Contacts of the helix formed by residues 321 - 326 (chain C) in PDB entry 3HB0
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 PHE 321 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316C ALA 3.4 1.4 + - - -
317C ASP 4.2 7.7 + - - -
318C THR 5.2 0.2 - - - -
319C HIS 3.7 9.3 - - - -
320C LEU* 1.3 79.6 - - - +
322C PHE* 1.3 60.3 + - - +
323C ASN 3.2 2.7 - - - -
324C ASP* 2.9 15.5 + - + +
325C LEU* 2.8 27.9 + - + +
350C PHE* 3.8 44.2 - + + -
383C ARG* 3.7 43.1 - - + -
386C ARG* 3.9 33.4 - - + -
387C VAL* 3.9 11.2 - - + -
390C MET* 6.5 0.4 - - + -
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Residues in contact with PHE 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313C PHE* 4.6 18.6 - + + -
316C ALA* 3.2 29.4 + - + +
317C ASP* 3.1 27.1 - - - +
320C LEU 2.9 5.3 + - - -
321C PHE* 1.3 77.1 - - - +
323C ASN* 1.3 56.6 + - - +
325C LEU* 4.4 2.0 - - - +
326C GLU* 2.8 78.6 + - + +
329C ASP* 3.7 11.7 - - - -
450C GLN* 4.3 9.6 - - - -
452C ILE* 3.7 20.0 - - + -
453C PRO* 3.4 31.4 - - + -
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Residues in contact with ASN 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317C ASP* 3.5 24.6 + - + +
321C PHE* 3.2 1.4 - - - +
322C PHE* 1.3 78.7 - - - +
324C ASP* 1.3 65.0 + - - +
326C GLU* 4.6 9.1 + - - +
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Residues in contact with ASP 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321C PHE* 2.9 20.1 + - + +
323C ASN* 1.3 86.5 - - - +
325C LEU* 1.3 61.4 + - - +
326C GLU 3.4 1.3 + - - -
327C ASP 4.7 1.9 + - - -
328C CYS* 3.6 12.3 - - - -
355C PHE* 3.6 33.7 - - + +
356C HIS* 4.5 14.0 + - - +
383C ARG* 3.3 27.6 + - - +
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Residues in contact with LEU 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320C LEU 4.0 8.3 - - - +
321C PHE* 2.8 23.7 + - + +
322C PHE* 3.8 1.3 - - - +
324C ASP* 1.3 74.0 - - - +
326C GLU* 1.3 62.1 + - - +
327C ASP 3.5 0.7 - - - -
328C CYS* 3.4 6.0 + - - -
329C ASP* 3.1 26.3 + - - +
355C PHE* 4.7 0.4 - - + -
380C LEU* 3.3 33.4 - - + -
383C ARG* 4.2 24.7 - - + -
384C TYR* 3.5 40.8 - - + +
387C VAL* 4.7 4.0 - - + -
452C ILE* 3.7 27.6 - - + -
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Residues in contact with GLU 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322C PHE* 2.8 63.6 + - + +
323C ASN* 5.0 7.7 - - - +
324C ASP 3.4 2.4 - - - -
325C LEU* 1.3 73.5 - - - +
327C ASP* 1.3 75.5 + - - +
328C CYS 3.2 4.2 + - - -
329C ASP* 3.7 5.0 + - - +
450C GLN* 3.2 29.0 + - - +
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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