Contacts of the strand formed by residues 212 - 219 (chain A) in PDB entry 4Y1W
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 THR 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A LEU* 3.7 43.0 - - + +
165A LYS* 5.0 6.6 - - - +
166A ARG 3.8 17.0 + - - +
167A VAL* 3.5 12.1 - - + +
168A LEU 3.1 22.5 + - - -
205A ILE* 4.9 0.9 - - + -
206A GLU 3.4 7.9 - - - +
207A ARG* 4.2 13.0 - - + +
208A THR 5.1 0.9 + - - -
211A HIS* 1.3 78.2 + - - +
213A TYR* 1.3 66.0 + - - +
214A ILE* 4.2 13.2 - - + -
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Residues in contact with TYR 213 (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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21A PHE* 3.7 39.5 - + + -
24A ILE* 3.9 16.2 + - + +
25A LYS* 3.9 29.7 - - + +
168A LEU* 3.3 37.2 - - + +
205A ILE* 3.5 0.9 - - - +
206A GLU* 2.9 41.0 + - - +
211A HIS* 3.3 48.8 + + + +
212A THR* 1.3 80.6 - - - +
214A ILE* 1.3 67.3 + - - +
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Residues in contact with ILE 214 (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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21A PHE* 3.6 3.6 - - - -
121A VAL* 6.2 0.9 - - + -
126A LEU* 4.1 22.4 - - + -
129A LEU* 4.2 17.0 - - + -
135A LEU* 5.1 0.2 - - + -
167A VAL* 3.8 23.3 - - + -
168A LEU 3.0 6.9 + - - -
169A PHE* 3.2 25.7 - - + -
170A GLU 3.0 22.0 + - - +
202A ILE* 4.0 17.0 - - + -
204A GLN 3.5 7.2 - - - +
205A ILE* 4.4 10.5 - - + -
212A THR* 4.2 6.7 - - + -
213A TYR* 1.3 79.7 - - - +
215A GLY* 1.3 71.9 + - - +
216A VAL* 3.9 15.0 - - + -
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Residues in contact with GLY 215 (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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21A PHE* 3.4 16.4 - - - -
170A GLU* 3.3 10.5 - - - -
202A ILE* 3.5 2.1 - - - -
203A THR* 2.8 34.4 + - - -
204A GLN* 2.8 16.3 + - - +
214A ILE* 1.3 74.1 - - - +
216A VAL* 1.3 63.5 + - - +
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Residues in contact with VAL 216 (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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135A LEU* 4.4 2.5 - - + -
169A PHE* 3.9 19.5 - - + -
170A GLU 3.0 8.6 + - - +
171A VAL* 3.9 31.6 - - + -
172A LYS* 2.8 33.4 + - - +
200A PHE* 3.8 29.2 - - + +
201A ARG 3.1 12.3 - - - +
202A ILE* 4.1 11.0 - - + -
203A THR* 3.8 5.1 + - - -
214A ILE* 3.9 17.7 - - + -
215A GLY* 1.3 78.6 - - - +
217A GLU* 1.3 54.0 + - - +
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Residues in contact with GLU 217 (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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172A LYS* 3.3 20.2 - - + +
174A ASN* 4.3 12.5 + - - +
200A PHE* 3.4 3.9 - - - -
201A ARG* 2.8 68.2 + - + +
203A THR* 3.9 18.4 - - + +
216A VAL* 1.3 74.7 - - - +
218A THR* 1.3 64.9 + - - +
219A VAL* 3.4 10.1 + - + +
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Residues in contact with THR 218 (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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171A VAL* 4.4 0.4 - - + -
172A LYS 3.0 11.0 + - - +
173A ILE* 3.8 7.0 - - + -
174A ASN* 2.8 53.4 + - - +
175A GLN* 3.4 29.4 + - - +
194A PHE* 3.5 26.7 - - + -
199A HIS 3.7 7.9 - - - +
200A PHE* 3.9 14.3 - - + -
217A GLU* 1.3 73.3 - - - +
219A VAL* 1.3 64.3 + - - +
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Residues in contact with VAL 219 (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 VAL* 4.4 3.8 - - + -
175A GLN* 3.7 10.6 - - - +
199A HIS* 3.1 41.2 + - + +
200A PHE 4.2 0.4 - - - +
201A ARG* 3.7 29.6 - - + +
217A GLU* 3.7 18.8 - - + +
218A THR* 1.3 81.2 - - - +
220A LYS* 1.3 63.3 + - - +
221A ALA 3.7 0.5 + - - -
223A ALA* 5.8 2.2 - - + -
224A VAL* 3.8 19.5 - - + -
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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