Contacts of the helix formed by residues 317 - 325 (chain A) in PDB entry 3TVX
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 ASN 317 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A GLU* 3.4 26.4 + - - +
315A GLY 3.4 4.5 + - - +
316A LEU* 1.3 73.2 - - - +
318A ILE* 1.3 61.3 + - - +
319A PHE* 3.1 23.5 + - - +
320A CYS* 3.2 24.9 + - - +
321A VAL* 3.2 22.9 + - - +
539A GLU* 4.4 15.0 + - - -
540A LEU* 3.4 25.0 - - + +
543A GLN* 5.4 2.0 - - - +
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Residues in contact with ILE 318 (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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316A LEU* 3.6 18.3 + - + +
317A ASN* 1.3 71.1 + - - +
319A PHE* 1.3 66.9 + - + +
321A VAL* 3.2 7.9 + - + +
322A SER* 2.8 28.2 + - - -
329A SER* 4.3 3.6 - - - -
333A ILE* 3.9 29.4 - - + -
375A LEU* 3.7 16.8 - - + -
378A ALA* 3.9 31.6 - - + +
379A ASP* 4.2 14.6 - - + +
382A GLN* 5.1 0.4 - - + -
540A LEU* 4.9 1.9 - - + +
544A TRP* 3.5 37.9 - - + -
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Residues in contact with PHE 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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317A ASN* 3.1 5.3 + - - +
318A ILE* 1.3 76.7 - - + +
320A CYS* 1.3 61.5 + - - +
322A SER* 3.4 7.4 + - - -
323A ASP* 3.0 34.4 + - - +
375A LEU* 4.0 17.3 - - + -
540A LEU* 3.5 36.1 - - + -
543A GLN* 3.7 41.7 - - + +
544A TRP* 3.6 44.9 - + - -
547A ARG* 3.5 32.5 - - - -
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Residues in contact with CYS 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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307A GLU* 3.3 34.1 - - + +
317A ASN* 3.2 27.6 + - - +
319A PHE* 1.3 76.6 - - - +
321A VAL* 1.3 61.1 + - - +
323A ASP* 3.2 9.8 + - - +
324A TYR* 2.9 51.4 + - + -
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Residues in contact with VAL 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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304A LEU* 4.1 13.4 - - + +
307A GLU* 4.3 12.8 - - + -
308A LEU* 5.0 3.6 - - + -
316A LEU* 3.8 22.9 - - + -
317A ASN 3.2 14.5 + - - +
318A ILE* 3.2 13.0 + - + +
320A CYS* 1.3 78.1 - - - +
322A SER* 1.3 57.1 + - - +
324A TYR* 3.3 1.3 + - - -
325A ALA* 2.8 34.3 + - - +
329A SER* 4.2 19.5 - - - -
332A CYS* 4.3 16.4 - - + -
333A ILE* 4.0 23.6 - - + -
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Residues in contact with SER 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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318A ILE 2.8 13.7 + - - -
319A PHE* 3.5 9.9 - - - -
320A CYS 3.2 0.2 - - - -
321A VAL* 1.3 75.8 - - - +
323A ASP* 1.3 63.3 + - - +
325A ALA 3.2 4.7 + - - -
327A GLY* 2.8 46.5 + - - -
329A SER* 4.1 13.1 + - - +
375A LEU* 3.9 26.2 - - - +
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Residues in contact with ASP 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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300A GLN* 4.1 8.4 + - - -
319A PHE* 3.0 21.2 + - - +
320A CYS* 3.4 12.2 - - - +
322A SER* 1.3 79.3 - - - +
324A TYR* 1.3 73.0 + - + +
325A ALA 3.4 0.2 + - - -
326A GLY* 3.6 8.8 + - - -
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Residues in contact with TYR 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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298A THR* 2.4 32.1 + - - -
300A GLN* 3.9 36.2 + - - +
303A LEU* 3.4 55.0 - - + +
304A LEU* 3.9 25.0 - - + +
307A GLU* 4.4 8.3 - - + -
320A CYS* 2.9 45.9 + - + +
323A ASP* 1.3 82.0 - - + +
325A ALA* 1.3 54.9 + - - +
326A GLY 3.4 1.7 + - - -
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Residues in contact with ALA 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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296A VAL* 3.7 29.3 - - + +
297A LYS 4.6 6.8 - - - +
298A THR* 4.5 1.8 - - - -
304A LEU* 4.4 9.0 - - + -
321A VAL 2.8 19.0 + - - +
322A SER 3.2 1.5 + - - +
324A TYR* 1.3 76.9 - - - +
326A GLY* 1.3 64.3 + - - +
327A GLY 3.2 2.0 - - - -
328A ARG* 3.1 30.9 + - - +
332A CYS* 4.3 9.0 - - + -
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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