9 - - - -
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Residues in contact with ALA 208 (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 ASP* 3.8 6.1 - - + +
157E ALA* 4.5 1.3 - - - +
207E PHE* 1.3 71.4 - - - +
209E LEU* 1.3 65.6 + - - +
210E ARG* 3.3 3.6 - - + +
211E TYR* 3.2 38.8 + - + +
212E LEU* 3.5 8.1 + - - +
251E LEU* 3.8 8.4 - - + +
252E ALA 5.4 0.2 + - - -
254E LYS* 4.0 10.5 - - + +
144F GLN* 3.7 18.2 + - - +
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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