Contacts of the helix formed by residues 317 - 326 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B GLU* 3.7 20.7 + - - +
310B ASN* 5.8 0.4 - - - +
315B GLY 3.4 4.6 + - - +
316B LEU* 1.3 79.4 - - - +
318B ILE* 1.3 60.5 + - - +
319B PHE* 3.1 25.2 + - - +
320B CYS* 3.2 25.8 + - - +
321B VAL* 3.3 21.5 + - - +
539B GLU* 6.2 0.2 - - - +
540B LEU* 3.5 24.5 - - + +
543B GLN* 5.5 1.6 - - - +
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Residues in contact with ILE 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B LEU* 3.8 23.7 + - + +
317B ASN* 1.3 73.2 + - - +
319B PHE* 1.3 65.1 + - + +
321B VAL* 3.5 8.6 - - + +
322B SER* 2.9 28.4 + - - -
329B SER* 4.6 2.0 - - - +
333B ILE* 3.9 23.8 - - + -
375B LEU* 3.5 18.3 - - + +
378B ALA* 3.8 32.1 - - + +
379B ASP* 4.2 13.0 - - + +
382B GLN* 4.9 1.8 - - + +
540B LEU* 5.3 1.4 - - + +
544B TRP* 3.6 37.2 - - + -
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Residues in contact with PHE 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B ASN* 3.1 12.3 + - - +
318B ILE* 1.3 77.0 - - + +
320B CYS* 1.3 60.2 + - - +
322B SER* 3.5 6.7 + - - -
323B ASP* 3.0 34.3 + - - +
375B LEU* 3.8 16.6 - - + -
540B LEU* 3.7 17.9 - - + -
543B GLN* 3.6 49.6 - - + +
544B TRP* 3.4 54.7 - + - -
547B ARG* 3.8 28.9 - - - -
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Residues in contact with CYS 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B GLU* 3.3 36.6 - - + +
317B ASN* 3.2 24.5 + - - +
319B PHE* 1.3 75.8 - - - +
321B VAL* 1.3 67.2 + - - +
323B ASP* 3.1 13.1 + - - +
324B TYR* 2.8 44.8 + - + -
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Residues in contact with VAL 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LEU* 3.8 19.9 - - + +
307B GLU* 4.4 17.0 - - + -
308B LEU* 4.8 5.8 - - + -
316B LEU* 4.4 8.3 - - + -
317B ASN 3.3 15.1 + - - +
318B ILE* 3.5 15.9 - - + +
320B CYS* 1.3 75.2 - - - +
322B SER* 1.3 52.6 + - - +
324B TYR* 3.1 3.0 + - - -
325B ALA* 2.7 38.7 + - + +
329B SER* 4.6 14.1 - - - +
332B CYS* 4.3 13.7 - - - -
333B ILE* 4.2 28.3 - - + -
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Residues in contact with SER 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ILE 2.9 17.6 + - - -
319B PHE* 3.6 7.0 - - - -
321B VAL* 1.3 74.4 - - - +
323B ASP* 1.3 62.9 + - - +
325B ALA* 4.5 2.0 - - - -
326B GLY* 3.0 18.5 + - - -
327B GLY* 3.0 24.6 + - - -
329B SER* 3.8 20.3 + - - +
375B LEU* 3.7 24.4 - - - +
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Residues in contact with ASP 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B ASP* 5.3 1.0 - - - +
300B GLN* 4.6 8.2 + - - -
319B PHE* 3.0 23.5 + - - +
320B CYS* 3.1 14.3 + - - +
322B SER* 1.3 77.9 - - - +
324B TYR* 1.3 74.0 + - + +
326B GLY* 3.3 10.4 + - - -
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Residues in contact with TYR 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B THR* 2.6 31.0 + - - -
299B ASP* 4.4 4.6 - - - +
300B GLN* 3.3 36.9 + - + +
303B LEU* 3.6 60.3 - - + +
304B LEU* 3.8 25.0 - - + +
307B GLU* 4.1 7.2 - - + -
320B CYS* 2.8 49.7 + - + +
321B VAL 3.5 0.4 - - - -
323B ASP* 1.3 81.9 - - + +
325B ALA* 1.3 56.6 + - - +
326B GLY 3.4 0.6 + - - -
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Residues in contact with ALA 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B VAL* 3.8 29.4 - - + +
297B LYS 4.5 8.6 - - - +
298B THR* 5.0 0.9 - - - -
299B ASP* 5.7 0.4 - - - -
304B LEU* 4.6 5.6 - - + -
321B VAL* 2.7 18.9 + - + +
322B SER* 4.0 2.9 - - - +
323B ASP 3.2 0.2 - - - -
324B TYR* 1.3 77.1 - - - +
326B GLY* 1.3 65.1 + - - +
327B GLY 3.4 0.4 - - - -
328B ARG* 3.5 32.2 + - - +
329B SER 4.5 0.4 - - - +
332B CYS* 4.3 7.4 - - + -
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Residues in contact with GLY 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B ASP* 5.3 5.7 + - - -
322B SER 3.0 4.7 + - - -
323B ASP 3.3 10.6 + - - -
324B TYR 3.4 1.2 - - - -
325B ALA* 1.3 79.6 - - - +
327B GLY* 1.3 57.4 + - - +
328B ARG* 3.3 10.6 + - - +
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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