Contacts of the strand formed by residues 219 - 226 (chain A) in PDB entry 5R52
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 ALA 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.0 10.3 - - + -
63A LEU* 3.4 37.7 - - + -
119A ASP* 5.3 3.4 + - + +
120A PRO 3.5 9.4 + - - +
121A LEU* 3.6 4.6 - - + -
122A GLY 3.0 19.2 + - - -
156A HIS* 5.4 0.3 + - - -
209A ILE* 3.9 7.6 - - + -
210A ALA 3.3 11.0 - - - +
211A ARG* 4.2 0.7 - - - +
217A GLY 3.5 3.3 + - - +
218A ARG* 1.3 75.2 + - - +
220A SER* 1.3 62.5 + - - +
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Residues in contact with SER 220 (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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121A LEU* 4.3 0.2 - - - -
122A GLY* 3.3 22.2 + - - -
123A VAL 4.6 0.8 + - - -
156A HIS* 4.8 5.4 + - - -
209A ILE* 3.4 6.5 - - - -
210A ALA* 2.8 32.9 + - - -
218A ARG* 5.2 4.3 + - - -
219A ALA* 1.3 75.8 + - - +
221A ALA* 1.3 62.2 + - - +
222A GLU* 3.3 23.9 + - - +
274A SER* 4.2 17.0 - - - -
405A DMS 4.7 3.9 - - - +
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Residues in contact with ALA 221 (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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121A LEU* 3.9 17.1 - - + +
122A GLY 2.8 14.1 + - - +
123A VAL* 3.2 7.2 - - + -
124A GLY 2.9 24.4 + - - -
182A LEU* 6.1 2.2 - - + -
206A LEU* 3.9 12.6 - - + -
208A GLY 3.7 5.6 - - - -
209A ILE* 4.3 9.6 - - + -
220A SER* 1.3 69.9 - - - +
222A GLU* 1.3 58.9 + - - +
223A PHE* 3.6 24.0 - - + -
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Residues in contact with GLU 222 (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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124A GLY* 3.3 20.3 - - - -
206A LEU* 3.6 2.6 - - - +
207A LEU* 2.8 36.1 + - + +
208A GLY 2.9 10.4 + - - +
210A ALA* 4.6 5.2 - - + +
220A SER* 3.3 30.0 - - - +
221A ALA* 1.3 76.1 - - - +
223A PHE* 1.3 53.8 + - - +
274A SER* 3.3 23.3 - - - +
277A GLY 4.2 2.0 - - - -
278A ALA* 3.4 33.0 - - + +
281A LEU* 4.0 26.7 - - + -
405A DMS 3.4 7.2 - - - +
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Residues in contact with PHE 223 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A VAL* 3.9 15.9 - - + -
124A GLY 2.9 14.9 + - - +
125A ALA* 3.3 2.2 - - - -
126A ALA* 2.9 26.2 + - - -
182A LEU* 4.4 18.8 - - + -
183A PHE* 3.8 39.7 - + - -
186A VAL* 4.1 21.1 - - + -
204A PRO* 3.8 24.7 - - + -
205A LEU 3.2 14.6 - - - +
206A LEU* 3.9 18.2 - - + -
207A LEU* 3.9 7.6 - - - +
221A ALA* 3.6 33.4 - - + -
222A GLU* 1.3 74.7 - - - +
224A TYR* 1.3 60.0 + - - +
225A VAL* 4.7 1.8 - - + -
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Residues in contact with TYR 224 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A ALA 3.5 13.9 - - - -
128A ALA* 3.9 20.0 - - + +
134A LEU* 5.3 0.2 - - + -
202A SER* 4.8 0.3 + - - -
203A GLN 4.5 1.0 - - - +
204A PRO* 3.5 1.6 - - - +
205A LEU* 2.8 46.9 + - + +
207A LEU* 3.9 23.0 - - + +
223A PHE* 1.3 73.5 - - - +
225A VAL* 1.3 65.6 + - - +
226A GLN* 3.0 31.0 + - + -
282A TYR* 3.8 32.2 + + - -
286A GLN* 3.5 35.4 + - + -
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Residues in contact with VAL 225 (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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125A ALA* 4.5 9.6 - - + -
126A ALA 3.0 8.6 + - - +
127A LEU* 3.3 22.9 - - + +
128A ALA* 2.9 25.8 + - - +
186A VAL* 4.8 2.7 - - + -
187A LEU* 4.1 11.7 - - + -
190A ILE* 4.2 18.6 - - + -
201A LEU* 4.2 6.7 - - + -
202A SER* 3.8 21.1 - - - +
204A PRO* 3.9 25.6 - - + -
223A PHE* 4.7 3.4 - - + -
224A TYR* 1.3 84.5 - - - +
226A GLN* 1.3 68.7 + - - +
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Residues in contact with GLN 226 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A ALA* 3.3 14.2 + - - +
129A THR 3.1 27.1 + - - -
130A ALA* 3.9 4.0 + - - +
132A ASP* 5.5 2.8 + - - +
200A THR 3.8 0.3 - - - +
201A LEU* 3.6 3.5 - - - -
202A SER* 2.8 45.9 + - - +
224A TYR* 3.0 30.1 + - + +
225A VAL* 1.3 76.6 - - - +
227A CYS* 1.3 77.4 + - - +
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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