Contacts of the helix formed by residues 233 - 245 (chain A) in PDB entry 1ND4
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 GLY 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A ILE 3.3 0.9 + - - +
229A ALA* 2.9 23.5 + - - -
230A GLU 4.7 0.2 - - - -
231A GLU 3.9 0.2 - - - -
232A LEU* 1.3 78.6 - - - +
234A GLY* 1.3 65.9 + - - -
235A GLU* 3.1 11.4 - - - -
236A TRP* 3.1 14.9 + - - +
237A ALA 3.3 6.9 + - - -
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Residues in contact with GLY 234 (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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229A ALA* 3.9 10.4 + - - +
233A GLY* 1.3 72.1 - - - -
235A GLU* 1.3 63.8 + - - +
237A ALA* 3.0 20.4 + - - +
238A ASP* 3.0 20.7 + - - +
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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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232A LEU 4.5 1.7 - - - +
233A GLY* 3.1 19.1 - - - -
234A GLY* 1.3 74.2 + - - -
236A TRP* 1.3 85.7 + - + +
238A ASP* 3.5 13.8 + - - +
239A ARG* 3.1 23.9 + - - +
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Residues in contact with TRP 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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109A PRO* 3.5 25.5 - - + +
110A ALA* 3.7 34.3 - - + -
113A VAL* 3.6 18.9 - - + +
228A ILE* 3.7 6.3 - - + -
232A LEU* 3.3 42.6 + - + -
233A GLY 3.1 7.5 + - - +
234A GLY 3.1 0.8 - - - -
235A GLU* 1.3 96.0 + - + +
237A ALA* 1.3 60.5 + - - +
238A ASP 3.1 0.4 - - - -
239A ARG* 3.6 28.4 - - + +
240A PHE* 2.9 28.1 + - - +
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Residues in contact with ALA 237 (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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225A THR* 3.9 32.0 - - - +
228A ILE* 3.6 9.8 - - + +
229A ALA* 3.9 18.8 - - + +
233A GLY 3.3 2.6 + - - -
234A GLY* 3.0 11.1 + - - +
236A TRP* 1.3 79.5 - - - +
238A ASP* 1.3 63.6 + - - +
240A PHE* 3.5 6.7 + - - +
241A LEU* 3.3 26.1 + - - +
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Residues in contact with ASP 238 (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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234A GLY 3.0 20.7 + - - +
235A GLU* 3.6 13.5 - - - +
236A TRP 3.1 0.2 - - - -
237A ALA* 1.3 78.4 - - - +
239A ARG* 1.3 64.7 + - - +
241A LEU* 3.2 17.5 + - - +
242A VAL* 3.1 27.2 + - + +
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Residues in contact with ARG 239 (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 VAL* 4.2 3.1 - - + -
235A GLU 3.1 13.0 + - - +
236A TRP* 3.3 34.9 + - + +
238A ASP* 1.3 76.3 - - - +
240A PHE* 1.3 64.4 + - - +
242A VAL* 3.2 25.8 + - - +
243A LEU* 2.9 63.9 + - + +
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Residues in contact with PHE 240 (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 VAL* 3.8 24.2 - - + +
116A MET* 3.7 13.5 - - + -
117A ALA* 3.6 26.2 - - + -
120A MET* 3.9 18.6 - - + -
221A ILE* 4.0 22.9 - - + -
224A ALA* 3.9 17.7 - - + -
225A THR* 3.8 24.5 - - + -
228A ILE* 3.7 26.0 - - + -
236A TRP 2.9 13.6 + - - +
237A ALA 3.5 8.1 - - - +
238A ASP 3.2 0.2 - - - -
239A ARG* 1.3 76.7 - - - +
241A LEU* 1.3 57.6 + - + +
243A LEU* 3.3 4.8 + - - +
244A TYR* 2.7 42.3 + - + +
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Residues in contact with LEU 241 (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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218A TYR* 5.9 0.4 - - + -
221A ILE* 3.6 31.2 - - + -
225A THR* 3.8 15.3 - - + -
237A ALA 3.3 14.1 + - - +
238A ASP* 3.2 18.9 + - - +
240A PHE* 1.3 84.8 - - + +
242A VAL* 1.3 57.2 + - + +
244A TYR* 3.2 2.9 + - + +
245A GLY 2.8 11.8 + - - -
246A ILE* 2.8 53.1 + - + +
249A PRO* 3.6 33.0 - - + -
254A ILE* 5.5 4.5 - - + -
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Residues in contact with VAL 242 (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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238A ASP* 3.1 17.7 + - + +
239A ARG* 3.5 29.8 - - - +
241A LEU* 1.3 75.1 - - + +
243A LEU* 1.3 66.8 + - + +
245A GLY* 3.2 13.7 + - - -
246A ILE 4.2 8.9 + - - +
247A ALA* 6.3 0.7 - - - -
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Residues in contact with LEU 243 (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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110A ALA 5.0 0.9 - - - +
113A VAL* 3.9 25.4 - - + +
114A SER* 4.1 20.6 - - - +
117A ALA* 3.8 12.1 - - + -
121A ARG* 3.1 20.1 + - - +
239A ARG* 2.9 57.8 + - - +
240A PHE 3.7 3.4 - - - +
242A VAL* 1.3 76.3 - - + +
244A TYR* 1.3 65.7 + - - +
245A GLY* 3.5 0.3 + - - -
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Residues in contact with TYR 244 (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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117A ALA* 3.8 8.7 - - + +
120A MET* 3.7 25.8 - - + -
121A ARG* 3.4 40.8 - - + +
124A HIS* 2.7 37.3 - + - +
217A ARG* 2.9 28.7 + - - -
221A ILE* 3.6 16.8 - - + -
240A PHE* 2.7 31.8 + + + +
241A LEU* 3.7 4.7 - - + +
243A LEU* 1.3 73.1 - - - +
245A GLY* 1.3 59.6 + - - +
246A ILE* 3.6 39.7 - - + -
108B ALA* 5.5 0.5 - - - +
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Residues in contact with GLY 245 (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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241A LEU 2.8 7.5 + - - -
242A VAL 3.2 7.8 + - - -
243A LEU 3.2 2.6 - - - -
244A TYR* 1.3 82.3 - - - +
246A ILE* 1.3 61.9 + - - +
108B ALA* 3.6 18.5 - - - +
110B ALA* 5.9 0.3 - - - +
111B GLU* 3.1 27.8 - - - +
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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