Contacts of the strand formed by residues 224 - 230 (chain A) in PDB entry 7NPA
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 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A TRP* 2.8 25.5 + - - +
214A LEU* 4.1 3.8 - - + -
219A ILE* 3.9 13.9 - - + -
220A ASN 3.9 0.4 - - - +
221A MET* 3.0 29.1 + - - +
222A ASP 3.4 2.1 - - - +
223A ASP* 1.3 78.6 - - - +
225A GLU* 1.3 60.4 + - - +
226A LYS 3.4 26.7 - - - +
227A PHE* 3.6 22.7 - - + -
236A VAL* 3.6 24.2 - - + -
237A TYR 3.5 7.4 - - - +
238A VAL* 4.1 3.6 - - + -
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Residues in contact with GLU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A TRP* 3.5 11.5 - - - -
131A LYS* 5.7 4.9 - - - +
223A ASP 3.5 6.5 + - - +
224A VAL* 1.3 73.2 - - - +
226A LYS* 1.3 66.2 + - + +
237A TYR* 2.8 19.3 + - + +
238A VAL* 5.2 0.9 - - - -
239A ASN* 4.3 5.6 + - - -
240A GLY* 4.1 21.0 + - - -
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Residues in contact with LYS 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A GLY 3.8 5.1 + - - -
84A GLN* 2.8 58.2 + - - +
113A TRP* 3.9 7.2 - - + -
131A LYS* 4.3 20.0 - - + +
224A VAL* 3.4 11.3 - - - +
225A GLU* 1.3 83.2 - - + +
227A PHE* 1.3 69.9 + - - +
228A ASP* 5.2 4.9 + - - -
236A VAL* 3.8 0.5 - - - -
237A TYR* 3.0 50.9 + - + -
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Residues in contact with PHE 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A GLN* 2.8 22.5 + - - +
113A TRP* 3.7 44.0 - + - -
132A SER 4.7 2.9 + - - +
134A TYR* 3.5 27.1 - + + -
210A LEU* 4.1 20.0 - - + -
214A LEU* 3.7 35.2 - - + -
221A MET* 4.0 13.9 - - + -
224A VAL* 3.6 18.8 - - + -
226A LYS* 1.3 80.8 - - - +
228A ASP* 1.3 61.8 + - - +
234A LEU* 4.1 18.6 - - + -
235A LEU 3.4 8.3 - - - -
236A VAL* 3.9 15.3 - - + -
237A TYR* 5.0 0.7 - - - -
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Residues in contact with ASP 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A GLN* 3.2 18.5 + - - +
85A ASP* 4.4 1.4 - - - +
134A TYR* 3.4 8.8 + - - -
226A LYS* 5.2 5.9 + - - -
227A PHE* 1.3 76.3 - - - +
229A ILE* 1.3 72.2 + - - +
230A LYS* 2.8 45.5 + - - +
234A LEU* 3.4 7.1 - - - +
235A LEU* 2.7 54.8 + - + +
237A TYR* 4.4 10.3 + - + -
273A CYS* 4.8 1.2 - - - -
278A ASP* 5.5 0.3 - - - +
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Residues in contact with ILE 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A TYR* 3.3 39.1 + - + +
202A THR* 4.3 13.7 - - + +
203A GLU* 4.5 15.5 - - + +
205A PHE* 4.2 17.0 - - + -
228A ASP* 1.3 82.6 + - - +
230A LYS* 1.3 70.1 + - - +
232A GLY 5.5 0.7 - - - +
233A LYS 3.3 2.7 - - - +
234A LEU* 4.0 10.1 - - + -
247A LEU* 3.7 39.9 - - + -
273A CYS* 3.9 13.5 - - - -
274A VAL* 6.0 0.3 - - - +
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Residues in contact with LYS 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ASP* 3.0 25.6 + - - -
228A ASP* 2.8 41.3 + - - +
229A ILE* 1.3 74.4 - - - +
231A LYS* 1.3 86.7 + - + +
232A GLY 3.2 2.2 - - - -
233A LYS* 3.0 24.9 + - - +
235A LEU* 4.0 18.8 - - + +
273A CYS* 3.3 26.5 - - - +
278A ASP* 4.3 19.3 - - - +
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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