Contacts of the helix formed by residues 351 - 355 (chain B) in PDB entry 1BQD
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 351 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338B VAL* 4.2 18.3 - - - +
342B GLN* 4.5 0.6 - - - +
349B ASP* 3.3 26.7 + - - -
350B PHE* 1.3 76.6 - - - +
352B PHE* 1.3 61.1 + - - +
353B ILE 3.0 2.0 + - - -
354B ILE* 3.2 21.2 + - - +
355B LYS* 3.8 8.9 - - - +
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Residues in contact with PHE 352 (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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165B ASN 5.3 1.6 - - - +
166B HIS* 3.5 45.8 - + + +
349B ASP* 3.5 26.4 + - - +
350B PHE* 2.7 16.0 + + - -
351B SER* 1.3 77.9 + - - +
353B ILE* 1.3 84.7 + - + +
355B LYS* 3.0 42.1 + - + +
356B GLN* 3.4 32.9 - - - +
362B PHE 3.6 20.2 - - - -
363B SER 4.0 19.5 - - - -
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Residues in contact with ILE 353 (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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334B ARG* 3.0 56.8 + - + +
337B PHE* 4.2 27.4 - - + -
338B VAL* 3.6 7.2 - - + -
350B PHE* 2.7 26.4 + - + +
352B PHE* 1.3 104.0 - - + +
354B ILE* 1.3 59.4 + - - +
355B LYS 3.4 0.3 + - - -
356B GLN* 3.5 6.3 + - - -
361B SER* 4.0 22.4 - - - -
362B PHE 4.8 2.9 - - - +
363B SER* 4.9 6.3 - - - -
387B VAL* 5.5 3.1 - - + -
389B VAL* 5.3 2.7 - - + -
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Residues in contact with ILE 354 (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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331B GLN 6.0 0.4 - - - +
334B ARG* 3.3 34.5 - - + +
335B GLN* 3.3 38.1 - - + +
338B VAL* 3.5 21.8 - - + -
351B SER* 3.6 16.2 - - - +
352B PHE 3.1 1.0 - - - -
353B ILE* 1.3 77.5 - - - +
355B LYS* 1.3 60.4 + - + +
356B GLN 3.4 3.5 + - - +
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Residues in contact with LYS 355 (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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166B HIS 3.5 23.0 + - - -
167B THR* 5.0 6.9 + - - -
197B GLY 4.5 1.7 - - - +
198B ILE* 5.1 5.7 - - - +
351B SER* 3.8 9.6 - - - +
352B PHE* 3.0 36.9 + - + +
354B ILE* 1.3 78.2 - - + +
356B GLN* 1.3 71.9 + - - +
357B ASN* 4.1 8.8 + - - +
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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