Contacts of the strand formed by residues 219 - 223 (chain C) in PDB entry 1AX4
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 PHE 219 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C LEU* 5.3 0.4 - - + -
111C LEU* 3.6 31.6 - - + -
114C TYR* 5.7 6.3 - + + -
115C LYS* 5.4 0.6 - - - +
185C VAL 3.9 16.4 + - - +
186C ALA* 3.2 4.3 - - - +
187C ILE 2.9 24.4 + - - -
214C LYS* 4.0 1.8 - - - +
217C GLY 3.8 2.4 + - - -
218C ILE* 1.3 75.4 - - - +
220C VAL* 1.3 61.7 + - - +
221C VAL* 3.9 15.5 - - + -
258C ASP* 3.5 33.7 - - + -
259C ALA* 3.7 27.6 - - + -
278C ILE* 5.3 1.8 - - + -
281C ASN* 4.6 16.8 - - + -
284C ILE* 4.5 26.0 - - + -
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Residues in contact with VAL 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C ILE* 3.4 20.2 - - + +
189C SER* 3.9 19.3 - - - +
209C VAL* 5.0 2.9 - - + +
210C TYR* 3.8 21.3 - - + -
213C ALA* 3.4 33.0 - - + -
218C ILE 4.0 1.6 - - - +
219C PHE* 1.3 78.4 - - - +
221C VAL* 1.3 64.5 + - - +
256C TYR 3.8 18.4 - - - +
257C ALA* 4.0 7.0 - - + -
258C ASP* 2.7 45.2 + - - +
259C ALA 3.3 4.9 + - - -
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Residues in contact with VAL 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C LEU* 4.1 8.3 - - + -
108C PHE* 4.5 9.6 - - + -
111C LEU* 3.6 30.7 - - + -
186C ALA* 4.4 7.4 - - + -
187C ILE 2.9 10.4 + - - +
188C VAL* 3.2 12.9 - - + -
189C SER* 2.8 25.8 + - - -
219C PHE* 3.9 12.8 - - + -
220C VAL* 1.3 78.2 - - - +
222C MET* 1.3 62.8 + - - +
223C ASP* 3.6 1.1 + - - +
259C ALA* 3.5 6.1 - - + +
260C LEU* 4.3 0.2 - - - -
261C THR* 3.9 39.7 - - + +
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Residues in contact with MET 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C SER* 3.4 22.9 - - - +
191C VAL* 3.8 29.4 - - + -
206C LEU* 4.2 9.6 - - + -
221C VAL* 1.3 72.7 - - - +
223C ASP* 1.3 59.9 + - - +
224C SER* 2.8 28.0 + - - +
253C MET* 3.1 37.9 - - + +
254C TYR* 3.6 26.7 - - + +
256C TYR 4.4 4.7 - - - +
257C ALA* 3.8 22.3 - - + +
259C ALA 2.9 12.6 + - - +
260C LEU* 3.3 1.0 - - - -
261C THR 3.2 15.6 + - - -
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Residues in contact with ASP 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C GLU* 3.9 2.3 - - - +
108C PHE* 6.4 0.2 - - + -
132C PHE* 4.4 1.2 + - - +
135C THR* 3.5 15.3 + - + +
188C VAL* 3.9 20.8 - - + +
189C SER 2.8 11.6 + - - +
190C THR* 4.0 8.8 + - - +
191C VAL* 3.1 28.8 + - - +
221C VAL* 3.6 3.8 + - - +
222C MET* 1.3 67.3 - - - +
224C SER* 1.3 58.3 + - - +
225C ALA* 3.5 5.9 + - - +
261C THR* 3.6 18.1 - - - +
262C MET* 5.5 0.3 - - - -
263C SER 5.7 0.2 + - - -
266C LLP 2.6 53.3 + - - +
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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