Contacts of the helix formed by residues 323 - 328 (chain D) in PDB entry 1JPM
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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132D THR* 3.7 0.4 + - - -
133D ASP 3.7 15.9 - - - +
134D TYR* 3.5 21.5 - - + -
135D THR* 2.7 45.6 + - - -
160D LYS* 5.1 1.7 + - - -
321D ASP* 3.7 12.7 + - - +
322D PHE* 1.3 75.3 - - - +
324D ALA* 1.3 72.5 + - - +
325D PRO* 3.4 2.5 - - - -
326D LEU* 2.9 26.8 + - + +
327D MET* 3.5 12.5 - - - +
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Residues in contact with ALA 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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296D SER* 4.0 3.8 - - - +
297D MET 3.8 20.2 - - - +
298D ILE* 4.6 7.2 - - + +
299D GLU 3.6 18.3 - - - +
304D ILE* 4.0 9.9 - - + -
322D PHE* 3.4 0.4 - - - +
323D ASP* 1.3 82.9 + - - +
325D PRO* 1.3 65.5 - - + +
327D MET* 2.8 32.3 + - - +
328D LEU* 4.0 7.1 + - - +
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Residues in contact with PRO 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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299D GLU 4.0 5.2 - - - +
300D THR 3.9 7.6 - - - +
301D LYS* 4.0 16.8 - - + +
304D ILE* 3.2 32.1 - - + -
322D PHE 3.8 1.6 - - - +
323D ASP 3.5 1.6 - - - -
324D ALA* 1.3 94.4 - - + +
326D LEU* 1.3 57.2 + - + +
327D MET 3.1 4.4 + - - -
328D LEU* 3.3 26.5 + - + +
330D THR 5.2 0.7 - - - +
331D ASP* 6.5 0.2 - - - -
339D TYR* 3.4 34.1 - - + +
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Residues in contact with LEU 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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16D THR* 4.5 5.7 + - - +
132D THR* 5.3 0.9 - - + -
134D TYR* 3.7 39.7 + - + -
156D PHE* 4.0 17.0 - - + -
323D ASP* 2.9 17.7 + - - +
325D PRO* 1.3 78.2 - - + +
327D MET* 1.3 62.8 + - - +
328D LEU 3.4 6.3 + - - +
339D TYR* 3.9 50.0 - - + -
341D GLY 5.2 0.4 - - - +
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Residues in contact with MET 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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15D LEU* 3.6 13.2 - - + +
16D THR* 2.8 32.8 + - - +
17D LYS* 3.5 36.5 + - + +
134D TYR* 3.5 34.1 - - + +
135D THR* 5.4 10.8 - - + +
137D SER* 4.9 5.6 - - - +
298D ILE* 6.3 2.0 - - + -
323D ASP* 3.5 22.2 - - - +
324D ALA* 2.8 15.9 + - - +
326D LEU* 1.3 77.7 - - - +
328D LEU* 1.3 63.4 + - + +
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Residues in contact with LEU 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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13D VAL* 3.6 24.9 - - + +
14D PRO 3.7 2.0 - - - +
15D LEU* 4.0 14.4 - - + -
16D THR* 3.5 8.9 - - - +
29D ALA* 3.6 29.6 - - + -
298D ILE* 5.2 3.1 - - + -
299D GLU 4.2 4.5 - - - +
300D THR* 3.8 37.5 - - + +
301D LYS 5.2 0.7 - - - +
324D ALA 4.1 7.4 - - - +
325D PRO* 3.3 19.1 + - + +
326D LEU 4.4 3.3 - - - +
327D MET* 1.3 80.9 - - + +
329D LYS* 1.3 63.5 + - - +
330D THR* 3.4 17.2 + - - +
331D ASP* 5.9 0.7 - - - -
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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