Contacts of the strand formed by residues 221 - 227 (chain B) in PDB entry 4YO0
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 ASN 221 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B LYS* 2.9 39.1 + - - +
134B THR* 4.5 21.9 + - + +
216B VAL 3.7 0.9 - - - +
217B THR* 3.2 1.7 - - - -
218B HIS* 2.8 39.0 + - - +
219B GLU 3.4 1.7 + - - +
220B GLY* 1.3 82.5 + - - +
222B THR* 1.3 61.7 + - - +
223B VAL* 5.2 2.0 - - + +
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Residues in contact with THR 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B GLN* 3.6 34.1 - - + +
216B VAL 3.3 6.3 - - - +
217B THR* 3.0 22.0 + - - +
220B GLY 4.1 2.6 + - - -
221B ASN* 1.3 74.3 - - - +
223B VAL* 1.3 70.1 + - - +
224B GLU* 5.0 4.9 - - + +
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Residues in contact with VAL 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B THR* 3.8 29.4 - - + -
135B PRO* 4.0 20.0 - - + +
137B LEU* 3.6 27.0 - - + +
215B GLN* 3.6 0.2 - - - -
216B VAL* 2.8 34.9 + - + +
221B ASN* 5.2 1.6 - - + +
222B THR* 1.3 81.0 - - - +
224B GLU* 1.3 68.7 + - - +
225B LYS* 5.9 2.7 - - + -
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Residues in contact with GLU 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B LEU* 3.8 3.6 - - - -
171B LYS* 5.6 1.4 + - - +
213B THR* 3.7 21.6 + - + +
214B CYS 3.2 14.1 - - - +
215B GLN* 3.4 27.7 - - + +
222B THR* 5.0 4.0 - - + +
223B VAL* 1.3 80.8 - - - +
225B LYS* 1.3 70.2 + - - +
226B SER* 4.9 2.5 + - - +
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Residues in contact with LYS 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B THR* 6.0 0.2 - - - +
137B LEU* 3.2 42.3 + - + +
138B THR* 4.8 2.5 - - - +
139B VAL* 3.9 31.6 - - + +
213B THR* 3.3 2.3 - - - -
214B CYS* 2.8 33.6 + - - +
223B VAL* 5.9 3.4 - - + -
224B GLU* 1.3 81.4 - - - +
226B SER* 1.3 64.9 + - - +
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Residues in contact with SER 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B VAL* 3.9 12.9 - - - +
211B SER* 4.0 14.2 + - - -
212B PHE 3.0 9.4 - - - -
213B THR* 2.8 26.6 + - - +
224B GLU* 4.9 2.4 + - - +
225B LYS* 1.3 74.0 - - - +
227B LEU* 1.3 66.2 + - - +
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Residues in contact with LEU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B VAL* 3.6 32.3 - - + +
140B PHE 3.2 29.2 - - - +
141B PRO* 3.6 31.4 - - + -
154B LEU* 3.9 25.1 - - + -
155B VAL 4.6 1.8 - - - +
170B TRP* 4.9 7.0 - - + -
206B TRP* 4.0 14.4 - - + -
211B SER* 3.4 4.9 + - - -
212B PHE* 2.7 42.6 + - + +
226B SER* 1.3 74.4 - - - +
228B SER* 1.3 60.5 + - - +
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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