Contacts of the helix formed by residues 295 - 299 (chain E) in PDB entry 2QC8
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 ASP 295 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38E GLU* 4.7 1.2 - - - +
239E ASP* 5.2 0.4 - - - -
240E PRO* 3.5 25.5 - - + +
289E ASP* 3.4 16.8 + - + -
290E PRO* 4.2 4.0 - - - +
291E LYS* 3.5 35.7 + - - +
293E GLY 3.3 0.6 - - - -
294E LEU* 1.3 75.4 - - - +
296E ASN* 1.3 62.3 + - - +
297E ALA 3.0 5.6 + - - -
298E ARG* 3.1 41.1 + - - +
299E ARG 4.0 0.5 + - - -
345E ASN* 3.0 23.3 + - - +
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Residues in contact with ASN 296 (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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240E PRO* 4.3 1.0 - - - +
285E ILE* 5.1 3.9 + - + +
288E TYR* 3.8 14.1 + - - +
289E ASP* 2.9 14.8 + - - +
293E GLY* 3.5 5.6 + - - +
295E ASP* 1.3 71.6 - - - +
297E ALA* 1.3 61.2 + - - +
298E ARG 3.0 3.3 + - - -
299E ARG* 3.0 33.7 + - - +
300E LEU* 2.8 51.0 + - + +
309E ILE* 4.0 6.3 - - + -
341E ARG 2.9 25.0 + - - -
342E PRO* 4.1 0.2 - - - +
343E SER* 3.2 26.5 + - - +
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Residues in contact with ALA 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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293E GLY 3.1 12.3 + - - +
294E LEU* 3.3 21.8 - - + +
295E ASP 3.0 1.4 - - - -
296E ASN* 1.3 77.3 - - - +
298E ARG* 1.3 59.6 + - + +
300E LEU 4.4 8.0 + - - +
301E THR* 4.5 5.4 - - - +
309E ILE* 3.8 19.5 - - + +
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Residues in contact with ARG 298 (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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239E ASP* 2.9 42.8 + - - -
240E PRO* 4.1 1.8 - - - +
241E LYS* 3.4 49.3 + - + +
294E LEU 4.4 6.4 + - - +
295E ASP* 3.1 47.5 + - - +
296E ASN 3.0 1.0 - - - -
297E ALA* 1.3 78.9 - - + +
299E ARG* 1.3 57.9 + - - +
301E THR* 3.7 11.3 - - - +
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Residues in contact with ARG 299 (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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240E PRO* 3.7 16.8 - - + +
241E LYS* 4.3 9.0 + - - +
249E GLY* 4.6 3.4 - - - -
250E ALA 3.3 28.6 + - - +
251E GLY* 3.5 8.4 - - - -
253E HIS* 4.5 0.2 + - - -
295E ASP 4.0 0.6 + - - -
296E ASN* 3.0 23.6 + - - +
298E ARG* 1.3 79.1 - - - +
300E LEU* 1.3 65.8 + - - +
301E THR* 2.7 24.0 + - - +
303E PHE 4.6 0.3 - - - +
306E THR* 3.2 20.5 + - + +
340E ARG 3.4 12.5 + - - -
341E ARG 2.6 34.6 + - - -
342E PRO 2.8 20.1 + - - -
343E SER* 4.2 1.2 - - - +
601E P3S 2.9 46.9 + - - +
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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