Contacts of the helix formed by residues 294 - 303 (chain A) in PDB entry 1ZM9
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 294 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292A LYS* 2.9 3.1 + - + -
293A LYS* 1.3 87.1 - - - +
295A GLU* 1.3 59.7 + - - +
297A PRO* 3.3 8.4 - - - +
298A VAL* 3.3 22.3 - - - +
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Residues in contact with GLU 295 (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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283A ARG* 4.9 13.5 + - - -
287A ALA* 4.2 14.2 - - + +
292A LYS* 3.0 22.7 + - + +
294A ASP* 1.3 80.2 - - - +
296A ILE* 1.3 58.4 + - - +
297A PRO 3.2 0.2 - - - -
298A VAL* 2.8 13.2 + - + +
299A LEU* 2.6 54.9 + - + +
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Residues in contact with ILE 296 (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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287A ALA* 4.1 6.5 - - - +
288A ILE* 3.9 47.3 - - + +
291A PHE* 4.4 6.3 - - + -
292A LYS 3.3 25.6 - - - +
293A LYS* 4.2 7.2 - - + +
295A GLU* 1.3 74.4 - - - +
297A PRO* 1.3 64.9 - - + +
299A LEU* 3.8 5.8 - - - +
300A LEU* 2.8 50.8 + - + +
307A LEU* 5.8 2.2 - - + -
315A GLU* 6.3 1.6 - - + -
319A LEU* 4.2 20.9 - - + -
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Residues in contact with PRO 297 (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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293A LYS 2.8 29.4 - - - +
294A ASP* 3.3 10.8 - - - +
295A GLU 3.3 1.1 - - - -
296A ILE* 1.3 92.9 - - + +
298A VAL* 1.3 68.2 + - + +
300A LEU* 3.7 7.2 - - + +
301A GLU* 3.1 26.4 + - - +
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Residues in contact with VAL 298 (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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294A ASP 3.3 20.6 - - - +
295A GLU* 2.8 17.8 + - + +
297A PRO* 1.3 76.5 - - + +
299A LEU* 1.3 64.9 + - - +
300A LEU 3.2 0.7 + - - -
301A GLU* 3.3 5.7 + - - +
302A LYS* 3.3 22.6 + - + +
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Residues in contact with LEU 299 (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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280A PRO* 5.2 2.7 - - + +
283A ARG* 3.6 25.4 - - + +
284A LEU* 3.5 48.7 - - + +
287A ALA* 3.5 21.1 - - + -
288A ILE* 6.0 0.2 - - + -
295A GLU* 2.6 34.1 + - + +
296A ILE* 3.8 3.8 - - - +
298A VAL* 1.3 75.2 - - - +
300A LEU* 1.3 63.3 + - - +
302A LYS* 3.4 34.1 + - - +
303A LEU* 3.5 14.8 + - + +
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Residues in contact with LEU 300 (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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284A LEU* 3.6 25.8 - - + -
288A ILE* 4.5 3.8 - - + -
296A ILE* 2.8 43.3 + - + +
297A PRO* 3.7 7.2 - - + +
299A LEU* 1.3 69.9 - - - +
301A GLU* 1.3 66.9 + - - +
303A LEU* 2.9 15.4 + - - +
304A GLU 3.1 8.0 + - - -
305A ILE* 3.1 36.2 + - + +
307A LEU* 3.6 41.7 - - + +
323A VAL* 3.8 16.2 - - + -
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Residues in contact with GLU 301 (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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297A PRO 3.1 14.9 + - - +
298A VAL* 3.8 6.6 - - - +
300A LEU* 1.3 78.3 - - - +
302A LYS* 1.3 62.0 + - - +
304A GLU* 3.0 17.4 + - - +
305A ILE 4.7 3.1 + - - +
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Residues in contact with LYS 302 (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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283A ARG* 5.4 8.9 - - - +
298A VAL* 3.3 12.7 + - + +
299A LEU* 3.5 27.0 - - - +
300A LEU 3.0 1.0 + - - -
301A GLU* 1.3 78.8 - - - +
303A LEU* 1.3 66.7 + - + +
304A GLU* 3.1 2.2 + - - +
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Residues in contact with LEU 303 (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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228A ARG* 4.3 20.5 + - - +
229A TYR* 6.0 0.9 - - - +
280A PRO* 4.2 24.2 - - + +
284A LEU* 3.3 44.6 - - + -
299A LEU* 3.5 14.1 + - + +
300A LEU 2.9 8.2 + - - +
302A LYS* 1.3 84.2 - - + +
304A GLU* 1.3 70.1 + - - +
305A ILE* 3.3 15.7 + - + +
327A PHE* 4.1 24.7 - - + -
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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