Contacts of the helix formed by residues 347 - 357 (chain A) in PDB entry 5E3H
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 347 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296A PHE* 4.8 0.2 - - - -
297A ALA 3.6 11.1 + - - +
298A ASN* 4.9 0.7 - - - -
299A GLN 5.8 0.7 - - - -
300A ILE* 4.4 9.0 - - - +
303A TYR* 4.6 6.6 - - - +
324A ILE 3.7 9.4 + - - -
325A SER* 4.5 1.7 - - - -
346A LEU* 1.3 78.9 - - - +
348A PRO* 1.3 79.1 - - + +
349A GLN* 3.7 8.5 - - + +
350A ILE* 3.2 24.0 + - - +
351A LEU 3.7 3.1 + - - -
13C C 3.3 41.4 + - - +
14C G 3.4 18.9 + - - +
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Residues in contact with PRO 348 (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 PHE* 4.2 5.8 - - + -
297A ALA 3.7 12.8 - - - +
298A ASN* 3.9 15.7 - - + -
346A LEU 3.9 2.2 - - - +
347A THR* 1.3 91.2 - - + +
349A GLN* 1.3 64.3 + - - +
350A ILE 3.0 0.4 - - - -
351A LEU* 2.9 16.2 + - - +
352A VAL* 3.0 15.4 + - - +
381A HIS* 4.9 0.9 - - + -
382A PRO* 3.6 19.1 - - + -
383A TYR* 3.6 38.6 - - + -
386A ILE* 3.6 19.0 - - + +
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Residues in contact with GLN 349 (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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347A THR 3.3 1.0 - - - -
348A PRO* 1.3 80.3 - - + +
350A ILE* 1.3 58.0 + - - +
352A VAL* 3.8 13.9 - - - +
353A ASN* 3.0 62.0 + - - +
382A PRO* 3.5 28.3 - - + +
2B G 5.8 1.8 - - - +
3B A 4.7 16.3 + - - +
13C C 3.2 26.7 - - + +
14C G 3.4 28.6 + - - +
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Residues in contact with ILE 350 (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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324A ILE* 3.3 43.3 - - + +
325A SER* 3.3 30.3 - - - +
326A GLY* 3.7 2.7 - - - +
329A ALA* 4.5 6.3 - - + -
334A VAL* 5.3 4.5 - - + -
346A LEU* 4.5 10.8 - - + -
347A THR* 3.2 13.2 + - - +
348A PRO 3.0 0.6 - - - -
349A GLN* 1.3 76.7 - - - +
351A LEU* 1.3 61.4 + - - +
352A VAL 3.2 0.2 - - - -
353A ASN* 3.4 5.5 + - - +
354A ASN* 2.9 49.4 + - - +
14C G 3.8 26.2 - - - +
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Residues in contact with LEU 351 (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 PHE* 3.5 32.3 - - + -
346A LEU* 3.7 19.9 - - + +
347A THR 3.7 1.6 + - - -
348A PRO 2.9 7.4 + - - +
350A ILE* 1.3 76.8 - - - +
352A VAL* 1.3 60.7 + - - +
354A ASN* 4.5 2.0 - - - +
355A LEU* 3.0 49.5 + - + +
360A ILE* 3.5 28.9 - - + -
363A LEU* 4.0 12.6 - - + -
366A PHE* 4.3 19.3 - - + -
386A ILE* 3.6 23.6 - - + -
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Residues in contact with VAL 352 (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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348A PRO 3.0 15.4 + - - +
349A GLN* 3.8 18.2 - - - +
351A LEU* 1.3 77.5 - - - +
353A ASN* 1.3 63.0 + - - +
355A LEU* 3.3 9.2 + - - +
356A LYS* 3.0 33.5 + - + +
382A PRO* 3.6 29.2 - - + +
385A MET* 3.9 23.3 - - + -
386A ILE* 3.8 9.2 - - + +
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Residues in contact with ASN 353 (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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349A GLN* 3.0 42.5 + - - +
350A ILE* 3.8 7.9 - - - +
351A LEU 3.3 0.2 - - - -
352A VAL* 1.3 79.7 - - - +
354A ASN* 1.3 61.3 + - - +
356A LYS* 3.4 8.2 + - - +
357A LYS* 2.9 32.8 + - - +
14C G 3.3 26.9 + - - -
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Residues in contact with ASN 354 (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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334A VAL* 3.2 37.7 - - - +
350A ILE* 2.9 41.7 + - - +
351A LEU 4.0 0.7 - - - +
353A ASN* 1.3 79.0 - - - +
355A LEU* 1.3 61.5 + - - +
357A LYS* 4.0 3.1 - - - -
358A GLY 3.3 0.3 + - - -
359A THR* 2.5 36.8 + - - +
360A ILE* 3.0 44.0 + - + -
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Residues in contact with LEU 355 (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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351A LEU* 3.0 33.9 + - + +
352A VAL* 3.7 7.9 - - - +
354A ASN* 1.3 77.4 - - - +
356A LYS* 1.3 65.2 + - - +
358A GLY* 3.1 13.7 + - - -
360A ILE* 3.5 34.5 - - + +
361A PRO 4.8 1.3 - - - +
362A SER* 4.7 7.0 - - - -
363A LEU* 4.0 23.8 - - + -
385A MET 5.4 0.4 - - - +
386A ILE* 4.8 9.0 - - - -
389A ASN* 3.6 44.8 + - + +
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Residues in contact with LYS 356 (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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352A VAL* 3.0 23.1 + - + +
353A ASN* 3.9 7.0 - - - +
355A LEU* 1.3 77.4 - - - +
357A LYS* 1.3 61.8 + - - +
358A GLY* 3.4 1.0 + - - -
828A GLU* 3.3 25.0 + - - -
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Residues in contact with LYS 357 (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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353A ASN 2.9 19.7 + - - +
354A ASN* 4.4 1.1 - - - +
356A LYS* 1.3 76.7 - - - +
358A GLY* 1.3 59.1 + - - +
359A THR* 3.2 22.5 + - + +
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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