Contacts of the helix formed by residues 354 - 363 (chain A) in PDB entry 5H1Y
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 PHE 354 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265A PRO* 3.8 20.6 - - + -
321A PRO* 3.9 35.4 - - + -
322A GLY* 5.4 4.3 - - - -
323A ARG* 6.2 2.0 - - - -
349A MET* 3.1 33.9 + - + +
352A MET* 3.8 37.5 - - + -
353A GLY* 1.3 78.7 - - - +
355A GLU* 1.3 63.8 + - - +
356A GLY 3.4 1.6 - - - -
357A ASP* 3.4 17.1 + - - +
358A ILE* 3.0 29.5 + - + +
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Residues in contact with GLU 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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349A MET 4.4 2.4 + - - -
350A ILE* 4.0 26.5 - - + +
353A GLY* 3.1 5.4 - - - +
354A PHE* 1.3 76.3 - - - +
356A GLY* 1.3 60.8 + - - +
358A ILE* 3.2 6.3 + - - +
359A ARG* 2.9 68.2 + - + +
381A LYS* 3.9 24.4 + - - +
385A PHE* 4.4 10.3 - - + +
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Residues in contact with GLY 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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353A GLY 4.4 3.6 + - - -
354A PHE 3.4 0.4 - - - -
355A GLU* 1.3 79.6 - - - +
357A ASP* 1.3 61.8 + - - +
359A ARG* 3.2 8.3 + - - +
360A THR* 2.8 34.5 + - - -
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Residues in contact with ASP 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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321A PRO* 4.4 16.8 - - + +
322A GLY* 3.9 17.3 + - - -
325A MET* 3.4 38.2 - - - +
353A GLY 5.2 1.7 + - - -
354A PHE* 3.4 21.2 + - - +
355A GLU 3.4 0.4 - - - -
356A GLY* 1.3 75.5 - - - +
358A ILE* 1.3 57.7 + - - +
360A THR* 3.4 2.8 + - - -
361A ILE* 2.9 33.4 + - - +
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Residues in contact with ILE 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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263A ILE* 4.7 9.0 - - + -
321A PRO* 4.2 14.4 - - + -
343A LEU* 4.4 10.8 - - + -
349A MET* 3.5 47.1 - - + -
350A ILE* 5.3 3.6 - - + -
354A PHE* 3.0 20.6 + - + +
355A GLU* 3.6 4.7 - - - +
357A ASP* 1.3 75.9 - - - +
359A ARG* 1.3 64.8 + - - +
360A THR 3.2 0.2 - - - -
361A ILE* 3.3 9.1 + - + +
362A PHE* 3.0 37.6 + - + -
385A PHE* 3.7 28.5 - - + -
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Residues in contact with ARG 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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355A GLU* 2.9 51.9 + - - +
356A GLY* 3.7 6.5 - - - +
358A ILE* 1.3 76.7 - - - +
360A THR* 1.3 63.7 + - - +
362A PHE* 3.3 30.6 - - + +
363A SER* 3.3 7.4 + - - -
384A ASN 4.9 1.0 + - - -
385A PHE* 3.6 29.6 - - + +
388A SER* 3.3 33.9 + - - -
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Residues in contact with THR 360 (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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325A MET* 3.9 19.7 - - + -
329A GLN* 3.9 24.2 - - - +
356A GLY 2.8 19.9 + - - -
357A ASP 3.5 9.2 - - - -
359A ARG* 1.3 74.7 - - - +
361A ILE* 1.3 66.8 + - - +
363A SER* 2.7 28.8 + - - +
364A TYR* 3.4 17.5 - - + -
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Residues in contact with ILE 361 (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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261A LEU* 4.6 3.1 - - + -
263A ILE* 4.0 22.0 - - + -
321A PRO* 3.6 33.2 - - + +
324A LEU* 3.9 29.8 - - + -
325A MET* 4.3 9.9 - - - -
328A LEU* 4.1 23.3 - - + -
335A LEU* 4.0 8.6 - - + +
341A LEU* 5.3 0.4 - - + -
357A ASP 2.9 22.3 + - - +
358A ILE* 3.3 11.0 + - - +
360A THR* 1.3 76.1 - - - +
362A PHE* 1.3 66.4 + - + +
364A TYR* 3.0 19.5 + - - +
365A PHE* 3.9 10.0 - - + -
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Residues in contact with PHE 362 (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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263A ILE* 5.9 0.2 - - + -
341A LEU* 3.4 30.7 - - + -
343A LEU* 3.9 12.3 - - + -
358A ILE* 3.0 37.9 + - + -
359A ARG* 3.3 22.4 - - + +
360A THR 3.1 0.4 - - - -
361A ILE* 1.3 76.8 - - + +
363A SER* 1.3 57.1 + - - +
364A TYR 3.0 5.9 + - - -
365A PHE* 3.1 27.4 + - - +
369A ARG* 3.5 28.8 + - - +
371A THR* 4.9 1.1 - - + -
385A PHE* 3.8 18.6 - + - -
388A SER* 6.0 0.7 - - - -
389A ALA* 3.7 33.7 - - + -
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Residues in contact with SER 363 (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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359A ARG 3.3 6.6 + - - -
360A THR* 2.7 25.9 + - - +
362A PHE* 1.3 77.1 - - - +
364A TYR* 1.3 67.4 + - - +
365A PHE 3.3 7.8 + - - +
366A LYS* 5.9 1.2 - - - +
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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