Contacts of the helix formed by residues 226 - 236 (chain A) in PDB entry 1Q0R
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 PRO 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A LEU 4.2 2.4 - - - +
224A LEU 3.6 2.4 - - - +
225A PRO* 1.3 91.5 - - + +
227A PRO* 1.3 74.0 - - + +
228A SER* 3.1 20.0 + - - +
229A ARG* 3.2 27.6 + - + +
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Residues in contact with PRO 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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130A LEU 3.6 13.5 - - - +
131A ASP* 4.0 23.5 - - + +
133A ASP* 5.6 10.8 - - + +
225A PRO 3.7 2.2 - - - +
226A PRO* 1.3 84.6 - - + +
228A SER* 1.3 64.3 + - - +
229A ARG 3.1 1.3 + - - -
230A ALA* 3.1 21.4 + - - +
231A ALA 4.5 0.3 + - - -
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Residues in contact with SER 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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226A PRO* 3.1 21.4 - - - +
227A PRO* 1.3 81.6 - - - +
229A ARG* 1.3 64.7 + - - +
230A ALA 3.3 0.7 + - - -
231A ALA* 3.5 18.8 + - - +
232A GLU* 4.3 7.4 + - - +
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Residues in contact with ARG 229 (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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110A VAL* 4.2 14.9 - - - +
113A LEU* 3.6 22.9 - - + +
114A ASP* 2.8 42.8 + - - -
130A LEU* 3.8 18.7 - - + +
225A PRO* 4.2 15.5 - - + +
226A PRO* 3.5 31.6 - - + +
227A PRO 3.1 0.8 - - - -
228A SER* 1.3 77.0 - - - +
230A ALA* 1.3 66.1 + - - +
231A ALA 3.2 0.2 - - - -
232A GLU* 2.8 62.7 + - - +
233A LEU 3.8 1.0 + - - -
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Residues in contact with ALA 230 (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 LEU* 4.0 11.3 - - + +
131A ASP* 3.5 39.0 - - + +
227A PRO 3.1 15.6 + - - +
229A ARG* 1.3 77.7 - - - +
231A ALA* 1.3 61.5 + - - +
233A LEU* 3.1 26.2 + - - +
234A ARG* 4.5 1.6 + - - +
262A LEU* 4.4 20.0 - - + +
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Residues in contact with ALA 231 (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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227A PRO 4.5 0.6 + - - -
228A SER* 3.5 13.3 + - - +
229A ARG 3.2 0.8 - - - -
230A ALA* 1.3 79.1 - - - +
232A GLU* 1.3 61.5 + - + +
234A ARG* 3.2 44.2 + - - +
235A GLU* 5.5 0.5 - - - +
262A LEU* 6.0 0.2 - - - -
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Residues in contact with GLU 232 (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 LEU* 3.5 19.6 - - + +
228A SER* 4.4 4.9 + - - +
229A ARG* 2.8 64.3 + - - +
231A ALA* 1.3 72.2 - - + +
233A LEU* 1.3 60.4 + - - +
234A ARG 3.1 7.0 + - - -
235A GLU* 3.1 26.5 + - + +
236A VAL 4.4 0.5 + - - -
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Residues in contact with LEU 233 (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 GLN* 3.5 43.1 - - + +
112A ALA* 4.5 2.7 - - + -
113A LEU* 3.7 26.7 - - + -
130A LEU* 4.3 5.4 - - + -
229A ARG 3.8 2.9 + - - +
230A ALA* 3.1 25.2 + - - +
232A GLU* 1.3 73.1 - - - +
234A ARG* 1.3 62.7 + - - +
235A GLU 3.1 2.5 - - - -
236A VAL* 3.1 33.8 + - + +
262A LEU* 3.4 34.5 - - + +
263A ILE* 3.8 18.9 - - + -
264A PRO* 3.6 4.9 - - - +
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Residues in contact with ARG 234 (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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230A ALA 5.1 0.7 - - - +
231A ALA* 3.2 33.3 + - - +
232A GLU 3.1 0.4 - - - -
233A LEU* 1.3 76.7 - - - +
235A GLU* 1.3 67.7 + - - +
236A VAL 3.4 0.2 - - - -
262A LEU* 3.5 15.5 + - + +
264A PRO* 3.2 26.2 - - + +
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Residues in contact with GLU 235 (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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116A HIS* 5.1 2.3 + - - -
231A ALA 5.5 0.4 - - - +
232A GLU* 3.5 17.9 - - + +
233A LEU 3.1 1.0 - - - -
234A ARG* 1.3 86.5 - - + +
236A VAL* 1.3 62.0 + - - +
237A THR* 3.5 14.3 + - - +
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Residues in contact with VAL 236 (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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112A ALA* 4.0 28.0 - - + +
113A LEU* 4.5 3.4 - - + -
116A HIS* 4.2 9.4 - - + -
122A LEU* 5.6 1.1 - - + -
233A LEU* 3.1 43.6 + - + +
234A ARG 4.3 0.2 - - - +
235A GLU* 1.3 77.9 - - - +
237A THR* 1.3 64.0 + - - +
238A VAL* 4.0 25.6 - - + +
240A THR* 4.2 3.4 - - - +
263A ILE* 3.9 20.2 - - + -
264A PRO* 3.7 20.4 - - - +
265A THR* 4.0 5.5 + - - +
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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