Contacts of the helix formed by residues 293 - 297 (chain E) in PDB entry 2BQZ
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 LEU 293 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E GLU* 2.9 26.5 + - + +
218E MET* 3.7 49.8 - - + +
219E LYS* 4.7 2.0 - - - +
220E ILE* 3.6 36.8 - - + -
230E VAL* 3.6 18.4 - - + +
243E VAL* 4.6 6.1 - - + -
291E ASN 4.0 12.6 - - - +
292E ARG* 1.3 72.3 - - - +
294E GLY* 1.3 65.5 + - - +
295E ARG 3.2 3.1 - - - -
296E LEU* 3.0 22.8 + - + +
297E ILE* 3.7 2.2 + - - +
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Residues in contact with GLY 294 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243E VAL* 3.9 22.9 - - - +
244E GLU 3.7 21.3 + - - -
245E TYR* 3.8 17.8 - - - -
246E HIS 5.3 0.4 - - - -
292E ARG* 3.6 2.6 - - - +
293E LEU* 1.3 76.3 - - - +
295E ARG* 1.3 58.7 + - - +
296E LEU 3.1 4.7 + - - -
297E ILE* 3.2 21.4 + - - +
320E LEU* 5.0 1.5 - - - +
334E TYR* 4.6 2.1 + - - -
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Residues in contact with ARG 295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228E ARG* 4.5 0.2 - - - +
245E TYR* 3.8 13.2 - - - +
246E HIS 4.9 5.9 - - - +
271E TYR* 3.3 42.1 - - + -
286E ALA* 2.8 41.6 + - + -
287E THR 3.2 23.8 + - - -
288E ARG 3.3 11.0 + - - -
289E GLU* 3.0 45.2 + - - +
290E THR* 3.8 22.1 + - - +
292E ARG* 3.4 26.4 + - + +
294E GLY* 1.3 75.1 - - - +
296E LEU* 1.3 74.0 + - + +
297E ILE 3.4 0.2 - - - -
1354E SAH 3.6 2.1 - - - +
20F MLZ 3.5 14.1 - - - -
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Residues in contact with LEU 296 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220E ILE* 3.6 41.1 - - + -
228E ARG* 3.5 46.1 - - + +
229E GLY* 3.6 19.8 - - - -
230E VAL* 3.8 9.6 - - + -
271E TYR* 4.6 0.9 - - - +
290E THR 6.0 1.8 - - - +
292E ARG 4.5 4.3 - - - +
293E LEU* 3.0 18.3 + - + +
295E ARG* 1.3 104.3 - - + +
297E ILE* 1.3 62.8 + - - +
298E ASN 3.5 1.9 + - - -
1354E SAH 3.5 21.1 - - + +
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Residues in contact with ILE 297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E MET* 5.3 0.7 - - - -
230E VAL* 3.7 25.8 - - + +
243E VAL* 3.7 18.8 - - + -
293E LEU 3.7 2.2 - - - +
294E GLY* 3.2 15.8 + - - +
296E LEU* 1.3 78.4 - - - +
298E ASN* 1.3 59.5 + - - +
305E CYS* 5.9 0.4 - - - -
320E LEU* 3.4 25.1 - - + -
332E LEU* 3.4 44.4 - - + +
333E LEU 4.1 0.9 - - - +
334E TYR* 3.5 29.6 + - + -
336E TYR* 2.7 28.6 + - - -
1354E SAH 4.0 1.2 - - - +
20F MLZ 4.6 2.1 - - - -
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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