Contacts of the helix formed by residues 218 - 228 (chain A) in PDB entry 5X6E
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 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A ASP* 3.1 17.0 - - + +
141A GLY 5.2 0.2 - - - +
144A CYS 4.4 1.6 - - - +
145A GLY* 4.1 24.5 - - - -
148A LEU* 4.2 10.6 - - + +
214A LEU 2.9 13.6 + - - +
215A LYS* 3.4 8.4 - - - +
217A TYR* 1.3 81.2 - - - +
219A PRO* 1.3 61.4 - - - +
221A LEU* 4.2 12.1 - - + -
222A ASP* 3.5 18.7 + - - +
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Residues in contact with PRO 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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133A ASP* 3.3 16.8 - - - +
136A ILE* 6.0 3.8 - - + -
137A ASN* 6.2 0.2 - - - +
215A LYS* 3.2 16.4 - - + +
216A ARG* 3.7 10.8 - - - +
217A TYR 3.5 5.8 - - - +
218A ALA* 1.3 87.6 - - - +
220A LYS* 1.3 62.5 + - + +
222A ASP* 3.6 7.4 + - + +
223A GLU* 3.4 23.9 + - - +
52B SER* 5.1 12.8 - - - +
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Residues in contact with LYS 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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129A ALA* 3.6 16.1 - - - +
132A ASN* 3.4 26.0 - - + +
133A ASP* 2.8 24.1 + - - +
219A PRO* 1.3 76.1 - - + +
221A LEU* 1.3 54.8 + - - +
223A GLU* 3.2 25.5 + - + +
224A TRP* 3.0 25.1 + - - +
50B SER* 3.4 21.8 - - - +
81B GLY* 4.5 1.8 - - - -
82B TYR* 2.9 43.1 + - - +
83B TYR* 3.6 25.2 - - + +
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Residues in contact with LEU 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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126A TYR* 5.1 6.7 - - + +
129A ALA* 3.2 20.0 - - + +
130A LYS* 3.5 28.7 - - + +
133A ASP* 3.1 34.9 + - + +
134A PHE* 4.8 6.5 - - + -
145A GLY* 4.4 5.6 - - - +
148A LEU* 4.2 10.8 - - + -
149A ILE* 3.5 38.8 - - + -
218A ALA* 3.7 11.0 + - + +
219A PRO 3.4 0.2 - - - -
220A LYS* 1.3 75.6 - - - +
222A ASP* 1.3 65.4 - - - +
224A TRP* 3.2 11.6 + - + +
225A PHE* 3.0 31.6 + - + -
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Residues in contact with ASP 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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148A LEU* 4.2 9.7 - - + +
152A TYR* 3.2 0.7 + - - -
215A LYS* 2.8 39.9 + - + +
218A ALA 3.5 11.2 + - - +
219A PRO* 3.7 10.1 - - + +
220A LYS 3.4 0.4 - - - -
221A LEU* 1.3 77.1 - - - +
223A GLU* 1.3 61.9 + - - +
225A PHE* 2.9 21.6 + - - +
226A TYR* 3.1 10.3 + - - +
233A TRP* 2.4 39.8 + - - -
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Residues in contact with GLU 223 (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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219A PRO 3.4 11.7 + - - +
220A LYS* 3.2 38.0 + - + +
221A LEU 3.2 0.2 - - - -
222A ASP* 1.3 81.8 - - - +
224A TRP* 1.3 57.3 + - - +
226A TYR* 3.2 7.0 + - + +
227A LEU* 2.9 42.0 + - + +
81B GLY* 5.7 1.2 - - - -
82B TYR* 3.1 40.8 + - + +
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Residues in contact with TRP 224 (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 LYS* 3.2 24.7 - - + -
125A SER* 2.5 39.7 + - - -
126A TYR* 3.0 46.5 - + + +
129A ALA* 4.1 9.6 - - + -
220A LYS 3.0 13.4 + - - +
221A LEU* 3.2 12.1 + - + +
223A GLU* 1.3 76.3 - - - +
225A PHE* 1.3 98.5 + + - +
227A LEU* 4.7 4.7 - - - +
228A ALA* 2.8 33.4 + - + +
229A CYS* 3.6 26.5 - - - -
301A GSH 4.3 17.9 - - + -
73B PHE* 5.7 0.2 - + - -
80B VAL 4.5 6.7 - - - -
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Residues in contact with PHE 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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126A TYR* 5.4 1.3 - + - -
148A LEU* 4.1 5.2 - - + -
149A ILE* 4.0 35.7 - - + -
152A TYR* 3.5 46.4 - + + -
153A VAL* 4.1 16.8 - - + -
221A LEU* 3.0 25.8 + - + -
222A ASP* 2.9 11.0 + - - +
224A TRP* 1.3 102.8 - + - +
226A TYR* 1.3 54.4 + - - +
228A ALA 2.7 18.6 - - - +
229A CYS* 2.8 31.1 - - + +
232A THR* 5.1 4.5 - - + -
233A TRP* 3.0 25.7 - - + +
301A GSH 5.2 1.8 - - - -
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Residues in contact with TYR 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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222A ASP* 3.1 9.5 + - - +
223A GLU* 3.2 10.9 + - + +
225A PHE* 1.3 78.3 - - - +
227A LEU* 1.3 83.0 + - + +
230A PRO* 3.7 20.6 - - + +
233A TRP* 3.3 50.9 - + + -
82B TYR* 5.3 3.4 - - - -
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Residues in contact with LEU 227 (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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223A GLU* 2.9 25.6 + - + +
224A TRP* 4.5 3.4 - - + +
226A TYR* 1.3 96.3 - - + +
228A ALA* 1.3 57.9 + - - +
230A PRO* 3.8 10.7 - - - +
73B PHE* 4.4 5.4 - - + -
76B THR* 5.1 1.9 + - - +
78B THR* 3.8 19.6 + - - +
79B SER* 3.3 33.2 - - - +
80B VAL* 3.8 4.0 - - - +
81B GLY* 3.4 30.3 - - - +
82B TYR* 3.5 37.2 - - + +
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Residues in contact with ALA 228 (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 LYS* 4.0 16.6 - - + -
224A TRP* 2.8 33.6 + - + +
225A PHE 2.7 28.4 - - - +
227A LEU* 1.3 79.3 - - - +
229A CYS* 1.3 57.3 + - - +
230A PRO* 3.3 2.4 - - - -
73B PHE* 3.4 30.9 - - + -
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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