Contacts of the strand formed by residues 189 - 195 (chain A) in PDB entry 1YI1
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 LEU 189 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A VAL* 4.4 21.8 - - + -
151A ALA* 3.6 33.0 - - + +
152A GLU* 4.1 11.4 - - + +
161A PRO* 4.7 1.1 - - - +
162A GLY* 3.5 22.4 - - - +
164A CYS* 5.1 3.1 - - - -
178A GLY 4.5 2.9 - - - +
179A LEU* 4.4 9.4 - - + -
182A ALA* 3.6 21.5 - - + -
187A VAL* 3.1 11.5 + - + +
188A PRO* 1.3 74.9 - - - +
190A VAL* 1.3 73.9 + - - +
191A ALA 5.2 0.4 - - - +
242A ALA* 3.4 7.0 - - - +
248A GLY 3.3 4.2 + - - -
249A PRO* 3.4 15.7 - - + +
250A VAL 3.0 22.5 + - - -
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Residues in contact with VAL 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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161A PRO* 5.0 3.6 - - + -
162A GLY 2.8 12.6 + - - +
163A ILE* 3.3 16.3 - - + +
164A CYS 3.2 23.0 + - - +
189A LEU* 1.3 81.4 - - - +
191A ALA* 1.3 63.0 + - - +
192A ILE* 4.4 18.8 - - + -
235A ILE* 5.7 1.6 - - + -
238A ALA* 4.2 16.6 - - + +
239A PHE* 4.1 40.4 - - + -
242A ALA* 3.9 17.0 - - + -
250A VAL* 3.3 9.2 - - + +
252A VAL* 5.2 3.6 - - + -
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Residues in contact with ALA 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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164A CYS* 3.3 25.1 - - - +
175A LEU* 4.6 10.3 - - + -
179A LEU* 4.1 22.7 - - + -
189A LEU* 4.2 1.3 - - + +
190A VAL* 1.3 73.4 - - - +
192A ILE* 1.3 64.0 + - - +
250A VAL 2.9 10.2 + - - +
251A LEU* 3.2 13.2 - - + +
252A VAL* 2.8 27.9 + - - +
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Residues in contact with ILE 192 (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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103A LEU* 3.8 44.0 - - + -
107A LEU* 4.2 24.7 - - + -
126A ILE* 4.1 18.6 - - + -
163A ILE* 4.9 2.9 - - + -
164A CYS 3.0 6.4 + - - +
165A ILE* 3.2 23.9 - - + +
166A ALA 2.8 24.3 + - - -
175A LEU* 5.2 0.3 - - - +
190A VAL* 4.4 13.0 - - + +
191A ALA* 1.3 78.9 - - - +
193A THR* 1.3 64.7 + - - +
235A ILE* 4.4 7.0 - - + -
252A VAL* 3.5 16.8 - - + +
254A VAL* 4.1 5.8 - - + -
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Residues in contact with THR 193 (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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166A ALA* 3.1 9.2 - - + -
167A THR 4.1 3.1 - - - -
172A ALA* 3.9 20.6 - - + -
175A LEU* 3.5 32.3 - - + -
191A ALA 4.2 0.4 - - - -
192A ILE* 1.3 79.8 - - - +
194A GLY* 1.3 67.0 + - - +
211A ILE* 4.0 3.8 - - - +
251A LEU* 4.0 18.8 - - + +
252A VAL 3.1 8.5 + - - +
253A ASP* 2.9 24.0 + - - +
254A VAL* 2.9 27.3 + - - +
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Residues in contact with GLY 194 (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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122A ALA* 3.9 11.9 - - - -
123A SER* 4.4 5.0 - - - -
126A ILE* 5.1 3.0 - - - +
166A ALA 2.9 14.0 + - - -
167A THR 3.7 0.9 - - - -
168A SER* 3.2 25.7 - - - -
172A ALA* 5.5 0.2 - - - +
193A THR* 1.3 80.0 - - - +
195A GLN* 1.3 60.2 - - - +
211A ILE* 5.9 0.2 - - - +
253A ASP* 3.7 3.3 - - - +
254A VAL* 3.5 8.7 - - - -
259A GLN* 3.9 12.6 - - - -
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Residues in contact with GLN 195 (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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122A ALA* 4.0 8.9 - - - +
168A SER* 3.9 6.7 - - - -
194A GLY* 1.3 75.0 - - - -
196A VAL* 1.3 113.1 + - + +
201A ILE* 4.1 18.6 - - + +
208A GLU* 3.7 17.2 - - - +
209A THR 3.4 20.3 - - - +
210A PRO* 5.3 0.5 - - - +
211A ILE* 4.5 1.4 + - - +
224A LEU* 4.8 0.2 - - + -
253A ASP* 3.2 34.7 - - - +
254A VAL 3.0 6.3 + - - +
255A PRO* 3.9 14.4 - - + -
256A LYS* 2.8 28.4 + - - +
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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