Contacts of the helix formed by residues 326 - 333 (chain L) in PDB entry 5XTE
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 SER 326 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310L ILE 4.6 0.7 - - - -
311L ILE 2.3 35.1 + - - -
312L GLY* 3.4 19.2 + - - -
313L HIS 4.8 3.6 - - - -
325L SER* 1.3 83.4 + - - +
327L PRO* 1.3 60.5 - - - +
328L LEU 3.4 2.9 + - - -
329L ALA* 2.8 15.5 + - - -
330L SER* 2.4 35.0 + - - -
390L ARG* 5.1 5.8 - - - +
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Residues in contact with PRO 327 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101K ARG* 5.7 0.7 - - - +
310L ILE* 3.4 24.7 - - + +
311L ILE* 4.8 1.3 - - - +
325L SER 3.6 3.9 - - - +
326L SER* 1.3 88.7 - - - +
328L LEU* 1.3 57.0 + - - +
330L SER* 3.3 10.5 + - - -
331L GLY* 2.9 23.4 + - - -
371L VAL* 4.7 1.2 - - - +
375L GLN* 3.4 34.5 + - + +
378L ARG* 6.0 2.7 - - - +
387L GLU* 4.7 4.3 - - - +
390L ARG* 4.4 9.4 - - - +
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Residues in contact with LEU 328 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311L ILE* 3.4 39.3 - - + +
326L SER* 3.2 0.8 + - - -
327L PRO* 1.3 82.1 - - - +
329L ALA* 1.3 57.2 + - - +
331L GLY* 3.6 1.5 + - - +
332L ALA* 2.9 24.1 + - - +
338L CYS* 5.1 8.1 - - - -
341L PHE* 3.4 32.5 - - + -
343L THR* 4.6 1.8 - - - +
356L ALA* 5.4 2.0 - - + -
358L PHE* 6.5 0.4 - - + -
368L MET* 4.7 3.4 - - - +
371L VAL* 3.6 27.1 - - + -
372L LEU* 3.6 35.0 - - + +
375L GLN* 4.3 7.8 - - + -
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Residues in contact with ALA 329 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314L TYR* 3.4 33.9 - - + -
322L VAL 3.8 6.0 - - - +
324L LEU 4.6 0.7 - - - -
325L SER* 3.4 19.5 - - - +
326L SER* 2.8 19.4 + - - +
328L LEU* 1.3 77.0 - - - +
330L SER* 1.3 57.4 + - - +
331L GLY 3.1 1.8 - - - -
332L ALA* 3.2 9.2 - - - +
333L VAL* 2.8 28.4 + - - +
341L PHE* 3.5 3.6 - - + -
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Residues in contact with SER 330 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101K ARG* 4.8 2.2 - - - -
322L VAL 3.6 10.5 - - - -
323L HIS* 3.1 38.2 + - - +
324L LEU 4.2 0.4 + - - -
326L SER 2.4 23.9 + - - -
327L PRO* 3.5 12.3 - - - -
329L ALA* 1.3 72.1 - - - +
331L GLY* 1.3 58.4 + - - +
333L VAL 3.1 17.2 - - - +
334L ALA* 3.4 11.8 - - - +
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Residues in contact with GLY 331 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327L PRO 2.9 15.2 + - - -
328L LEU 3.7 2.5 - - - -
330L SER* 1.3 77.4 - - - +
332L ALA* 1.3 62.5 + - - +
333L VAL 3.2 0.8 + - - -
334L ALA* 4.3 8.9 + - - +
335L ASN 5.1 0.7 + - - -
337L LEU* 3.1 28.9 + - - +
371L VAL* 4.5 15.9 - - - -
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Residues in contact with ALA 332 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314L TYR* 4.3 6.1 - - + -
328L LEU 2.9 16.8 + - - +
329L ALA* 3.0 11.4 + - - +
331L GLY* 1.3 79.3 - - - +
333L VAL* 1.3 59.3 + - - +
336L LYS* 3.4 1.0 - - - +
337L LEU* 2.4 30.3 + - - -
338L CYS* 3.2 41.0 + - + +
341L PHE* 3.5 13.0 - - + -
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Residues in contact with VAL 333 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314L TYR* 3.3 35.0 - - + +
316L CYS* 3.8 7.0 - - - -
322L VAL* 2.8 59.4 - - + +
323L HIS* 3.8 0.7 + - - -
329L ALA 2.8 5.2 + - - +
330L SER 3.1 6.1 - - - +
332L ALA* 1.3 85.0 - - - +
334L ALA* 1.3 60.7 + - - +
336L LYS* 3.6 39.0 - - + +
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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