Contacts of the strand formed by residues 209 - 219 (chain A) in PDB entry 1YB2
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 MSE 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A VAL* 3.3 45.1 - - + +
177A ILE* 4.3 5.2 - - + -
178A ALA* 3.9 18.6 - - + +
181A MSE 3.7 23.3 - - - +
187A ALA* 4.1 15.3 - - - -
189A PHE* 4.0 11.9 - - + -
204A LEU* 3.2 25.7 + - + +
205A SER* 3.8 7.8 + - - -
207A SER* 3.3 18.6 - - - +
208A GLY* 1.3 82.7 - - - +
210A HIS* 1.3 61.1 + - - +
211A HIS 4.1 1.0 + - - -
245A ALA* 4.1 17.3 - - + -
246A ILE 3.3 9.6 - - - +
247A LYS* 4.3 4.3 - - - +
248A LYS* 4.1 7.1 + - - -
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Residues in contact with HIS 210 (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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11A SER* 3.9 15.1 - - - -
12A GLU* 3.7 18.3 + - + +
45A GLU* 5.7 1.0 + - - -
52A SER* 4.6 22.6 - - - -
54A ILE* 3.8 27.4 - - + +
209A MSE 1.3 74.2 - - - +
211A HIS* 1.3 89.3 + - - +
212A LEU* 3.5 2.1 + - + -
245A ALA* 3.3 3.6 - - - -
246A ILE* 2.7 54.3 + - + +
248A LYS* 4.1 14.2 + - + +
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Residues in contact with HIS 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLU* 3.2 55.5 + - + +
201A VAL* 3.7 27.7 - - + +
204A LEU* 3.6 22.1 - - + +
209A MSE 4.1 1.8 + - - -
210A HIS* 1.3 89.0 + - - +
212A LEU* 1.3 61.1 + - - +
213A GLU* 3.2 25.2 - - - -
214A THR* 2.8 33.4 + - - -
243A THR* 3.8 8.8 - - + +
244A PHE 3.6 7.7 + - - -
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Residues in contact with LEU 212 (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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10A VAL* 3.6 33.7 - - + -
11A SER 4.0 16.0 - - - +
12A GLU* 3.5 28.4 - - - +
15A TYR* 4.2 10.6 + - - +
61A MSE 4.5 3.6 - - - -
62A TYR* 3.5 30.7 - - + +
65A ARG* 5.3 1.9 + - - -
186A VAL* 4.4 6.3 - - + -
210A HIS* 4.1 7.0 - - + +
211A HIS* 1.3 76.2 - - - +
213A GLU* 1.3 70.1 + - + +
244A PHE* 2.9 26.2 + - + +
245A ALA 4.3 4.7 - - - -
246A ILE* 3.8 23.8 - - + +
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Residues in contact with GLU 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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12A GLU* 5.3 0.2 - - - -
15A TYR* 5.9 3.4 - - - +
61A MSE 5.9 1.4 - - - +
65A ARG* 5.3 13.0 + - - +
211A HIS* 3.2 14.4 - - - -
212A LEU* 1.3 87.2 - - + +
214A THR* 1.3 57.4 + - - +
215A VAL* 4.1 22.2 - - + +
244A PHE* 2.8 49.9 + - + -
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Residues in contact with THR 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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197A SER* 3.2 26.7 - - - +
201A VAL* 3.3 7.5 - - + +
211A HIS* 2.8 26.6 + - - -
213A GLU* 1.3 73.3 - - - +
215A VAL* 1.3 74.0 - - - +
241A PHE* 5.0 2.9 - - + -
242A ILE 3.2 10.3 - - - +
243A THR* 2.8 21.9 + - - +
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Residues in contact with VAL 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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213A GLU* 4.1 27.1 - - + +
214A THR* 1.3 83.3 - - - +
216A GLU* 1.3 62.9 + - - +
217A LEU* 4.7 12.1 - - + -
240A ALA 3.7 0.5 - - - +
241A PHE* 3.4 5.0 - - - -
242A ILE* 2.9 59.0 + - + +
244A PHE* 4.8 9.2 - - + -
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Residues in contact with GLU 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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215A VAL* 1.3 76.3 - - - +
217A LEU* 1.3 62.4 + - - +
218A MSE 3.8 38.0 - - + +
239A THR* 3.9 16.5 + - + +
240A ALA 3.5 3.1 - - - -
241A PHE* 3.6 39.2 - - + -
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Residues in contact with LEU 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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215A VAL* 3.9 9.8 - - + -
216A GLU* 1.3 76.0 - - - +
218A MSE 1.3 68.4 + - - +
238A HIS 3.8 0.7 - - - +
239A THR* 3.3 3.6 - - - +
240A ALA* 2.9 42.0 + - + +
242A ILE* 3.9 26.9 - - + -
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Residues in contact with MSE 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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216A GLU* 3.8 46.1 + - + +
217A LEU* 1.3 81.9 - - - +
219A LYS* 1.3 61.7 + - - +
237A THR* 4.0 12.6 - - - +
238A HIS 3.3 3.1 - - - -
239A THR* 3.3 26.7 - - + +
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Residues in contact with LYS 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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217A LEU 4.3 0.4 - - - -
218A MSE 1.3 75.8 - - - +
220A ARG* 1.3 64.5 + - - +
221A ARG* 4.4 24.2 - - - +
237A THR* 3.4 2.9 + - - -
238A HIS* 2.8 68.3 + - + +
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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