Contacts of the helix formed by residues 319 - 327 (chain E) in PDB entry 4Q9U
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 LEU 319 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298E ILE* 5.8 1.3 - - - -
318E THR* 1.3 90.9 - - - +
320E ILE* 1.3 76.5 + - + +
322E ILE* 3.2 16.8 - - - +
323E VAL* 3.1 26.6 - - + +
358E ASN* 3.9 41.5 - - + +
359E LEU* 5.9 3.1 - - + -
361E CYS* 4.1 11.2 - - - -
362E ALA* 3.9 17.7 - - + -
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Residues in contact with ILE 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253E LEU* 3.7 22.7 - - + -
318E THR 4.6 6.3 - - - +
319E LEU* 1.3 99.2 - - + +
321E TYR* 1.3 58.3 + - - +
323E VAL* 4.3 0.6 - - - +
324E LEU* 3.0 41.9 + - + +
362E ALA* 4.2 9.4 - - + -
365E PHE* 3.4 41.1 - - + -
366E ILE* 4.3 14.8 - - + -
369E LEU* 5.1 3.1 - - + -
82F TYR* 4.3 26.2 - - + +
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Residues in contact with TYR 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248E VAL 6.1 0.4 - - - -
249E THR* 5.5 1.3 - - - -
250E PRO* 3.3 41.3 - - + +
253E LEU* 4.2 7.8 - - + +
255E VAL* 3.3 37.5 - - + -
257E VAL* 4.1 22.0 - - + -
259E GLU* 3.3 28.8 + - - -
268E VAL* 6.3 2.2 - - + -
318E THR* 3.1 12.2 + - - +
320E ILE* 1.3 78.9 - - - +
322E ILE* 1.3 67.8 + - - +
324E LEU* 4.3 2.9 - - + -
325E LYS* 3.4 44.5 + - + +
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Residues in contact with ILE 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271E ALA* 3.2 41.3 - - + +
272E ILE* 3.2 26.6 - - + +
275E ILE* 3.7 17.5 - - + -
294E CYS* 4.2 1.6 - - - -
298E ILE* 3.7 41.1 - - + -
318E THR 3.1 13.8 + - - +
319E LEU* 3.2 23.1 - - - +
321E TYR* 1.3 77.6 - - - +
323E VAL* 1.3 73.5 + - + +
324E LEU 3.1 0.2 + - - -
325E LYS* 3.2 0.7 + - - -
326E GLY 3.2 12.3 + - - -
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Residues in contact with VAL 323 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242E ILE* 4.9 7.6 - - + +
275E ILE* 6.0 5.4 - - + -
319E LEU* 3.1 20.5 + - + +
320E ILE* 4.3 2.2 - - - +
322E ILE* 1.3 83.6 - - + +
324E LEU* 1.3 59.1 + - + +
326E GLY* 2.7 23.8 + - - -
327E ASN 3.1 12.3 + - - -
328E PRO* 3.9 27.5 - - + +
331E LEU* 5.1 6.5 - - + -
359E LEU* 6.6 0.2 - - + -
362E ALA* 5.6 6.3 - - + -
363E VAL* 6.1 7.4 - - + -
366E ILE* 5.1 10.1 - - + -
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Residues in contact with LEU 324 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242E ILE* 3.8 38.0 - - + +
245E LEU* 3.8 38.4 - - + +
246E ARG* 6.0 1.8 - - - -
248E VAL* 5.1 7.4 - - + -
320E ILE* 3.0 23.2 + - + +
321E TYR* 4.4 4.0 - - + +
323E VAL* 1.3 81.1 - - + +
325E LYS* 1.3 63.3 + - + +
327E ASN 4.6 0.4 - - - -
366E ILE* 3.7 40.6 - - + -
369E LEU* 5.7 4.0 - - + -
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Residues in contact with LYS 325 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246E ARG 5.4 4.6 + - - -
248E VAL 4.4 15.6 + - - +
249E THR* 5.2 7.7 - - - +
250E PRO* 5.6 1.7 - - - +
259E GLU* 4.7 7.4 - - - -
272E ILE* 4.1 10.7 - - + +
321E TYR* 3.4 46.8 + - + +
322E ILE* 3.2 5.0 + - - +
324E LEU* 1.3 80.5 - - + +
326E GLY* 1.3 60.1 + - - +
327E ASN* 5.0 1.8 - - - +
583H ASP* 6.0 1.8 - - - +
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Residues in contact with GLY 326 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272E ILE* 3.4 27.0 - - - +
275E ILE* 6.0 0.7 - - - -
276E ILE* 4.2 14.1 - - - +
322E ILE 3.2 5.1 + - - -
323E VAL* 2.7 16.3 + - - -
325E LYS* 1.3 71.1 - - - +
327E ASN* 1.3 68.7 + - - +
328E PRO* 3.7 3.8 - - - -
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Residues in contact with ASN 327 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238E ILE* 4.2 1.2 - - - +
239E GLN* 3.7 19.8 + - - +
242E ILE* 3.1 43.1 - - + +
243E ARG* 3.5 29.3 - - - +
323E VAL 3.1 5.1 + - - -
325E LYS 3.8 2.6 - - - +
326E GLY* 1.3 78.2 - - - +
328E PRO* 1.3 71.9 - - - +
329E PRO* 3.8 3.1 - - - +
576H LYS* 5.4 5.5 - - - +
579H GLN* 3.6 25.2 + - - +
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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