Contacts of the helix formed by residues 389 - 396 (chain B) in PDB entry 5Y9F
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 MET 389 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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384B LEU* 3.8 44.6 - - + +
385B THR 3.4 13.2 - - - +
386B THR* 5.7 3.8 - - - -
388B VAL* 1.3 79.9 - - - +
390B SER* 1.3 56.1 + - - +
391B TYR 3.3 0.7 - - - -
392B ILE* 3.5 21.6 - - - +
393B HIS* 2.5 34.8 + - - +
400B LEU* 3.2 30.8 - - + +
404B ASN 5.2 5.8 - - - +
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Residues in contact with SER 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B THR* 5.6 0.9 - - - -
387B GLU* 2.7 35.8 + - - -
388B VAL 2.5 11.3 + - - -
389B MET* 1.3 74.2 - - - +
391B TYR* 1.3 57.5 + - - -
393B HIS* 3.3 9.3 + - - +
394B ASN* 2.9 28.4 + - - +
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Residues in contact with TYR 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LYS 4.0 15.3 - - - -
21B VAL* 3.3 15.5 - - + +
22B VAL* 2.8 51.8 + - + -
24B THR* 5.6 0.2 - - - +
27B TYR* 3.2 45.8 + + - -
242B TYR* 3.9 16.9 + + - -
387B GLU 2.9 21.5 + - - +
388B VAL* 4.4 4.5 - - - -
390B SER* 1.3 75.5 + - - +
392B ILE* 1.3 62.7 + - + +
394B ASN* 3.4 7.5 + - + +
395B MET* 2.9 32.4 + - - +
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Residues in contact with ILE 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B TYR* 4.3 21.1 - - + +
325B TRP* 4.6 6.1 - - + -
382B ILE* 4.1 26.2 - - + -
384B LEU* 4.4 2.9 - - + -
388B VAL* 4.2 4.7 - - + -
389B MET* 3.3 25.8 + - - +
391B TYR* 1.3 80.4 - - + +
393B HIS* 1.3 57.4 + - - +
395B MET* 3.1 7.4 + - + -
396B ASN 2.8 34.0 + - - +
399B ILE* 3.6 36.1 - - + -
400B LEU* 4.0 12.8 - - + -
403B TRP* 4.1 15.7 - - + -
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Residues in contact with HIS 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389B MET 2.5 22.4 + - - +
390B SER* 3.5 9.8 + - - +
391B TYR 3.2 0.2 - - - -
392B ILE* 1.3 72.9 - - - +
394B ASN* 1.3 65.5 + - - +
395B MET 3.3 0.5 + - - -
396B ASN 4.3 3.4 - - - -
397B THR* 3.2 60.3 + - + +
400B LEU* 3.8 17.7 - - + -
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Residues in contact with ASN 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B TYR* 3.9 14.4 + - - -
390B SER 2.9 17.1 + - - +
391B TYR* 3.8 8.9 - - + +
392B ILE 3.4 0.2 - - - -
393B HIS* 1.3 81.1 + - - +
395B MET* 1.3 62.8 + - - +
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Residues in contact with MET 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B THR* 5.6 2.0 - - + -
27B TYR* 4.1 18.6 - - - +
242B TYR* 3.5 48.0 + - + -
244B ASP* 3.6 27.4 - - - +
320B ASN* 4.4 2.2 - - + +
325B TRP* 3.4 37.0 - - + +
391B TYR* 2.9 21.7 + - + +
392B ILE* 3.1 9.4 + - - +
394B ASN* 1.3 81.2 - - - +
396B ASN* 1.3 75.6 + - + +
399B ILE* 4.7 6.3 - - + -
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Residues in contact with ASN 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B ASP* 5.0 6.8 - - - +
326B HIS* 5.0 3.3 - - - -
392B ILE 2.8 20.2 + - - +
393B HIS* 4.3 0.2 - - - -
395B MET* 1.3 85.3 + - + +
397B THR* 1.3 67.5 + - - +
398B THR* 3.1 23.3 - - + +
399B ILE* 3.0 39.3 + - + +
400B LEU 4.0 1.7 + - - -
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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