Contacts of the helix formed by residues 240 - 248 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A TYR* 3.8 19.7 - - + -
234A PHE* 3.6 45.1 - - + -
238A ALA 3.3 6.9 - - - +
239A GLU* 1.3 90.4 - - + +
241A GLU* 1.3 64.8 + - - +
242A ALA* 4.4 2.7 - - + +
243A MET* 3.8 19.1 - - + +
244A LEU* 3.1 20.8 + - - +
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Residues in contact with GLU 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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240A PRO* 1.3 71.6 - - - +
242A ALA* 1.3 56.1 + - - +
244A LEU* 3.2 10.3 + - + +
245A GLN* 2.7 43.2 + - + +
94B SER* 4.0 13.9 - - - -
97B GLU* 4.0 16.4 - - - +
146B ALA* 4.0 21.3 - - + +
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Residues in contact with ALA 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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191A LEU* 5.2 1.1 - - - -
193A LEU* 5.0 1.8 - - + -
198A TYR* 3.3 40.2 - - + +
240A PRO* 3.4 1.5 - - + +
241A GLU* 1.3 76.8 - - - +
243A MET* 1.3 63.9 + - - +
245A GLN* 3.2 10.3 + - - -
246A VAL* 3.3 10.2 - - - +
146B ALA* 3.7 21.6 + - - +
147B SER* 3.2 27.7 + - - -
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Residues in contact with MET 243 (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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180A TRP* 4.0 7.2 - - + -
183A PHE* 3.5 22.9 - - + -
191A LEU* 4.0 26.7 - - + +
198A TYR* 5.2 11.2 - - + -
200A TRP* 3.7 39.5 - - + -
234A PHE* 5.9 1.1 - - - -
239A GLU* 4.0 14.6 - - + -
240A PRO* 3.5 26.4 + - + +
241A GLU 3.3 0.2 - - - -
242A ALA* 1.3 80.5 - - - +
244A LEU* 1.3 62.2 + - - +
245A GLN 3.2 0.3 + - - -
246A VAL* 3.3 1.4 + - - +
247A LEU* 3.0 54.0 + - + +
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Residues in contact with LEU 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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180A TRP* 4.4 10.3 - - + -
239A GLU* 3.6 46.4 - - + +
240A PRO 3.1 9.6 + - - +
241A GLU* 3.6 8.1 - - + +
243A MET* 1.3 79.6 - - - +
245A GLN* 1.3 58.1 + - - +
248A GLY* 2.8 47.8 + - - +
249A PRO* 5.0 3.1 - - + -
250A LYS* 4.6 7.2 - - + +
92B GLU* 4.9 3.1 - - - +
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Residues in contact with GLN 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 GLU* 2.7 27.5 + - + +
242A ALA* 3.4 7.0 - - - +
243A MET 3.1 0.4 - - - -
244A LEU* 1.3 76.7 - - - +
246A VAL* 1.3 60.2 + - - +
248A GLY 4.2 0.9 + - - -
64B THR* 5.3 1.2 - - - +
65B GLY* 3.3 38.7 + - - +
92B GLU* 3.9 32.4 + - - +
94B SER 5.7 0.2 - - - +
97B GLU* 4.4 4.9 + - - -
142B LYS* 5.2 1.2 - - - +
143B GLY 4.2 9.3 + - - -
144B GLY* 3.3 17.8 + - - -
146B ALA* 3.4 19.8 - - + +
147B SER* 2.8 34.8 + - - +
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Residues in contact with VAL 246 (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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160A GLN* 4.9 7.9 - - - +
178A VAL* 3.9 26.2 - - + +
191A LEU* 4.2 15.5 - - + -
193A LEU* 4.6 11.2 - - + -
242A ALA 3.3 10.0 + - - +
243A MET 4.2 0.2 - - - +
245A GLN* 1.3 75.7 - - - +
247A LEU* 1.3 70.0 + - + +
142B LYS* 2.9 40.3 - - + +
143B GLY* 4.4 8.7 - - - +
147B SER* 3.2 29.6 - - - +
149B PHE* 4.3 10.5 - - + -
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Residues in contact with LEU 247 (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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162A LEU* 5.4 0.4 - - + -
178A VAL* 3.9 17.3 - - + +
179A SER* 3.6 40.5 - - - +
180A TRP* 3.5 36.4 + - + +
183A PHE* 4.0 11.9 - - + -
191A LEU* 4.7 8.5 - - + -
243A MET* 3.0 54.0 + - + +
246A VAL* 1.3 83.4 - - + +
248A GLY* 1.3 60.7 + - - +
142B LYS* 5.3 3.5 - - - +
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Residues in contact with GLY 248 (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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180A TRP* 2.9 16.5 + - - -
244A LEU* 2.8 33.0 + - - +
245A GLN 4.2 0.8 + - - -
246A VAL 3.6 1.0 - - - -
247A LEU* 1.3 79.0 - - - +
249A PRO* 1.3 71.7 - - - +
250A LYS 3.4 0.7 + - - -
92B GLU* 4.4 14.4 - - - -
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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