Contacts of the strand formed by residues 187 - 193 (chain A) in PDB entry 4JYY
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 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A VAL* 3.2 3.7 - - - -
164A ALA* 2.8 42.1 + - - -
166A LYS* 4.0 16.1 + - - +
182A VAL* 5.5 0.4 - - - -
186A LEU* 1.3 72.9 - - - +
188A PRO* 1.3 78.5 - - + +
189A ILE* 3.4 11.7 + - + +
226A ASN* 4.2 9.9 - - + +
229A ASN* 6.2 0.9 - - + -
230A LEU* 3.3 29.6 - - + +
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Residues in contact with PRO 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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109A TYR* 4.1 18.2 - - + +
113A PHE* 3.5 30.0 - - + -
161A TRP* 3.9 22.0 - - + -
162A LEU 3.7 5.6 - - - +
163A VAL* 4.3 5.1 - - + -
181A PRO* 4.6 11.7 - - + -
182A VAL* 3.9 23.3 - - + -
186A LEU 3.6 8.3 - - - +
187A THR* 1.3 90.5 - - + +
189A ILE* 1.3 64.6 + - - +
226A ASN* 3.8 8.3 - - - +
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Residues in contact with ILE 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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113A PHE* 3.6 1.5 - - - -
117A ILE* 3.5 4.5 - - - +
129A LEU* 3.9 23.8 - - + -
162A LEU* 2.7 32.5 + - + +
164A ALA* 4.0 19.1 - - + +
170A LEU* 4.1 14.8 - - + -
187A THR* 3.6 20.0 - - + +
188A PRO* 1.3 79.0 - - - +
190A ILE* 1.3 65.6 + - - +
223A ALA* 3.5 22.7 - - + +
226A ASN* 3.0 26.1 + - - -
227A TYR* 3.8 28.3 - - + +
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Residues in contact with ILE 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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113A PHE* 3.9 6.1 - - - -
117A ILE* 3.9 18.2 - - + -
143A PHE* 3.9 24.9 - - + -
147A PHE* 4.1 10.3 - - + -
161A TRP* 3.5 5.4 - - - -
162A LEU* 2.9 40.6 + - + +
189A ILE* 1.3 86.5 + - + +
191A GLY* 1.3 59.1 + - - +
214A TRP* 4.0 24.7 - - + -
215A PHE* 4.6 2.7 - - + -
218A VAL* 4.1 11.7 - - + -
220A TRP* 3.9 19.7 - - + -
223A ALA* 3.6 22.0 - - + -
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Residues in contact with GLY 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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113A PHE* 3.7 7.4 - - - -
114A PHE* 3.3 21.0 - - - -
117A ILE* 3.8 5.4 - - - +
147A PHE* 4.6 0.4 - - - -
159A TRP* 4.5 4.0 - - - -
160A ALA 3.1 11.4 - - - -
161A TRP* 3.6 17.9 - - - -
190A ILE* 1.3 79.6 - - - +
192A LEU* 1.3 59.4 + - - -
214A TRP* 3.3 12.9 - - - -
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Residues in contact with LEU 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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114A PHE* 3.8 1.1 - - + -
147A PHE* 3.9 19.2 - - + -
151A ALA* 4.1 9.6 - - + -
159A TRP* 3.3 6.5 - - - -
160A ALA* 2.8 34.7 + - + +
191A GLY* 1.3 74.3 - - - -
193A ASP* 1.3 66.6 + - - +
194A VAL* 3.4 11.2 + - + +
210A TYR* 3.4 29.4 - - + +
211A ILE* 3.8 38.8 - - + -
214A TRP* 3.4 43.3 - - + +
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Residues in contact with ASP 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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56A HIS* 2.9 9.5 + - - -
111A HIS* 3.5 2.8 + - - -
114A PHE* 3.5 20.7 - - + -
159A TRP* 3.4 33.6 - - + -
192A LEU* 1.3 70.1 - - - +
194A VAL* 1.3 58.2 + - - +
195A TRP* 3.0 32.1 + - - +
198A ALA* 3.6 11.9 - - + +
210A TYR* 2.9 26.2 + - - -
301A FE 2.0 32.3 - - - -
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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