Contacts of the helix formed by residues 350 - 359 (chain A) in PDB entry 5EO3
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 HIS 350 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A GLU* 4.5 13.7 - - - +
347A SER* 4.5 5.4 + - - -
348A SER* 3.4 3.2 - - - +
349A LEU* 1.3 127.3 + - + +
351A VAL* 1.3 67.5 - - + +
352A SER* 3.2 16.4 - - - +
353A GLY* 3.5 1.3 + - - +
354A GLU* 3.0 23.9 + - - +
275B VAL* 6.0 4.9 - - + -
279B ASP* 3.5 27.0 + - - +
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Residues in contact with VAL 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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350A HIS* 1.3 74.9 - - - +
352A SER* 1.3 59.0 + - - +
354A GLU* 3.2 7.9 + - - +
355A GLN* 2.8 35.9 + - - +
275B VAL* 4.1 12.8 - - + -
278B LEU* 4.1 23.3 - - + -
279B ASP* 3.0 23.3 + - - +
282B TYR* 4.1 27.4 - - + -
351B VAL* 4.1 20.6 - - + +
355B GLN* 4.1 23.2 - - + +
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Residues in contact with SER 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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274A GLU* 3.2 33.2 + - - +
275A VAL* 4.7 13.0 - - - +
278A LEU* 3.4 26.6 - - - +
346A PHE* 4.4 2.7 - - - -
350A HIS* 3.6 13.0 - - - +
351A VAL* 1.3 80.7 - - - +
353A GLY* 1.3 62.2 + - - +
355A GLN* 3.2 3.3 + - - +
356A LEU* 3.1 18.5 + - - +
275B VAL* 4.9 5.4 - - - +
351B VAL* 4.6 12.6 - - - -
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Residues in contact with GLY 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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274A GLU* 4.2 3.0 + - - -
314A SER* 4.3 2.9 + - - -
346A PHE* 4.2 13.7 - - - -
347A SER 3.3 26.3 + - - -
348A SER* 4.3 5.4 - - - -
350A HIS* 3.5 5.5 + - - +
351A VAL 3.4 0.2 - - - -
352A SER* 1.3 78.6 + - - +
354A GLU* 1.3 65.9 + - - +
356A LEU* 3.4 3.0 + - - +
357A SER* 2.9 26.2 + - - -
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Residues in contact with GLU 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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348A SER* 4.6 12.3 - - - +
350A HIS 3.0 19.0 + - - +
351A VAL* 3.2 10.3 + - - +
353A GLY* 1.3 76.1 - - - +
355A GLN* 1.3 63.4 + - + +
357A SER* 3.2 11.9 + - - -
358A GLN* 3.2 42.9 + - - +
355B GLN* 5.7 1.8 - - - +
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Residues in contact with GLN 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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278A LEU* 4.0 1.6 - - + +
282A TYR* 2.7 34.0 + - - +
351A VAL* 2.8 16.0 + - - +
352A SER 3.5 3.6 - - - +
354A GLU* 1.3 74.4 - - - +
356A LEU* 1.3 65.2 + - - +
357A SER 3.0 1.3 - - - -
358A GLN* 2.9 20.0 + - + +
359A LEU* 3.3 16.2 + - - +
351B VAL* 3.1 47.9 - - - +
354B GLU* 4.0 6.9 - - - -
355B GLN* 2.8 36.0 + - - +
358B GLN* 5.5 3.8 - - - +
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Residues in contact with LEU 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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278A LEU* 4.5 8.3 - - + +
312A LEU* 3.9 19.5 - - + +
313A ILE 3.8 7.4 - - - +
314A SER* 3.7 19.5 - - - +
346A PHE* 3.5 41.3 - - + -
352A SER 3.1 12.0 + - - +
353A GLY* 3.7 8.5 - - - +
355A GLN* 1.3 76.7 - - - +
357A SER* 1.3 58.7 + - - +
359A LEU* 2.8 28.0 + - + -
361A GLY* 3.0 30.0 + - - +
362A VAL 4.2 0.7 - - - +
363A ALA* 4.0 22.2 - - + +
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Residues in contact with SER 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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314A SER* 3.3 17.2 + - - -
316A GLU* 3.7 14.7 + - - +
348A SER* 4.8 6.0 - - - -
353A GLY 2.9 16.2 + - - -
354A GLU* 3.3 21.1 - - - -
355A GLN 3.0 0.2 - - - -
356A LEU* 1.3 78.2 - - - +
358A GLN* 1.3 62.1 + - - +
360A THR* 3.4 11.5 + - - -
361A GLY* 3.9 9.4 + - - +
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Residues in contact with GLN 358 (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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354A GLU* 3.2 29.1 + - - +
355A GLN* 2.9 15.7 + - + +
357A SER* 1.3 78.6 - - - +
359A LEU* 1.3 61.9 + - + +
360A THR* 3.2 6.5 + - - +
358B GLN* 5.8 3.4 - - - +
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Residues in contact with LEU 359 (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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278A LEU* 4.8 2.9 - - + -
281A PHE* 4.1 26.0 - - + -
282A TYR* 4.5 20.4 - - + +
285A LEU* 6.4 0.9 - - + -
294A TYR* 3.4 41.6 - - + -
355A GLN 3.5 14.8 - - - +
356A LEU* 2.8 23.9 + - + +
358A GLN* 1.3 82.0 - - + +
360A THR* 1.3 76.7 + - - +
361A GLY 3.3 4.1 + - - -
362A VAL 3.5 7.1 - - - +
363A ALA* 5.0 1.3 - - + -
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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