Contacts of the helix formed by residues 397 - 403 (chain B) in PDB entry 4YC3
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 397 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B ASP* 3.7 1.0 + - - -
389B VAL* 3.3 45.8 - - - +
392B GLY* 4.1 15.5 - - - -
394B THR* 3.0 26.5 - - - +
395B LYS 3.2 11.7 + - - +
396B HIS* 1.3 74.5 - - - +
398B THR* 1.3 65.3 + - - +
399B VAL 3.3 2.7 - - - -
400B LYS* 3.2 15.0 + - - +
401B ASN* 2.9 41.6 + - - +
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Residues in contact with THR 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ASP* 2.9 35.3 + - - -
209B VAL* 3.6 26.5 - - + -
210B GLN* 3.6 31.8 + - + +
213B MET* 4.1 11.1 - - - +
396B HIS 3.5 0.6 - - - -
397B MET* 1.3 77.7 + - - +
399B VAL* 1.3 58.4 + - - +
401B ASN* 3.4 6.8 + - - +
402B LYS* 2.8 28.2 + - - +
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Residues in contact with VAL 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ASP* 4.7 0.4 + - - -
209B VAL* 4.1 23.8 - - + -
324B TYR* 3.9 13.7 - - + -
327B GLU* 4.0 33.7 - - + +
328B LEU* 3.8 26.2 - - + +
330B MET* 4.7 0.2 - - + -
331B LEU* 3.9 28.7 - - + +
396B HIS 5.0 1.9 + - - +
397B MET 3.3 0.2 - - - -
398B THR* 1.3 75.2 - - - +
400B LYS* 1.3 64.6 + - - +
402B LYS* 3.3 6.1 + - - +
403B TYR* 3.1 27.1 + - + +
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Residues in contact with LYS 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B TYR* 3.3 28.7 - - - +
328B LEU* 4.8 1.6 - - + +
389B VAL* 3.8 36.4 + - + +
390B ASN* 3.4 29.0 + - - +
396B HIS 5.6 0.2 + - - -
397B MET* 3.2 17.5 + - - +
399B VAL* 1.3 77.2 - - - +
401B ASN* 1.3 71.9 + - - +
403B TYR 3.3 2.1 + - - -
404B ALA* 3.0 9.0 + - + +
412B SER* 2.6 41.2 + - - +
413B THR* 5.7 2.7 - - - +
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Residues in contact with ASN 401 (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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213B MET* 5.6 0.9 - - - -
397B MET* 2.9 36.8 + - - +
398B THR* 3.8 5.7 - - - +
400B LYS* 1.3 84.9 - - - +
402B LYS* 1.3 66.0 + - - +
404B ALA* 3.2 18.8 + - - +
405B THR* 3.7 10.9 - - - +
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Residues in contact with LYS 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B VAL* 4.3 6.3 - - + -
212B GLN* 3.2 16.6 + - - +
213B MET* 4.1 40.3 - - + +
219B GLN* 2.9 17.2 + - - -
327B GLU* 2.7 31.3 + - - +
398B THR 2.8 18.3 + - - +
399B VAL* 3.3 6.0 + - - +
401B ASN* 1.3 78.5 - - - +
403B TYR* 1.3 77.7 + - + +
404B ALA 3.3 0.7 + - - -
405B THR* 3.1 27.1 + - - +
407B LYS* 6.5 0.2 - - - -
408B HIS* 3.6 22.1 - - + +
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Residues in contact with TYR 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B GLN* 5.3 2.6 - - - +
320B THR* 4.3 9.9 - - + -
323B LYS* 4.0 20.3 + - + +
324B TYR* 3.7 45.1 - + + -
327B GLU* 2.6 37.1 + - + -
399B VAL* 3.1 17.1 + - + +
400B LYS 3.3 0.2 + - - -
402B LYS* 1.3 94.2 + - + +
404B ALA* 1.3 59.4 + - - +
405B THR 3.3 3.0 - - - +
408B HIS* 3.8 34.7 - + + +
410B LYS* 3.3 2.4 + - - -
411B ILE* 3.0 47.9 + - + +
412B SER* 3.1 12.7 + - - -
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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
------------------------------------------------------------
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