Contacts of the strand formed by residues 220 - 224 (chain A) in PDB entry 1Y24
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 GLY 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A GLU* 3.9 3.4 - - - -
179A THR 4.9 0.7 - - - -
201A TYR* 4.0 6.0 - - - -
219A GLY* 1.3 74.3 - - - -
221A PRO* 1.3 67.3 - - - +
222A GLY 3.8 0.9 - - - -
234A SER* 5.0 1.8 - - - -
235A TRP* 5.4 0.2 - - - -
238A LEU* 6.3 0.8 - - - +
245A THR* 5.2 0.4 + - - -
247A PHE* 3.3 8.8 + - - +
248A PHE* 3.2 13.2 - - - -
249A THR* 2.9 39.1 + - - -
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Residues in contact with PRO 221 (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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179A THR 4.1 8.3 - - - +
180A TRP 3.9 7.0 - - - -
183A PRO* 3.1 21.5 - - + +
198A PHE* 4.9 8.3 - - + -
201A TYR* 5.3 7.2 - - + -
220A GLY* 1.3 79.9 - - - +
222A GLY* 1.3 58.7 + - - +
223A ASP* 2.8 37.5 - - - +
230A ARG* 4.0 12.8 - - + +
231A SER* 5.0 0.4 - - - +
234A SER* 3.8 30.3 - - - +
248A PHE* 3.3 24.7 - - + -
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Residues in contact with GLY 222 (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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178A GLU* 3.1 27.9 + - - -
180A TRP 3.8 3.4 - - - -
181A ASN* 4.1 3.6 - - - +
182A GLU* 2.8 29.8 + - - +
221A PRO* 1.3 72.4 - - - +
223A ASP* 1.3 58.6 + - - +
249A THR* 2.8 22.9 + - - -
250A GLY* 5.0 1.6 - - - -
251A GLU* 5.1 2.7 - - - +
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Residues in contact with ASP 223 (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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182A GLU* 3.9 1.0 - - - +
183A PRO* 3.2 8.3 - - - +
184A ASP* 3.0 38.9 + - + +
221A PRO* 2.8 29.1 - - + +
222A GLY* 1.3 75.7 - - - +
224A SER* 1.3 66.0 + - - +
227A THR* 4.7 7.9 - - - +
230A ARG* 3.1 31.2 + - + +
248A PHE* 5.6 4.3 - - + -
249A THR 3.4 6.6 + - - +
250A GLY* 3.2 7.6 - - - -
251A GLU* 2.8 25.4 + - - -
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Residues in contact with SER 224 (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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182A GLU* 3.5 15.7 - - - +
184A ASP* 5.0 5.7 + - - +
185A HIS* 3.1 34.2 + - - -
222A GLY 3.9 1.6 + - - -
223A ASP* 1.3 83.2 - - - +
225A PHE* 1.3 72.9 + - - +
227A THR* 3.9 13.5 + - - +
251A GLU* 3.1 34.9 - - - +
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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