Contacts of the helix formed by residues 231 - 241 (chain B) in PDB entry 1DSU
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LEU* 4.0 13.9 - - + -
103B LEU* 5.0 4.9 - - + -
124B TRP* 4.2 11.8 - - - -
125B GLN* 4.1 12.7 - - + +
209B LEU* 3.4 33.7 - - + +
210B GLU* 3.1 14.5 + - - +
211B GLY 4.3 2.2 - - - -
212B VAL* 3.7 29.4 - - + -
229B THR 4.0 5.4 - - - +
230B ARG* 1.3 70.3 - - - +
232B ALA* 1.3 67.7 + - - +
234B TYR* 2.9 19.9 + - - +
235B ALA* 3.3 10.6 + - - -
238B ILE* 4.3 12.1 - - + +
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Residues in contact with ALA 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLN* 3.4 27.6 - - + +
126B ARG* 4.6 2.5 - - - +
127B VAL 3.4 26.7 - - - +
128B ASP* 3.9 12.6 - - - +
129B ARG 5.3 0.7 - - - -
210B GLU* 4.6 3.7 + - - +
230B ARG* 3.3 20.1 - - + +
231B VAL* 1.3 80.8 - - - +
233B SER* 1.3 61.7 + - - +
234B TYR 3.1 1.2 + - - -
235B ALA* 3.4 14.7 + - - +
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Residues in contact with SER 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ASP* 4.1 16.2 + - - +
179B ARG* 3.2 48.9 + - - +
230B ARG* 2.9 33.7 + - - +
231B VAL 3.2 0.2 - - - -
232B ALA* 1.3 76.4 - - - +
234B TYR* 1.3 60.6 + - - +
235B ALA 3.7 0.6 + - - -
236B ALA* 5.4 0.7 + - - +
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Residues in contact with TYR 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B HIS* 3.5 39.3 - + - -
101B HIS* 2.7 43.8 + - - -
103B LEU* 3.5 26.5 - - + -
179B ARG* 3.5 45.6 + - + +
180B LEU* 6.1 0.7 - - - +
229B THR* 3.6 20.2 - - + +
230B ARG 3.3 22.2 - - - -
231B VAL 2.9 9.1 + - - +
233B SER* 1.3 78.5 - - - +
235B ALA* 1.3 61.7 + - - +
236B ALA 3.3 2.9 - - - -
237B TRP* 3.1 11.3 + + + +
238B ILE* 2.9 29.1 + - + +
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Residues in contact with ALA 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B TRP* 3.4 30.8 + - + +
126B ARG* 4.1 23.6 - - + +
231B VAL 3.3 3.2 + - - +
232B ALA 3.4 14.4 + - - +
233B SER 3.7 0.4 + - - -
234B TYR* 1.3 77.0 - - - +
236B ALA* 1.3 58.0 + - - +
239B ASP* 2.9 39.0 + - - +
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Residues in contact with ALA 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B SER 5.4 0.8 + - - +
234B TYR 3.3 0.4 - - - -
235B ALA* 1.3 77.0 - - - +
237B TRP* 1.3 64.4 + - - +
239B ASP* 3.2 8.4 + - - +
240B SER* 3.0 23.5 + - - -
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Residues in contact with TRP 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LEU* 5.2 1.1 - - + -
89B VAL* 3.6 29.0 - - + +
90B PRO 3.8 3.1 + - - -
91B HIS* 3.6 45.3 - + + +
92B PRO* 3.6 25.1 - - + +
103B LEU* 3.8 29.8 - - + -
104B LEU 5.0 0.2 - - - -
105B LEU* 4.0 20.4 - - + -
234B TYR* 3.1 17.9 + - + +
236B ALA* 1.3 76.7 - - - +
238B ILE* 1.3 82.2 + - + +
240B SER* 2.7 29.1 + - - -
241B VAL* 3.1 28.1 + - + +
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Residues in contact with ILE 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B VAL* 5.5 4.9 - - + -
53B LEU* 4.6 18.2 - - + -
103B LEU* 4.9 3.6 - - + -
105B LEU* 4.2 21.1 - - + -
124B TRP* 3.6 40.2 - - + +
231B VAL* 4.3 16.6 - - + +
234B TYR* 2.9 30.8 + - + +
235B ALA 3.7 4.0 - - - +
237B TRP* 1.3 88.9 - - + +
239B ASP* 1.3 65.6 + - - +
241B VAL* 3.0 5.9 + - - +
242B LEU* 3.0 33.7 + - + +
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Residues in contact with ASP 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ARG* 5.5 2.3 + - - -
239A ASP* 5.4 5.1 - - - +
124B TRP* 3.5 23.3 + - - -
126B ARG* 6.0 0.9 - - - +
235B ALA* 2.9 25.6 + - - +
236B ALA* 3.5 7.0 - - - +
238B ILE* 1.3 76.2 - - - +
240B SER* 1.3 62.8 + - - +
242B LEU* 3.2 9.7 + - - +
243B ALA* 3.0 25.8 + - - +
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Residues in contact with SER 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B ALA 3.0 12.4 + - - -
237B TRP* 2.7 31.7 + - - -
239B ASP* 1.3 76.5 - - - +
241B VAL* 1.3 61.2 + - - +
243B ALA* 3.6 19.0 + - - +
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Residues in contact with VAL 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B TRP* 3.7 37.0 - - + -
87B ARG* 4.6 8.2 + - - +
89B VAL* 4.0 24.7 - - + -
105B LEU* 3.7 22.0 - - + -
237B TRP* 3.6 39.7 - - + +
238B ILE 3.0 2.7 + - - +
240B SER* 1.3 80.0 + - - +
242B LEU* 1.3 62.8 + - - +
243B ALA* 3.4 5.7 + - - +
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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