Contacts of the helix formed by residues 318 - 329 (chain A) in PDB entry 1R00
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 THR 318 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A ARG* 4.2 13.5 - - - +
316A VAL* 4.1 2.1 + - - +
317A ARG* 1.3 77.0 - - - +
319A ARG* 1.3 64.5 + - - +
320A ASP* 3.6 9.6 + - - +
321A GLU* 3.0 34.9 + - - +
322A VAL* 3.1 18.8 + - - +
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Residues in contact with ARG 319 (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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288A ARG* 4.3 28.2 - - - +
318A THR* 1.3 73.1 - - - +
320A ASP* 1.3 70.4 + - - +
322A VAL* 3.3 7.7 + - - +
323A VAL* 3.1 29.4 + - + +
336A GLU* 3.1 44.4 + - - +
338A THR* 3.9 21.6 + - - +
349A SER* 5.1 6.7 - - - +
351A LEU* 4.8 10.7 - - + +
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Residues in contact with ASP 320 (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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318A THR* 3.3 9.0 + - - +
319A ARG* 1.3 81.3 - - - +
321A GLU* 1.3 63.9 + - + +
323A VAL* 3.1 9.2 + - - +
324A ASP* 3.1 31.8 + - - +
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Residues in contact with GLU 321 (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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315A ARG* 3.0 31.2 + - - +
316A VAL 4.4 1.6 - - - +
317A ARG* 3.4 21.2 - - + -
318A THR* 3.0 41.5 + - - +
319A ARG 3.3 0.2 - - - -
320A ASP* 1.3 78.7 - - + +
322A VAL* 1.3 62.9 + - - +
323A VAL 3.2 0.2 + - - -
324A ASP* 3.3 6.8 + - - +
325A LEU* 3.0 24.9 + - - +
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Residues in contact with VAL 322 (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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258A LEU* 4.3 25.6 - - + -
270A LEU* 5.4 1.0 - - + +
285A VAL* 4.6 7.0 - - + -
287A ASP* 6.4 2.2 - - + -
317A ARG* 3.6 29.4 - - + +
318A THR 3.1 15.7 + - - +
319A ARG 3.3 7.2 + - - +
321A GLU* 1.3 76.1 - - - +
323A VAL* 1.3 56.0 + - - +
325A LEU* 3.5 10.4 - - + +
326A ALA* 2.9 28.4 + - + +
351A LEU* 3.6 26.9 - - + -
353A PHE* 4.6 7.0 - - + -
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Residues in contact with VAL 323 (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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319A ARG* 3.1 17.8 + - + +
320A ASP* 3.5 11.0 - - - +
321A GLU 3.1 0.2 - - - -
322A VAL* 1.3 76.9 - - - +
324A ASP* 1.3 66.4 + - - +
326A ALA* 3.5 2.6 + - - +
327A GLY* 2.9 22.5 + - - -
331A LEU 4.8 1.4 - - - +
333A LEU* 4.3 32.5 - - + +
351A LEU* 4.3 19.7 - - + -
353A PHE* 4.3 13.1 - - + -
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Residues in contact with ASP 324 (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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320A ASP* 3.1 20.2 + - - +
321A GLU* 4.0 6.1 - - - +
323A VAL* 1.3 79.9 - - - +
325A LEU* 1.3 66.9 + - - +
327A GLY* 3.0 3.6 + - - +
328A SER* 2.9 24.3 + - - -
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Residues in contact with LEU 325 (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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258A LEU* 5.4 5.8 - - + -
263A ASP* 3.9 31.0 - - + +
266A ALA* 4.1 13.0 - - + -
267A LEU* 3.9 16.3 - - + +
270A LEU* 4.3 15.4 - - + +
317A ARG* 3.9 40.2 - - - +
321A GLU 3.0 15.6 + - - +
322A VAL* 3.5 8.5 - - + +
324A ASP* 1.3 77.2 - - - +
326A ALA* 1.3 61.0 + - - +
328A SER* 3.3 16.5 + - - +
329A ALA* 3.4 12.1 + - - +
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Residues in contact with ALA 326 (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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270A LEU* 4.3 15.0 - - + +
322A VAL* 2.9 20.2 + - + +
323A VAL 3.7 1.3 - - - +
325A LEU* 1.3 75.4 - - - +
327A GLY* 1.3 61.9 + - - +
329A ALA* 3.1 10.7 + - - +
330A GLY 3.2 0.9 + - - -
331A LEU* 3.1 33.7 + - + +
353A PHE* 3.4 38.8 - - + -
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Residues in contact with GLY 327 (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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323A VAL 2.9 15.9 + - - -
324A ASP* 3.0 7.5 + - - -
326A ALA* 1.3 76.3 - - - +
328A SER* 1.3 58.8 + - - +
330A GLY* 3.3 12.8 + - - -
331A LEU 3.4 15.2 + - - -
356A VAL* 5.4 1.4 - - - +
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Residues in contact with SER 328 (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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267A LEU* 3.0 29.3 - - - +
271A ARG* 3.2 21.2 + - - -
324A ASP 2.9 12.4 + - - -
325A LEU* 3.3 6.1 + - - +
327A GLY* 1.3 76.1 - - - +
329A ALA* 1.3 58.5 + - - +
330A GLY 3.4 0.8 + - - -
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Residues in contact with ALA 329 (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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267A LEU* 3.8 14.1 - - + -
270A LEU* 3.7 31.0 - - + -
271A ARG* 4.1 20.0 - - - +
274A VAL* 3.5 20.9 - - - +
325A LEU 3.4 4.6 + - - +
326A ALA 3.1 11.3 + - - +
328A SER* 1.3 79.5 + - - +
330A GLY* 1.3 56.1 + - - +
331A LEU* 4.4 4.9 - - + -
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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