Contacts of the helix formed by residues 295 - 299 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38I GLU* 4.7 0.9 - - - +
239I ASP* 5.2 0.9 - - - -
240I PRO* 3.8 23.1 - - + +
289I ASP* 3.5 16.1 + - + +
290I PRO* 3.9 7.4 - - - +
291I LYS* 3.5 33.1 + - - +
293I GLY 3.3 0.2 - - - -
294I LEU* 1.3 77.5 - - - +
296I ASN* 1.3 64.4 + - - +
298I ARG* 3.1 44.8 + - - +
299I ARG 4.1 0.9 + - - -
345I ASN* 2.8 24.4 + - - +
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Residues in contact with ASN 296 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240I PRO* 4.6 1.0 - - - +
285I ILE* 5.1 3.0 + - + +
288I TYR* 3.8 9.7 + - - +
289I ASP* 3.1 18.2 + - - +
293I GLY* 3.2 5.3 + - - +
295I ASP* 1.3 77.7 - - - +
297I ALA* 1.3 54.1 + - - +
298I ARG 3.1 0.4 - - - -
299I ARG* 2.9 35.0 + - - +
300I LEU* 2.8 57.1 + - + +
309I ILE* 4.0 5.2 - - + -
341I ARG 3.1 19.8 + - - -
343I SER* 3.3 26.8 - - - +
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Residues in contact with ALA 297 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293I GLY 3.1 11.3 + - - +
294I LEU* 3.6 19.7 - - + +
295I ASP 3.1 0.8 + - - -
296I ASN* 1.3 77.0 - - - +
298I ARG* 1.3 60.6 + - + +
299I ARG 3.5 0.3 + - - -
300I LEU 4.5 4.2 - - - +
301I THR* 4.4 10.7 - - - +
309I ILE* 3.8 20.0 - - + -
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Residues in contact with ARG 298 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239I ASP* 2.9 43.2 + - - -
240I PRO* 4.0 4.6 - - - +
241I LYS* 3.2 49.5 + - + +
294I LEU 4.3 6.8 + - - +
295I ASP* 3.1 39.4 + - - +
296I ASN 3.1 1.2 - - - -
297I ALA* 1.3 79.5 - - + +
299I ARG* 1.3 56.2 + - - +
301I THR* 4.2 7.7 - - - +
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Residues in contact with ARG 299 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240I PRO* 3.6 27.2 - - + +
241I LYS* 4.4 7.9 + - - +
249I GLY* 4.7 3.8 - - - -
250I ALA 3.2 21.8 + - - +
251I GLY* 3.4 13.0 - - - -
253I HIS* 4.5 0.6 + - - -
295I ASP 4.1 0.2 + - - -
296I ASN* 2.9 23.2 + - - +
298I ARG* 1.3 78.8 - - - +
300I LEU* 1.3 66.0 + - - +
301I THR* 2.9 16.6 + - - +
303I PHE 4.7 0.2 - - - +
304I HIS* 5.9 0.7 - - - +
306I THR* 3.3 25.4 + - + +
340I ARG 3.6 12.1 + - - -
341I ARG* 2.8 25.9 + - - +
342I PRO 2.7 26.5 + - - -
343I SER* 4.4 0.4 - - - +
601I P3S 2.9 38.9 + - - +
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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