Contacts of the helix formed by residues 391 - 396 (chain B) in PDB entry 4UB6
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 SER 391 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B ASP* 3.6 8.7 + - - -
382B PRO* 4.3 12.1 - - - -
388B SER* 3.6 14.0 + - - -
390B TYR* 1.3 81.6 - - - +
392B PHE* 1.3 64.2 + - - +
393B GLU* 3.4 16.4 + - - +
394B GLN* 2.6 40.8 + - - +
395B GLN* 3.0 20.6 + - - +
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Residues in contact with PHE 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B PHE* 5.1 0.2 - + - -
368B VAL* 4.4 0.4 - - + -
370B LEU* 3.9 21.1 - - + -
379B ALA* 4.0 9.9 - - + -
380B ASP* 3.6 34.2 + - - -
381B ILE* 4.2 9.9 - - + -
382B PRO* 5.5 0.2 - - - +
391B SER* 1.3 72.9 - - - +
393B GLU* 1.3 63.4 + - - +
396B GLY* 2.9 24.9 + - - -
397B VAL* 3.1 33.2 + - + +
414B PRO* 4.7 9.3 - - + +
417B VAL* 3.8 24.9 - - + -
418B LYS* 3.6 46.3 - - + +
421B ALA* 3.7 23.3 - - + -
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Residues in contact with GLU 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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349B LYS* 5.1 1.9 + - - -
382B PRO* 5.8 0.5 - - - +
391B SER* 3.4 19.2 - - - +
392B PHE* 1.3 81.4 + - - +
394B GLN* 1.3 65.7 + - + +
395B GLN 3.3 0.3 + - - -
396B GLY* 3.6 7.3 + - - -
414B PRO* 3.8 27.0 - - + +
418B LYS* 2.9 35.9 + - - -
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Residues in contact with GLN 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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349B LYS* 3.1 24.1 + - - -
388B SER* 3.0 28.1 + - - -
389B LYS* 3.3 15.4 + - - +
391B SER* 2.6 47.4 + - - +
393B GLU* 1.3 76.7 - - - +
395B GLN* 1.3 72.1 + - - +
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Residues in contact with GLN 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ASN* 3.6 12.9 + - + +
349B LYS* 3.0 34.5 + - - +
350B GLU* 5.0 8.7 - - - +
378B LYS 3.4 25.9 + - - +
379B ALA* 4.4 0.4 - - + -
389B LYS 3.0 23.8 + - - -
390B TYR* 3.9 12.4 - - - +
391B SER 3.0 17.4 + - - +
394B GLN* 1.3 87.1 + - - +
396B GLY* 1.3 61.2 + - - +
397B VAL* 3.3 15.7 + - + -
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Residues in contact with GLY 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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348B ASN 3.7 1.4 - - - -
349B LYS* 3.5 28.0 + - - +
392B PHE 2.9 7.9 + - - -
393B GLU 3.6 5.4 + - - -
394B GLN 3.4 3.6 + - - -
395B GLN* 1.3 78.1 - - - +
397B VAL* 1.3 65.9 + - - +
398B THR* 3.4 13.0 + - - +
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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