Contacts of the helix formed by residues 218 - 228 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133N ASP* 3.1 22.2 - - + +
141N GLY 4.9 0.7 - - - +
144N CYS 4.5 0.7 - - - +
145N GLY* 3.6 33.0 - - - +
148N LEU* 4.4 6.7 - - + +
214N LEU 3.0 13.2 + - - +
215N LYS 3.4 5.7 - - - +
217N TYR* 1.3 78.2 - - - +
219N PRO* 1.3 64.8 - - - +
221N LEU* 3.7 6.2 - - + +
222N ASP* 3.3 17.2 + - - +
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Residues in contact with PRO 219 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52M SER* 5.8 8.7 - - - -
132N ASN* 4.8 3.8 - - - +
133N ASP* 3.2 12.3 - - + +
136N ILE* 4.7 13.5 - - + -
215N LYS 3.3 13.0 - - - +
216N ARG* 4.1 8.1 - - - +
217N TYR 3.4 9.2 - - - +
218N ALA* 1.3 89.3 - - - +
220N LYS* 1.3 64.1 + - + +
222N ASP* 3.2 7.2 + - + +
223N GLU* 3.0 28.4 + - - +
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Residues in contact with LYS 220 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31M GLN* 5.8 2.2 - - - +
50M SER* 3.1 23.3 - - - +
51M ILE 5.6 3.6 - - - +
82M TYR* 3.3 19.6 + - - +
83M TYR* 3.5 27.0 + - + +
129N ALA* 3.5 15.3 - - + +
132N ASN* 3.2 23.8 - - + +
133N ASP* 3.1 16.7 + - - +
219N PRO* 1.3 82.9 - - + +
221N LEU* 1.3 58.0 + - - +
223N GLU* 2.6 43.9 + - - +
224N TRP* 2.9 27.9 + - - +
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Residues in contact with LEU 221 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126N TYR* 4.2 16.6 - - + -
129N ALA* 3.9 12.3 - - + +
130N LYS* 4.0 19.5 - - - +
133N ASP* 2.6 23.0 + - + +
134N PHE* 4.2 12.8 - - + -
145N GLY* 3.7 35.7 - - - +
148N LEU* 4.3 8.7 - - + -
149N ILE* 3.9 28.0 - - + -
218N ALA* 3.7 7.4 - - + +
220N LYS* 1.3 70.3 - - - +
222N ASP* 1.3 66.2 + - - +
224N TRP* 3.2 12.2 + - + +
225N PHE* 3.1 25.7 + - + -
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Residues in contact with ASP 222 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148N LEU* 4.0 18.9 - - + +
152N TYR* 2.9 28.6 + - - -
215N LYS* 3.4 27.6 + - + +
218N ALA 3.3 10.1 + - - +
219N PRO* 3.2 11.3 + - + +
221N LEU* 1.3 77.5 - - - +
223N GLU* 1.3 65.7 + - - +
225N PHE* 3.1 14.9 + - - +
226N TYR* 3.2 9.4 + - - +
233N TRP* 3.0 19.6 + - - -
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Residues in contact with GLU 223 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81M GLY* 3.9 4.5 - - - -
82M TYR* 2.9 44.7 + - + +
83M TYR* 5.2 0.3 + - - -
219N PRO 3.0 16.7 + - - +
220N LYS* 2.6 43.6 + - - +
222N ASP* 1.3 81.0 + - - +
224N TRP* 1.3 65.1 + - - +
226N TYR* 3.0 18.7 + - + +
227N LEU* 3.1 26.8 + - + +
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Residues in contact with TRP 224 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80M VAL 4.1 7.9 - - - -
122N LYS* 3.2 31.2 - - + -
125N SER* 2.5 47.6 + - - -
126N TYR* 3.3 37.3 - + + +
129N ALA* 4.2 7.6 - - + -
220N LYS 2.9 15.5 + - - +
221N LEU* 3.2 11.2 + - + +
223N GLU* 1.3 77.2 - - - +
225N PHE* 1.3 92.3 + + - +
227N LEU* 3.2 4.2 + - - +
228N ALA* 2.7 47.6 + - + +
229N CYS* 4.3 18.2 - - - -
301N GSH 3.9 18.4 - - + -
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Residues in contact with PHE 225 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126N TYR* 5.1 1.1 - + - -
148N LEU* 4.4 4.9 - - + -
149N ILE* 4.3 38.4 - - + -
152N TYR* 3.4 35.7 - + + -
153N VAL* 4.0 23.3 - - + -
221N LEU* 3.1 26.6 + - + -
222N ASP 3.1 8.8 + - - +
224N TRP* 1.3 107.3 - + - +
226N TYR* 1.3 55.5 + - - +
228N ALA 2.9 10.7 - - - +
229N CYS* 2.9 26.9 - - + +
230N PRO* 3.2 4.0 - - - +
232N THR* 4.0 16.6 - - - -
233N TRP* 3.1 24.4 - - + +
301N GSH 5.0 1.3 - - - -
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Residues in contact with TYR 226 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82M TYR* 4.7 9.2 - + - -
222N ASP* 3.2 10.4 + - - +
223N GLU* 3.0 14.4 + - + +
225N PHE* 1.3 79.5 - - - +
227N LEU* 1.3 79.9 + - + +
230N PRO* 3.7 16.9 - - + +
233N TRP* 3.9 45.5 - + + +
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Residues in contact with LEU 227 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73M PHE* 4.1 5.2 - - - -
78M THR* 4.6 12.9 + - - +
79M SER* 3.6 27.3 - - - +
80M VAL 4.2 5.8 - - - +
81M GLY* 3.6 32.5 - - - +
82M TYR* 3.4 36.1 - - + +
223N GLU* 3.1 29.7 + - + +
224N TRP* 4.1 2.7 - - - +
226N TYR* 1.3 101.8 - - + +
228N ALA* 1.3 58.8 + - - +
230N PRO* 4.7 7.0 - - - +
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Residues in contact with ALA 228 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73M PHE* 3.7 26.2 - - + -
80M VAL 5.8 0.2 - - - +
122N LYS* 4.3 14.6 - - + -
224N TRP* 2.7 45.1 + - + +
225N PHE* 2.9 15.4 - - - +
227N LEU* 1.3 73.9 - - + +
229N CYS* 1.3 68.6 + - - +
230N PRO* 3.4 1.8 - - - -
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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