Contacts of the strand formed by residues 181 - 191 (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 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A MSE 3.3 16.8 - - - +
160A TYR 4.0 4.3 - - - +
163A VAL* 3.7 18.8 - - + -
177A ILE* 3.3 22.9 - - - +
178A ALA* 3.1 13.2 + - - +
179A SER 3.5 0.2 - - - -
180A MSE 1.3 77.2 - - - +
182A LYS* 1.3 63.8 + - - +
183A PRO 3.5 0.3 - - - -
185A SER* 3.3 36.6 - - - +
186A VAL 3.5 3.6 - - - +
187A ALA* 3.4 32.8 - - + +
209A MSE 3.7 25.1 - - - +
245A ALA 4.3 0.9 - - - +
247A LYS* 3.3 32.0 + - + +
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Residues in contact with LYS 182 (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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93A ASP* 4.9 5.3 + - - -
159A MSE 3.7 34.0 + - + -
160A TYR 3.1 17.6 + - - +
161A ASP* 2.6 37.8 + - - +
180A MSE 4.1 0.8 + - - -
181A MSE 1.3 71.8 - - - +
183A PRO* 1.3 79.5 - - + +
184A GLY 3.3 0.2 + - - -
185A SER* 2.7 29.7 + - - -
247A LYS* 3.6 3.7 - - - +
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Residues in contact with PRO 183 (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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42A PRO* 3.4 30.4 - - - +
159A MSE 4.9 7.6 - - + -
181A MSE 3.5 3.5 - - - +
182A LYS* 1.3 90.2 - - + +
184A GLY* 1.3 60.5 + - - +
185A SER 3.4 0.3 + - - -
247A LYS* 3.8 15.7 - - + +
248A LYS 5.1 0.7 - - - +
249A SER* 3.9 26.5 - - - +
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Residues in contact with GLY 184 (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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42A PRO* 4.1 7.2 - - - -
43A GLY* 3.7 18.0 - - - -
55A VAL 4.4 0.9 - - - -
56A SER* 4.0 9.1 + - - -
57A ASP 5.3 1.2 + - - -
182A LYS 3.3 0.2 + - - -
183A PRO* 1.3 70.8 - - - +
185A SER* 1.3 61.4 + - - +
186A VAL* 4.6 3.8 - - - +
246A ILE* 3.5 22.8 - - - +
247A LYS 2.8 19.5 + - - -
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Residues in contact with SER 185 (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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160A TYR 3.8 5.7 + - - -
161A ASP* 3.3 27.3 - - - -
162A ALA* 5.1 0.5 - - - -
181A MSE 3.3 24.7 - - - +
182A LYS* 2.7 29.6 + - - -
183A PRO 3.2 1.2 + - - -
184A GLY* 1.3 79.6 - - - +
186A VAL* 1.3 59.4 + - - +
246A ILE* 3.4 3.8 - - - -
247A LYS 2.9 25.3 + - - -
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Residues in contact with VAL 186 (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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59A SER* 6.0 2.0 - - - +
61A MSE 4.3 23.3 - - + -
62A TYR* 3.4 27.1 - - + +
86A CYS* 5.6 4.5 - - + -
161A ASP 4.3 3.2 + - - -
162A ALA* 3.5 9.6 - - + +
163A VAL 3.2 20.4 + - - +
181A MSE 3.5 3.7 - - - +
184A GLY 4.6 4.3 - - - +
185A SER* 1.3 80.2 - - - +
187A ALA* 1.3 74.9 + - - +
188A THR* 4.4 3.9 + - - +
212A LEU* 4.4 4.5 - - + -
244A PHE* 4.3 11.9 - - + -
245A ALA 3.2 13.9 - - - +
246A ILE* 4.7 2.5 - - + -
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Residues in contact with ALA 187 (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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163A VAL* 3.3 17.5 - - + +
177A ILE* 4.9 0.7 - - + -
181A MSE 3.4 26.2 - - + +
186A VAL* 1.3 75.4 - - - +
188A THR* 1.3 61.3 + - - +
189A PHE* 3.8 25.9 - - + -
209A MSE 4.1 5.8 - - - -
243A THR 3.6 1.2 - - - +
244A PHE* 3.4 5.0 - - - -
245A ALA 2.8 31.1 + - - +
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Residues in contact with THR 188 (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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86A CYS* 4.4 13.4 - - + +
163A VAL 2.8 13.6 + - - -
164A ILE* 3.6 11.4 - - + +
165A ALA* 2.8 33.6 + - - +
186A VAL* 4.4 4.9 + - - +
187A ALA* 1.3 74.6 - - - +
189A PHE* 1.3 59.8 + - - +
190A TYR* 3.7 21.3 - - + +
242A ILE* 3.6 26.7 - - + -
243A THR 3.4 3.1 - - - -
244A PHE* 3.3 25.8 - - + -
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Residues in contact with PHE 189 (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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163A VAL* 6.1 0.2 - - + -
165A ALA* 3.5 15.5 - - + -
170A PRO* 3.6 31.0 - - + -
174A VAL* 4.2 10.8 - - + -
177A ILE* 4.1 21.1 - - + -
187A ALA* 3.8 26.5 - - + -
188A THR* 1.3 73.8 - - - +
190A TYR* 1.3 61.7 + - - +
191A LEU* 3.8 17.5 - - + +
200A THR* 4.1 6.1 - - + -
204A LEU* 4.1 16.8 - - + -
209A MSE 4.0 24.9 - - + -
241A PHE 3.5 1.7 - - - +
242A ILE* 3.4 5.9 - - - +
243A THR* 2.8 57.9 + - + +
245A ALA* 4.5 2.7 - - + -
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Residues in contact with TYR 190 (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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104A MSE 4.9 13.1 - - + -
164A ILE* 4.4 18.6 - - + -
165A ALA 2.9 20.9 + - - +
166A ASP* 3.9 31.0 - - + +
167A ILE 4.4 4.2 - - - +
170A PRO* 5.7 0.2 - - - +
188A THR* 3.7 26.2 - - + +
189A PHE* 1.3 75.2 - - - +
191A LEU* 1.3 69.0 + - - +
192A PRO* 4.9 0.2 - - - +
240A ALA* 4.5 13.0 - - + -
241A PHE 3.6 1.8 - - - -
242A ILE* 3.6 34.5 - - + +
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Residues in contact with LEU 191 (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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167A ILE 4.2 2.9 - - - +
168A PRO 4.1 3.1 - - - +
170A PRO* 3.9 28.0 - - + -
171A TRP* 4.2 0.2 - - + -
189A PHE* 3.8 25.8 - - + +
190A TYR* 1.3 82.8 - - - +
192A PRO* 1.3 68.0 - - + +
193A ASN 3.4 4.5 - - - +
196A GLN* 3.8 24.5 - - + +
197A SER* 3.9 25.1 - - - +
200A THR* 3.5 23.6 - - + +
240A ALA* 4.0 3.3 - - - +
241A PHE* 2.9 37.3 + - + +
243A THR* 5.0 3.6 - - - +
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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