Contacts of the helix formed by residues 323 - 333 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154C ILE* 4.6 0.9 - - - +
321C GLY 3.7 2.9 + - - +
322C THR* 1.3 76.1 - - - +
324C VAL* 1.3 63.3 + - - +
325C ALA* 3.0 10.9 + - - +
326C SER* 2.8 40.1 + - - -
327C PHE* 3.7 7.6 + - - +
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Residues in contact with VAL 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C ILE* 3.9 29.6 - - + -
157C LYS* 3.6 38.1 - - + -
158C ILE* 6.3 0.2 - - + -
187C ILE* 4.3 11.0 - - + -
191C GLY* 3.5 31.2 - - - +
193C VAL* 4.8 4.3 - - + -
322C THR* 3.1 8.9 + - + +
323C ASP* 1.3 71.1 - - - +
325C ALA* 1.3 63.4 + - - +
327C PHE* 3.1 5.2 + - - +
328C VAL* 3.1 33.9 + - + +
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Residues in contact with ALA 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C ALA 3.3 23.3 - - - +
190C LEU* 3.6 17.7 - - - +
191C GLY* 3.8 6.7 - - - -
323C ASP* 3.0 9.3 + - - +
324C VAL* 1.3 79.0 - - - +
326C SER* 1.3 61.0 + - - +
328C VAL* 3.6 2.7 + - - +
329C LYS* 3.1 35.0 + - - +
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Residues in contact with SER 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323C ASP* 2.8 33.2 + - - -
325C ALA* 1.3 73.6 - - - +
327C PHE* 1.3 66.2 + - - +
329C LYS* 3.2 7.8 + - - +
330C LEU* 2.9 24.8 + - - +
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Residues in contact with PHE 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C PHE* 3.7 31.0 - + - -
143C VAL* 4.5 1.3 - - + -
148C GLN* 4.7 4.7 - - + -
149C THR 3.1 28.0 - - - -
150C ILE* 4.1 9.2 - - + -
151C PRO* 3.6 21.5 - - + -
154C ILE* 3.9 31.0 - - + -
323C ASP 3.7 3.5 + - - +
324C VAL 3.1 8.8 + - - +
326C SER* 1.3 78.1 - - - +
328C VAL* 1.3 57.9 + - + +
330C LEU* 3.3 23.1 - - + +
331C ILE* 2.9 51.1 + - + +
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Residues in contact with VAL 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU* 5.4 0.4 - - + -
139C PHE* 4.1 16.4 - - + -
187C ILE* 3.5 33.9 - - + -
188C ASN* 3.7 27.6 - - - +
189C ALA* 3.9 12.3 - - + -
324C VAL* 3.1 21.5 + - + +
325C ALA 3.8 6.5 - - - +
327C PHE* 1.3 76.0 - - + +
329C LYS* 1.3 58.5 + - - +
332C LEU* 2.9 49.8 + - + +
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Residues in contact with LYS 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU* 4.7 15.9 - - + -
189C ALA* 3.8 34.6 + - + +
190C LEU* 6.3 0.2 - - - +
325C ALA* 3.1 23.8 + - - +
326C SER* 3.9 6.7 - - - +
327C PHE 3.2 0.2 - - - -
328C VAL* 1.3 75.8 - - - +
330C LEU* 1.3 70.1 + - - +
332C LEU* 5.0 1.1 - - - -
333C ALA* 2.8 31.4 + - + +
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Residues in contact with LEU 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C LYS* 4.3 7.9 - - - -
148C GLN* 2.9 29.2 - - - +
326C SER 2.9 12.9 + - - +
327C PHE* 3.3 28.9 - - + +
329C LYS* 1.3 79.7 - - - +
331C ILE* 1.3 66.6 + - + +
333C ALA* 3.5 10.7 + - - +
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Residues in contact with ILE 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A MSE 5.7 0.3 - - - +
139C PHE* 3.8 22.7 - - + +
142C GLN* 3.8 28.7 - - + +
143C VAL* 3.9 30.3 - - + +
146C LYS* 3.7 28.6 + - + +
148C GLN* 4.0 27.8 - - + +
327C PHE* 2.9 44.9 + - + +
328C VAL 4.1 0.2 - - - +
330C LEU* 1.3 81.1 - - + +
332C LEU* 1.3 62.8 + - + +
333C ALA 3.7 0.2 + - - -
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Residues in contact with LEU 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A MSE 4.2 36.0 - - + +
58A GLU 5.7 0.4 - - - +
59A LEU* 3.8 34.4 + - + +
133C ASP* 3.8 25.1 - - + -
134C THR* 3.7 20.2 - - - +
139C PHE* 4.0 20.9 - - + -
142C GLN* 4.2 19.3 - - + -
187C ILE* 5.6 0.7 - - + -
328C VAL* 2.9 34.1 + - + +
329C LYS 4.7 0.2 - - - +
331C ILE* 1.3 80.1 - - + +
333C ALA* 1.3 62.4 + - - +
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Residues in contact with ALA 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU* 4.9 12.8 - - + +
146C LYS* 4.1 19.8 + - - -
329C LYS* 2.8 22.4 + - + +
330C LEU* 4.2 5.2 - - - +
331C ILE 3.5 0.6 - - - -
332C LEU* 1.3 82.2 - - - +
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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