Contacts of the helix formed by residues 253 - 266 (chain A) in PDB entry 1XXE
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 HIS 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A THR* 5.0 2.5 - - - -
57A ASN 3.1 23.6 - - - +
58A HIS* 3.0 29.2 + - - -
59A SER 3.8 4.7 - - - +
60A THR* 3.6 7.0 + - + +
73A GLU* 2.6 38.4 + - - -
227A LYS* 4.0 19.4 + - - -
230A ASP* 3.5 18.4 + - + -
234A ASP* 2.9 25.9 + - - +
252A GLY* 1.3 71.7 - - - -
254A SER* 1.3 68.5 + - - +
256A ASN* 3.1 4.7 + - - +
257A VAL* 2.8 27.7 + - - +
320A TUX 4.0 4.1 + - - -
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Residues in contact with SER 254 (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 THR* 3.2 38.8 + - - -
57A ASN* 4.4 2.9 + - - -
135A GLU* 5.4 7.4 - - - -
252A GLY 3.6 0.2 - - - -
253A HIS* 1.3 79.1 - - - +
255A LEU* 1.3 65.5 + - - +
257A VAL* 3.1 5.6 + - - +
258A LYS* 2.9 22.3 + - - +
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Residues in contact with LEU 255 (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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132A VAL* 3.7 26.9 - - + +
134A ASP* 4.2 23.3 - - + +
135A GLU* 5.7 4.4 + - - +
137A ARG* 3.7 36.1 - - + +
138A LEU* 3.9 9.0 - - - +
139A ILE* 3.7 29.1 - - + +
251A GLY* 4.6 2.7 - - - -
252A GLY* 4.0 13.3 + - - +
253A HIS 3.3 0.6 - - - -
254A SER* 1.3 78.3 - - - +
256A ASN* 1.3 66.7 + - - +
258A LYS* 3.1 29.5 + - + +
259A LEU* 3.2 5.7 + - - +
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Residues in contact with ASN 256 (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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139A ILE* 2.7 30.0 - - - +
227A LYS* 5.3 7.1 - - - +
230A ASP* 6.1 0.2 - - - +
231A LEU* 3.3 40.3 - - + +
234A ASP* 4.2 15.5 + - + -
235A LEU* 5.9 0.2 - - - +
248A SER* 3.9 1.6 + - - -
251A GLY 4.4 3.1 + - - -
252A GLY* 2.6 31.5 + - - +
253A HIS* 3.1 10.2 + - - +
255A LEU* 1.3 74.8 - - - +
257A VAL* 1.3 65.1 + - - +
259A LEU* 2.8 22.9 + - - +
260A VAL* 3.2 9.1 + - - +
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Residues in contact with VAL 257 (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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50A HIS* 5.1 3.1 - - + -
53A VAL* 4.3 18.2 - - + -
56A THR* 4.4 12.3 - - + -
60A THR* 4.6 4.9 - - + -
234A ASP* 4.5 10.5 - - + +
237A LEU* 3.9 23.6 - - + -
253A HIS 2.8 18.1 + - - +
254A SER* 3.5 9.6 - - - +
256A ASN* 1.3 73.4 - - - +
258A LYS* 1.3 58.3 + - - +
260A VAL* 2.9 11.4 + - - +
261A LYS* 2.7 56.9 + - + +
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Residues in contact with LYS 258 (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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132A VAL* 5.1 13.0 - - + +
133A GLU 5.6 2.4 + - - -
134A ASP* 4.5 16.2 + - + +
254A SER 2.9 12.4 + - - +
255A LEU* 3.1 28.5 - - + +
256A ASN 3.0 0.2 + - - -
257A VAL* 1.3 77.8 - - - +
259A LEU* 1.3 64.2 + - - +
261A LYS* 2.9 11.5 + - + +
262A GLU* 2.9 31.7 + - + +
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Residues in contact with LEU 259 (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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130A ILE* 4.0 22.6 - - + +
132A VAL* 4.5 19.6 - - + +
139A ILE* 4.3 26.2 - - + +
141A ALA* 3.9 22.9 - - + +
231A LEU* 5.7 4.7 - - + -
235A LEU* 4.2 17.9 - - + -
246A PHE* 4.1 26.2 - - + -
