Contacts of the helix formed by residues 346 - 354 (chain A) in PDB entry 4Y5O
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 ARG 346 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A LYS* 3.5 20.3 + - - +
310A LEU* 4.1 16.1 - - + +
311A SER* 4.6 1.4 - - - +
314A GLU* 3.0 37.3 + - - -
342A TYR* 3.7 40.6 - - + +
343A GLY 3.2 8.3 + - - +
344A ASP 2.9 1.6 + - - -
345A SER* 1.3 110.5 + - - +
347A LYS* 1.3 63.0 + - - +
348A PHE* 3.3 24.7 - - + -
349A LEU* 3.4 12.2 + - + +
350A LEU* 3.2 18.4 - - - +
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Residues in contact with LYS 347 (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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343A GLY 4.2 1.1 + - - -
344A ASP* 3.2 18.2 + - - +
345A SER 3.6 1.4 - - - -
346A ARG* 1.3 74.1 - - - +
348A PHE* 1.3 67.8 - - - +
350A LEU* 2.9 13.1 + - - +
351A LEU* 2.9 37.6 + - + +
369A LEU* 5.6 6.3 - - + -
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Residues in contact with PHE 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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302A TYR* 4.6 1.6 - - - -
305A THR* 3.8 18.0 - - + +
306A LEU* 5.7 2.2 - - + -
309A LYS* 3.6 54.1 - - + -
310A LEU* 4.0 16.8 - - + -
345A SER 3.0 27.8 - - - -
346A ARG* 3.5 26.5 - - - -
347A LYS* 1.3 77.5 - - - +
349A LEU* 1.3 72.0 + - + +
351A LEU* 3.7 10.2 - - - +
352A GLY* 2.7 33.6 + - - -
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Residues in contact with LEU 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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302A TYR* 2.9 47.1 + - - +
306A LEU* 3.7 17.5 - - + -
310A LEU* 4.6 8.5 - - + -
318A PHE* 3.6 28.0 - - + -
338A LEU* 5.1 0.9 - - + -
342A TYR* 3.6 50.0 - - + -
346A ARG* 3.4 12.6 - - + +
347A LYS 3.1 0.8 - - - -
348A PHE* 1.3 98.1 - - + +
350A LEU* 1.3 69.9 + - + +
353A LEU* 3.2 11.1 + - + +
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Residues in contact with LEU 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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338A LEU* 4.9 11.4 - - + -
339A ARG* 6.0 0.4 - - - -
342A TYR* 4.1 31.0 - - + +
343A GLY 5.7 0.2 - - - +
346A ARG 3.2 19.1 - - - +
347A LYS* 2.9 10.4 + - - +
349A LEU* 1.3 90.3 - - + +
351A LEU* 1.3 62.0 + - + +
353A LEU* 3.1 12.7 + - - +
365A PHE* 3.2 34.0 - - + -
368A PHE* 3.7 37.0 - - + +
369A LEU* 5.7 11.9 - - + -
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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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347A LYS* 2.9 31.7 + - + +
348A PHE* 3.7 8.7 - - - +
350A LEU* 1.3 77.0 - - - +
352A GLY* 1.3 57.2 + - - +
354A ARG* 3.0 60.8 + - - +
355A PRO* 3.8 3.5 - - - +
365A PHE* 5.4 0.2 - - - -
369A LEU* 4.1 31.4 - - + +
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Residues in contact with GLY 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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302A TYR* 3.2 31.0 - - - +
348A PHE 2.7 21.5 + - - -
351A LEU* 1.3 73.6 - - - +
353A LEU* 1.3 59.0 + - - +
354A ARG 3.4 0.2 - - - -
355A PRO* 3.5 6.8 - - - +
356A PHE* 3.5 15.8 - - - -
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Residues in contact with LEU 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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302A TYR* 3.4 18.2 - - + +
318A PHE* 4.0 24.9 - - + -
322A LEU* 4.3 4.7 - - + -
334A PHE* 4.0 26.5 - - + -
338A LEU* 5.4 2.9 - - + -
349A LEU* 3.2 12.1 + - + +
350A LEU* 3.1 13.4 + - - +
351A LEU 3.0 0.6 - - - -
352A GLY* 1.3 79.0 - - - +
354A ARG* 1.3 64.2 + - - +
355A PRO* 3.3 2.2 - - - -
356A PHE* 3.0 18.5 + - + +
357A ILE* 3.4 18.4 - - + +
365A PHE* 4.3 10.3 - - + -
14B LEU* 3.7 30.5 - - + -
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Residues in contact with ARG 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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350A LEU 3.4 3.8 + - - +
351A LEU* 3.0 45.4 + - - +
353A LEU* 1.3 75.6 - - - +
355A PRO* 1.3 67.9 - - + +
357A ILE* 3.1 22.4 + - - +
362A SER* 5.1 4.9 - - - -
365A PHE* 3.8 22.9 - - + -
366A GLU* 3.9 40.2 - - + +
369A LEU* 5.2 7.7 - - - +
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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