Contacts of the strand formed by residues 223 - 229 (chain L) in PDB entry 2X1W
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 ILE 223 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221L TYR 3.2 12.6 + - - +
222L ARG* 1.3 71.0 - - - +
224L TYR* 1.3 62.0 + - - +
225L ASP 4.2 4.9 - - - +
226L VAL* 3.9 25.4 - - + -
248L ALA* 4.8 3.1 - - + -
249L ARG 3.7 10.3 - - - +
250L THR* 4.0 14.1 - - + -
256L ILE* 3.8 19.3 - - + -
309L ALA* 3.2 27.6 - - + +
311L SER* 4.0 4.0 - - - +
314L MET* 3.6 30.7 - - + +
316L LYS* 2.8 36.6 + - + +
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Residues in contact with TYR 224 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222L ARG* 4.4 24.4 - - + -
223L ILE* 1.3 73.2 - - - +
225L ASP* 1.3 66.9 + - - +
249L ARG* 2.8 17.5 + - + +
250L THR 3.4 26.0 - - - -
251L GLU* 3.5 12.7 + - - +
284L GLU* 3.3 27.5 + - - -
285L MET* 3.4 31.0 - - + -
316L LYS* 3.0 18.6 + - - +
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Residues in contact with ASP 225 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223L ILE* 3.6 0.8 - - - +
224L TYR* 1.3 81.2 - - - +
226L VAL* 1.3 64.0 + - - +
227L VAL* 4.1 18.3 - - + +
247L THR 3.7 1.2 - - - +
248L ALA* 3.5 2.8 - - - -
249L ARG* 3.0 71.5 + - - +
316L LYS* 4.7 4.5 - - - -
2701L NAG 4.6 13.9 - - - +
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Residues in contact with VAL 226 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223L ILE* 3.9 8.7 - - + -
225L ASP* 1.3 79.0 - - - +
227L VAL* 1.3 54.9 + - - +
246L CYS* 3.7 26.7 - - - -
247L THR 3.3 5.2 - - - +
248L ALA* 4.2 3.1 - - + -
307L CYS 3.9 16.2 - - - +
309L ALA* 3.8 19.3 - - + -
316L LYS* 3.4 40.1 - - + +
317L LYS* 4.4 2.2 - - - +
318L ASN* 2.7 39.9 + - + +
2701L NAG 3.8 8.3 + - - +
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Residues in contact with VAL 227 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225L ASP* 4.1 24.7 - - + +
226L VAL* 1.3 79.9 - - - +
228L LEU* 1.3 79.2 + - - +
229L SER* 5.4 2.2 - - - -
245L ASN 3.5 1.2 - - - +
246L CYS* 3.5 4.1 - - - -
247L THR* 2.8 45.1 + - - +
249L ARG* 5.7 1.6 - - - +
318L ASN* 4.0 1.8 - - - +
2701L NAG 4.0 33.2 - - - +
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Residues in contact with LEU 228 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226L VAL 4.3 0.4 + - - -
227L VAL* 1.3 88.4 - - - +
229L SER* 1.3 60.9 + - - +
230L PRO 3.5 11.9 - - - +
231L SER* 3.4 24.6 + - - +
244L LEU* 4.3 7.6 - - + -
245L ASN 3.2 12.1 - - - +
246L CYS* 3.9 10.3 - - + -
260L TRP* 3.8 28.3 - - + -
305L TYR 4.1 4.0 - - - +
307L CYS* 4.0 7.0 - - + -
318L ASN* 3.6 16.8 - - + +
319L SER* 3.3 47.3 - - - +
320L THR* 3.8 11.4 - - + +
2701L NAG 4.9 0.8 + - - -
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Residues in contact with SER 229 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F BMA 5.3 2.3 + - - -
227L VAL* 5.4 2.0 - - - -
228L LEU* 1.3 76.2 - - - +
230L PRO* 1.3 67.9 - - - +
231L SER 3.7 0.4 - - - +
243L VAL 4.2 0.5 - - - +
244L LEU* 3.7 1.8 - - - +
245L ASN* 2.8 46.3 + - - +
247L THR* 6.1 0.7 - - - -
1Q NAG 2.9 24.0 + - - +
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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