255A LEU 3.2 6.0 + - - +
256A ASN* 2.8 12.9 + - - +
258A LYS* 1.3 79.8 - - - +
260A VAL* 1.3 60.6 + - - +
262A GLU* 3.3 2.1 + - - +
263A LEU* 2.9 37.6 + - + +
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Residues in contact with VAL 260 (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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50A HIS* 4.0 24.0 - - + -
234A ASP 3.5 23.1 - - - +
235A LEU* 3.5 31.0 - - + +
237A LEU* 4.4 5.8 - - + -
238A LEU* 3.5 27.4 - - + -
256A ASN 3.2 8.7 + - - +
257A VAL* 2.9 11.7 + - - +
259A LEU* 1.3 77.4 - - + +
261A LYS* 1.3 58.5 + - - +
263A LEU* 3.6 7.7 - - - +
264A ALA* 2.7 29.3 + - - +
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Residues in contact with LYS 261 (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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50A HIS* 3.6 48.3 + - + +
51A GLU* 4.4 5.3 - - - +
53A VAL* 3.7 20.2 + - - +
257A VAL* 2.7 34.0 + - + +
258A LYS* 3.2 16.2 - - + +
260A VAL* 1.3 74.5 - - - +
262A GLU* 1.3 59.0 + - + +
264A ALA* 3.7 0.5 - - - +
265A LYS* 2.8 49.6 + - + +
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Residues in contact with GLU 262 (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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130A ILE* 3.4 26.9 - - + -
132A VAL* 5.2 6.7 - - + -
258A LYS* 2.9 21.5 + - + +
259A LEU 3.9 0.2 - - - +
261A LYS* 1.3 79.0 - - + +
263A LEU* 1.3 54.5 + - - +
265A LYS* 4.4 17.5 + - - +
266A LYS* 2.6 56.0 + - + +
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Residues in contact with LEU 263 (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 PHE* 4.1 14.5 - - + -
126A VAL* 4.4 25.1 - - + -
128A GLU* 4.6 3.6 - - + +
130A ILE* 3.9 24.5 - - + -
141A ALA* 4.7 1.1 - - + -
235A LEU* 4.5 9.6 - - + -
238A LEU* 5.3 4.5 - - + -
242A VAL* 5.6 0.7 - - + -
246A PHE* 4.2 17.9 - - + -
259A LEU* 2.9 45.8 + - + +
260A VAL* 3.6 5.8 - - - +
262A GLU* 1.3 78.4 - - - +
264A ALA* 1.3 57.6 + - - +
266A LYS* 4.4 4.3 - - + -
267A GLN* 3.1 45.9 + - - +
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Residues in contact with ALA 264 (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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50A HIS* 3.6 31.0 - - + +
124A PHE* 4.8 7.2 - - + -
238A LEU* 3.7 20.1 - - + +
260A VAL 2.7 20.3 + - - +
261A LYS 3.9 1.1 - - - +
263A LEU* 1.3 73.7 - - - +
265A LYS* 1.3 60.2 + - - +
267A GLN* 4.2 1.9 - - - +
268A LYS* 3.7 16.5 + - - +
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Residues in contact with LYS 265 (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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50A HIS* 5.5 4.3 - - + -
261A LYS* 2.8 35.7 + - + +
262A GLU* 4.0 16.0 + - - +
264A ALA* 1.3 79.7 - - + +
266A LYS* 1.3 65.7 + - - +
268A LYS* 3.1 20.7 - - - +
269A LEU* 5.8 0.3 - - - +
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Residues in contact with LYS 266 (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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128A GLU* 3.3 39.4 + - + +
129A PRO 4.0 14.5 + - - -
130A ILE* 4.6 17.6 - - + +
262A GLU* 2.6 47.0 + - - +
263A LEU* 3.9 6.3 - - + +
265A LYS* 1.3 72.3 - - - +
267A GLN* 1.3 64.8 + - - +
268A LYS 2.9 10.0 + - - -
269A LEU* 3.9 18.2 + - - +
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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