Contacts of the helix formed by residues 323 - 333 (chain D) in PDB entry 3ENM
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 ASP 323 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154D ILE* 4.9 1.4 - - - +
321D GLY 4.2 1.2 + - - -
322D THR* 1.3 76.7 - - - +
324D VAL* 1.3 58.2 - - - +
325D ALA* 3.4 10.6 + - - +
326D SER* 2.5 44.9 + - - -
327D PHE* 3.4 9.0 + - - +
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Residues in contact with VAL 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D ILE* 4.2 30.1 - - + -
157D LYS* 4.1 34.1 - - + +
187D ILE* 4.1 13.2 - - + -
191D GLY* 3.7 24.2 - - - +
193D VAL* 5.0 2.9 - - + -
322D THR* 3.2 9.6 + - + +
323D ASP* 1.3 71.3 - - - +
325D ALA* 1.3 66.3 + - - +
327D PHE* 2.9 3.3 + - + +
328D VAL* 2.7 40.9 + - + +
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Residues in contact with ALA 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D ALA 3.5 17.4 - - - +
190D LEU* 3.7 16.2 - - - +
191D GLY* 3.7 12.0 - - - +
323D ASP* 3.2 9.2 + - - +
324D VAL* 1.3 78.4 - - - +
326D SER* 1.3 57.7 + - - +
328D VAL* 3.2 3.2 + - - +
329D LYS* 2.9 41.1 + - - +
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Residues in contact with SER 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ILE* 6.2 4.0 - - - -
145A ASP* 4.8 11.6 + - - -
323D ASP* 2.5 38.9 + - - -
325D ALA* 1.3 72.1 - - - +
327D PHE* 1.3 67.6 + - - +
329D LYS* 3.3 12.8 + - - +
330D LEU* 2.9 23.3 + - - +
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Residues in contact with PHE 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D PHE* 3.7 31.0 - + - -
143D VAL* 4.1 4.9 - - + -
148D GLN* 4.1 11.4 - - + -
149D THR 3.4 26.0 - - - -
150D ILE* 4.0 16.2 - - + -
151D PRO* 3.7 13.7 - - + -
154D ILE* 3.2 37.9 - - + -
323D ASP 3.4 4.4 + - - +
324D VAL 2.9 6.3 + - - +
326D SER* 1.3 77.1 - - - +
328D VAL* 1.3 68.4 + - + +
330D LEU* 2.8 29.1 + - + +
331D ILE* 3.0 35.5 + - + +
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Residues in contact with VAL 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D PHE* 4.2 19.5 - - + -
187D ILE* 3.7 25.8 - - + -
188D ASN 3.6 24.9 - - - +
189D ALA* 4.1 5.4 - - - -
324D VAL* 2.7 41.3 + - + +
325D ALA* 3.6 4.7 - - - +
327D PHE* 1.3 73.1 - - + +
329D LYS* 1.3 61.9 + - - +
331D ILE* 3.0 3.5 + - - +
332D LEU* 3.0 46.7 + - + +
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Residues in contact with LYS 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C PRO* 6.0 5.6 - - - -
73C VAL* 5.7 7.6 - - + -
189D ALA* 4.3 26.5 + - + +
325D ALA* 2.9 31.7 + - - +
326D SER* 3.8 10.3 + - - +
328D VAL* 1.3 73.1 - - - +
330D LEU* 1.3 66.7 + - - +
332D LEU* 4.6 3.4 - - - +
333D ALA* 3.0 30.2 + - + +
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Residues in contact with LEU 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ILE* 4.5 12.3 - - + +
145A ASP* 4.3 19.7 - - - +
147A GLY* 4.9 9.0 - - - +
146D LYS* 4.4 11.6 + - + +
148D GLN* 4.0 31.6 - - - +
326D SER 2.9 14.1 + - - +
327D PHE* 2.8 23.0 + - + +
329D LYS* 1.3 77.9 - - - +
331D ILE* 1.3 69.5 + - + +
333D ALA 4.2 10.0 - - - -
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Residues in contact with ILE 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D PHE* 3.9 14.6 - - + -
142D GLN* 3.5 34.8 - - + +
143D VAL* 3.7 24.0 - - + +
146D LYS* 3.3 32.9 - - + +
148D GLN* 4.1 18.4 - - + -
327D PHE* 3.0 53.3 + - + +
328D VAL 3.0 5.6 + - - +
330D LEU* 1.3 85.7 - - + +
332D LEU* 1.3 63.9 + - + +
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Residues in contact with LEU 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ASP* 3.9 31.2 - - + +
134D THR* 4.6 14.8 - - + +
139D PHE* 4.1 22.4 - - + -
142D GLN* 4.5 16.9 - - + +
146D LYS* 5.1 1.9 - - - -
187D ILE* 5.7 0.2 - - + -
189D ALA* 5.6 2.0 - - + -
328D VAL* 3.0 37.1 + - + +
329D LYS* 4.6 2.9 - - - +
331D ILE* 1.3 81.9 - - + +
333D ALA* 1.3 64.2 + - - +
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Residues in contact with ALA 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D LYS* 4.5 13.0 + - - -
329D LYS* 3.0 17.0 + - + +
330D LEU 4.2 12.8 - - - -
331D ILE 4.5 1.6 - - - -
332D LEU* 1.3 83.1 - - - +
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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