Contacts of the helix formed by residues 240 - 248 (chain B) in PDB entry 1D0N
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 240 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B TYR* 3.9 16.2 - - + -
234B PHE* 3.6 45.3 - - + -
238B ALA 3.3 6.0 - - - +
239B GLU* 1.3 89.6 - - + +
241B GLU* 1.3 61.8 + - - +
242B ALA 4.5 2.2 - - - +
243B MET* 3.4 24.4 + - + +
244B LEU* 3.1 27.8 + - - +
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Residues in contact with GLU 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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94A SER* 4.0 23.0 + - - -
146A ALA* 3.9 25.0 - - + +
240B PRO* 1.3 69.7 - - - +
242B ALA* 1.3 68.1 + - - +
243B MET 3.1 1.8 - - - -
244B LEU* 3.3 6.7 + - - +
245B GLN* 2.9 28.7 + - + +
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Residues in contact with ALA 242 (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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146A ALA* 3.6 22.6 + - - +
147A SER* 3.4 17.0 + - - -
193B LEU* 4.4 3.3 - - + +
198B TYR* 3.4 38.6 - - + +
240B PRO* 3.5 1.4 - - - +
241B GLU* 1.3 79.9 - - - +
243B MET* 1.3 60.7 + - - +
245B GLN* 3.5 3.2 + - - -
246B VAL* 3.2 25.3 - - - +
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Residues in contact with MET 243 (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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180B TRP* 3.6 26.0 - - + -
183B PHE* 4.0 9.2 - - + -
191B LEU* 3.6 29.4 - - + -
193B LEU* 5.6 0.2 - - - -
198B TYR* 4.8 13.0 - - + +
200B TRP* 3.4 44.0 - - + -
234B PHE* 5.5 1.3 - - - -
239B GLU* 4.2 6.3 - - + -
240B PRO* 3.4 36.8 + - + +
241B GLU 3.1 0.4 - - - -
242B ALA* 1.3 77.1 - - - +
244B LEU* 1.3 64.4 + - - +
245B GLN 3.1 1.3 - - - -
246B VAL* 3.6 1.9 + - - +
247B LEU* 3.2 39.4 + - + +
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Residues in contact with LEU 244 (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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92A GLU* 4.3 4.2 - - - +
180B TRP* 4.1 11.7 - - + -
239B GLU* 3.6 37.5 - - + +
240B PRO 3.1 21.4 + - - +
241B GLU* 4.0 6.3 - - - +
243B MET* 1.3 76.4 - - - +
245B GLN* 1.3 57.3 + - - +
248B GLY* 2.7 48.7 + - - +
249B PRO* 4.9 3.8 - - + -
250B LYS* 4.5 8.5 - - + +
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Residues in contact with GLN 245 (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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64A THR* 5.3 1.2 - - - +
65A GLY* 3.0 43.1 + - - -
92A GLU* 3.7 33.3 + - - +
93A CYS* 5.4 0.2 - - - +
94A SER* 5.7 1.2 - - - +
142A LYS* 5.8 0.9 - - - +
143A GLY 4.3 10.4 + - - +
144A GLY* 3.4 14.0 + - - -
146A ALA* 3.6 18.8 + - - +
147A SER* 2.6 35.6 + - - +
241B GLU* 2.9 21.7 + - + +
242B ALA 3.6 5.4 - - - +
244B LEU* 1.3 79.9 - - - +
246B VAL* 1.3 59.9 + - - +
248B GLY 4.4 0.5 + - - -
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Residues in contact with VAL 246 (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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142A LYS* 2.8 37.7 + - + +
143A GLY* 4.4 13.9 - - - +
147A SER* 3.5 20.6 - - - +
149A PHE* 4.2 11.7 - - + -
160B GLN* 5.1 6.1 - - - +
178B VAL* 3.9 24.6 - - + +
191B LEU* 4.3 13.0 - - + -
193B LEU* 4.3 12.6 - - + -
242B ALA 3.2 18.1 + - - +
243B MET 3.6 0.4 + - - +
244B LEU 3.4 0.2 - - - -
245B GLN* 1.3 76.9 - - - +
247B LEU* 1.3 70.4 + - + +
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Residues in contact with LEU 247 (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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142A LYS* 4.4 8.8 + - - +
162B LEU* 5.3 0.9 - - + -
178B VAL* 3.8 27.6 - - + -
179B SER* 3.8 28.7 - - - +
180B TRP* 3.4 46.7 + - + +
183B PHE* 4.0 14.8 - - + -
191B LEU* 4.5 8.5 - - + -
243B MET* 3.2 41.2 + - + +
246B VAL* 1.3 84.4 - - + +
248B GLY* 1.3 60.3 + - - +
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Residues in contact with GLY 248 (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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92A GLU* 4.1 13.9 - - - -
180B TRP* 2.8 19.6 + - - -
244B LEU* 2.7 33.8 + - - +
245B GLN 4.4 1.0 + - - -
246B VAL 3.6 1.4 - - - -
247B LEU* 1.3 74.0 - - - +
249B PRO* 1.3 72.5 - - - +
250B LYS 3.4 0.5 + - - -
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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