Contacts of the helix formed by residues 231 - 241 (chain A) in PDB entry 1DST
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 VAL 231 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 4.0 15.7 - - + -
103A LEU* 4.8 5.8 - - + -
124A TRP* 4.0 9.8 - - - -
125A GLN* 3.9 16.2 - - + +
209A LEU* 3.4 33.0 - - + +
210A GLU 3.1 11.1 + - - +
211A GLY* 4.6 0.4 - - - -
212A VAL* 3.7 30.3 - - + -
229A THR 4.3 2.7 - - - +
230A ARG* 1.3 69.9 - - - +
232A ALA* 1.3 64.0 + - - +
233A SER 3.1 2.5 - - - -
234A TYR* 2.8 25.6 + - - +
235A ALA* 3.2 11.1 + - - -
238A ILE* 4.3 13.6 - - + +
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Residues in contact with ALA 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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125A GLN* 3.2 28.3 - - + +
126A ARG* 4.7 3.5 - - - +
127A VAL 3.5 25.8 - - - +
128A ASP* 3.9 23.3 - - - +
210A GLU* 4.7 4.2 + - - +
230A ARG* 3.3 10.0 - - + +
231A VAL* 1.3 81.8 - - - +
233A SER* 1.3 57.6 + - - +
234A TYR 3.1 3.7 + - - -
235A ALA* 3.4 15.1 + - - +
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Residues in contact with SER 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ASP* 4.1 6.9 + - - -
178A GLU 3.5 0.9 + - - -
179A ARG* 3.3 48.4 + - - +
230A ARG* 2.7 44.0 + - - +
231A VAL 3.1 0.2 - - - -
232A ALA* 1.3 77.6 - - - +
234A TYR* 1.3 65.2 + - - +
235A ALA 3.8 0.4 - - - -
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Residues in contact with TYR 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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91A HIS* 3.2 42.6 - + - -
100A ASP* 5.1 0.7 - - - +
101A HIS* 2.7 38.0 + - - -
103A LEU* 4.0 23.8 - - + -
179A ARG* 3.2 49.6 + - + +
229A THR* 3.6 20.2 - - + +
230A ARG 3.4 17.0 - - - -
231A VAL 2.8 8.4 + - - +
233A SER* 1.3 82.5 - - - +
235A ALA* 1.3 65.4 + - - +
236A ALA* 3.1 3.8 - - - -
237A TRP* 2.8 21.7 + - + +
238A ILE* 3.0 16.6 + - + +
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Residues in contact with ALA 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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124A TRP* 3.4 31.2 + - + +
126A ARG* 4.1 26.5 - - + +
231A VAL 3.2 4.2 + - - +
232A ALA 3.4 14.2 + - - +
233A SER 3.8 0.4 - - - -
234A TYR* 1.3 76.6 - - - +
236A ALA* 1.3 62.7 + - - +
238A ILE* 3.6 0.4 + - - -
239A ASP* 3.1 30.7 + - - +
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Residues in contact with ALA 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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234A TYR 3.0 1.6 + - - -
235A ALA* 1.3 77.4 - - - +
237A TRP* 1.3 63.2 + - - +
239A ASP* 3.5 5.6 + - - +
240A SER* 3.1 22.9 + - - -
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Residues in contact with TRP 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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53A LEU* 4.9 0.9 - - + -
89A VAL* 3.4 33.4 - - + +
90A PRO 3.7 3.1 - - - -
91A HIS* 3.3 48.5 - + - +
92A PRO* 3.2 29.4 - - + +
103A LEU* 3.7 34.5 - - + -
104A LEU 4.7 0.2 - - - -
105A LEU* 4.1 19.7 - - + -
234A TYR* 2.8 19.6 + - + +
236A ALA* 1.3 71.2 - - - +
238A ILE* 1.3 81.6 + - + +
240A SER* 3.1 26.8 + - - -
241A VAL* 3.1 24.7 + - + +
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Residues in contact with ILE 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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47A VAL* 5.5 3.8 - - + -
53A LEU* 4.7 19.7 - - + -
103A LEU* 5.1 2.0 - - + -
105A LEU* 4.2 17.7 - - + -
124A TRP* 3.4 53.4 - - + +
231A VAL* 4.3 20.9 - - + +
234A TYR* 3.0 20.4 + - + +
237A TRP* 1.3 90.6 - - + +
239A ASP* 1.3 61.8 + - - +
241A VAL* 3.3 0.9 + - - +
242A LEU* 3.1 41.2 + - + +
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Residues in contact with ASP 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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124A TRP* 3.5 10.4 + - - -
126A ARG* 2.9 42.9 + - - -
235A ALA 3.1 20.7 + - - +
236A ALA* 3.8 5.6 - - - +
238A ILE* 1.3 77.7 - - - +
240A SER* 1.3 60.8 + - - +
242A LEU* 3.2 10.2 + - - +
243A ALA* 3.1 24.1 + - - +
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Residues in contact with SER 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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236A ALA 3.1 14.2 + - - -
237A TRP* 3.1 21.4 + - - -
239A ASP* 1.3 75.0 - - - +
241A VAL* 1.3 65.7 + - - +
242A LEU 3.7 0.2 + - - -
243A ALA* 3.7 18.6 + - - +
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Residues in contact with VAL 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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51A TRP* 3.6 41.5 - - + -
89A VAL* 4.1 20.4 - - + -
105A LEU* 3.7 24.7 - - + -
237A TRP* 3.1 38.7 + - + +
238A ILE 3.8 1.3 - - - +
240A SER* 1.3 81.5 + - - +
242A LEU* 1.3 61.8 + - - +
243A ALA 3.5 4.7 + - - +
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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