Contacts of the strand formed by residues 223 - 229 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221O TYR 3.2 12.0 + - - +
222O ARG* 1.3 72.3 - - - +
224O TYR* 1.3 61.9 + - - +
225O ASP 4.2 4.0 - - - +
226O VAL* 3.9 25.8 - - + -
248O ALA* 4.9 2.7 - - + -
249O ARG 3.7 11.2 - - - +
250O THR* 4.0 13.9 - - + -
256O ILE* 3.8 19.3 - - + -
309O ALA* 3.2 28.0 - - + +
311O SER* 4.0 3.6 - - - +
314O MET* 3.6 32.2 - - + +
316O LYS* 2.8 37.6 + - + +
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Residues in contact with TYR 224 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222O ARG* 4.4 24.2 - - + -
223O ILE* 1.3 72.8 - - - +
225O ASP* 1.3 69.0 + - - +
249O ARG* 2.8 17.0 + - + +
250O THR* 3.4 28.3 - - - -
251O GLU* 3.5 22.9 + - - +
284O GLU* 3.6 15.0 + - - +
285O MET* 3.4 31.0 - - + -
316O LYS* 3.0 18.8 + - - +
2301O NAG 5.9 0.3 - - - +
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Residues in contact with ASP 225 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223O ILE* 3.6 1.1 - - - -
224O TYR* 1.3 81.4 - - - +
226O VAL* 1.3 65.4 + - - +
227O VAL* 4.1 16.1 - - + +
247O THR 3.8 0.9 - - - +
248O ALA* 3.5 2.3 - - - -
249O ARG* 3.0 72.2 + - - +
316O LYS* 4.7 4.5 - - - -
2301O NAG 3.5 17.9 + - - +
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Residues in contact with VAL 226 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223O ILE* 3.9 7.6 - - + -
225O ASP* 1.3 77.0 - - - +
227O VAL* 1.3 54.6 + - - +
246O CYS* 3.7 27.4 - - - -
247O THR 3.3 4.9 - - - +
248O ALA* 4.2 3.1 - - + -
307O CYS* 3.9 17.0 - - - +
309O ALA* 3.8 19.7 - - + -
316O LYS* 3.5 39.9 - - + +
317O LYS* 4.4 2.5 - - - +
318O ASN* 2.7 39.7 + - + +
2301O NAG 3.1 9.9 + - - +
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Residues in contact with VAL 227 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225O ASP* 4.1 24.0 - - + +
226O VAL* 1.3 79.2 - - - +
228O LEU* 1.3 79.3 + - - +
229O SER* 5.4 1.5 - - - -
245O ASN 3.5 1.2 - - - +
246O CYS* 3.5 3.6 - - - -
247O THR* 2.8 46.2 + - - +
249O ARG* 5.7 1.3 - - - +
318O ASN* 4.0 1.3 - - - +
2301O NAG 3.4 38.1 - - - +
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Residues in contact with LEU 228 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226O VAL 4.3 0.4 + - - -
227O VAL* 1.3 87.4 - - - +
229O SER* 1.3 62.3 + - - +
230O PRO 3.5 11.9 - - - +
231O SER* 3.5 21.6 + - - +
244O LEU* 4.3 7.4 - - + -
245O ASN 3.2 12.1 - - - +
246O CYS* 3.9 10.3 - - + -
260O TRP* 3.8 28.5 - - + -
305O TYR 4.1 3.8 - - - +
307O CYS* 3.9 7.6 - - + +
318O ASN* 3.6 15.5 - - + +
319O SER* 3.3 47.8 - - - +
320O THR* 3.8 11.7 - - + +
2301O NAG 4.8 1.6 + - - -
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Residues in contact with SER 229 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3H BMA 3.9 11.5 + - - -
227O VAL* 5.4 2.0 - - - -
228O LEU* 1.3 76.8 - - - +
230O PRO* 1.3 68.9 - - - +
231O SER 3.8 0.2 - - - +
243O VAL 4.2 0.3 - - - +
244O LEU* 3.7 1.1 - - - -
245O ASN* 2.8 46.1 + - - +
247O THR* 6.2 0.2 - - - -
1U NAG 3.1 23.6 + - - +
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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