Contacts of the helix formed by residues 326 - 331 (chain C) in PDB entry 2BZN
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 GLU 326 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320C GLY 4.0 0.5 - - - +
321C ALA* 4.0 4.5 - - + -
322C ALA* 3.5 27.0 + - - +
323C LYS* 2.9 37.6 + - + +
325C LYS* 1.3 82.9 - - + +
327C LEU* 1.3 63.7 + - - +
328C SER 3.6 0.7 - - - -
329C ARG* 3.4 26.5 + - - +
330C ARG* 2.9 60.6 + - - +
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Residues in contact with LEU 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 4.3 2.2 - - + -
229C ALA* 3.8 27.1 - - - +
232C PHE* 3.8 18.4 - - + +
233C GLY* 4.1 3.4 - - - +
312C ILE* 4.8 4.3 - - + -
315C THR* 4.2 18.4 - - + -
316C CYS* 4.4 18.6 - - - -
319C VAL* 3.6 28.0 - - + -
321C ALA* 4.2 4.5 - - - -
323C LYS 3.7 1.6 + - - -
324C LEU* 2.9 30.1 + - + +
325C LYS 3.4 0.2 - - - -
326C GLU* 1.3 74.0 - - - +
328C SER* 1.3 62.0 + - - +
330C ARG* 3.1 4.4 + - - -
331C THR* 2.7 39.4 + - - +
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Residues in contact with SER 328 (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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34C ARG* 5.5 4.2 + - - -
232C PHE 3.6 14.4 + - - -
233C GLY* 3.4 24.9 - - - +
234C ALA 4.7 0.4 - - - -
235C GLY* 4.0 14.6 - - - -
324C LEU 4.6 1.2 + - - -
325C LYS 4.8 6.1 + - - -
327C LEU* 1.3 78.6 - - - +
329C ARG* 1.3 64.4 + - - +
331C THR* 3.3 17.0 + - - +
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Residues in contact with ARG 329 (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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20C LYS* 5.0 2.1 + - - -
325C LYS* 5.1 4.0 + - - +
326C GLU* 3.4 30.7 + - - +
327C LEU 3.1 0.6 - - - -
328C SER* 1.3 83.4 + - - +
330C ARG* 1.3 102.8 + - - +
331C THR 3.3 3.0 + - - +
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Residues in contact with ARG 330 (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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18C ARG 4.9 0.2 - - - +
20C LYS* 2.8 35.4 + - + +
21C ARG 5.5 3.6 + - - -
319C VAL* 3.8 30.3 + - + +
320C GLY* 3.1 35.8 + - - -
321C ALA* 3.6 9.4 - - - +
326C GLU* 2.9 36.3 + - - +
327C LEU 3.1 3.3 + - - +
329C ARG* 1.3 104.5 - - - +
331C THR* 1.3 55.7 + - - +
332C THR 3.6 0.5 + - - -
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Residues in contact with THR 331 (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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17C LEU* 3.6 22.5 - - + +
20C LYS* 3.9 0.6 + - - -
233C GLY* 3.3 28.2 - - - +
319C VAL* 5.4 1.6 - - - -
327C LEU* 2.7 23.0 + - - +
328C SER 3.3 15.2 + - - +
329C ARG 3.3 2.3 - - - +
330C ARG* 1.3 76.2 - - - +
332C THR* 1.3 66.4 + - - +
333C PHE* 3.7 37.1 + - + -
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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