Contacts of the helix formed by residues 297 - 300 (chain E) in PDB entry 3SZ9
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 ASN 297 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110E ASN* 4.5 0.7 - - - +
112E LYS* 3.0 32.8 + - - +
113E PRO* 6.1 1.3 - - - -
116E ILE* 5.9 1.5 - - - +
169E ASN* 3.1 23.8 + - - +
170E PHE* 3.5 9.7 - - + -
295E PHE 3.3 0.4 + - - -
296E PHE* 1.3 92.8 - - + +
298E GLN* 1.3 83.3 + - - +
300E GLN* 3.0 43.2 + - - +
301E CYS* 3.8 12.8 - - - -
329E ARG* 4.9 2.2 - - - +
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Residues in contact with GLN 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E ASN* 4.5 1.6 + - - -
112E LYS* 3.7 18.9 - - - +
113E PRO* 3.5 14.2 - - - +
295E PHE 3.1 8.2 + - - -
297E ASN* 1.3 100.6 + - - +
299E GLY* 1.3 59.3 + - - +
300E GLN* 3.1 17.6 + - - +
329E ARG* 4.9 1.8 - - - +
340E GLU 4.4 1.6 - - - +
341E GLN* 3.7 17.0 - - + -
342E GLY* 2.9 45.4 + - - +
343E PRO 3.5 13.2 + - - +
344E GLN* 3.1 30.7 + - - +
402E GLY* 3.6 0.5 - - - -
403E PRO* 3.6 13.7 - - - -
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Residues in contact with GLY 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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294E LEU 3.4 23.8 - - - -
295E PHE* 3.2 6.8 + - - +
296E PHE 3.0 8.2 + - - -
298E GLN* 1.3 77.2 - - - +
300E GLN* 1.3 57.6 + - - +
301E CYS* 3.2 11.6 + - - +
304E ALA* 4.3 7.0 - - - +
401E PHE* 3.3 21.8 - - - -
402E GLY 3.4 14.9 + - - +
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Residues in contact with GLN 300 (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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110E ASN* 5.1 7.9 + - - +
168E TRP* 3.5 27.6 - - + -
169E ASN* 3.2 13.0 + - + +
170E PHE* 3.6 0.5 - - - -
296E PHE 3.8 0.2 + - - -
297E ASN* 3.0 41.7 + - - +
298E GLN* 3.5 22.6 - - - +
299E GLY* 1.3 74.9 - - - +
301E CYS* 1.3 59.6 + - - +
343E PRO 4.6 2.2 + - - -
344E GLN* 3.0 20.5 + - - +
345E VAL* 3.1 26.4 + - - +
349E GLN* 5.0 2.3 - - - +
401E PHE* 3.4 41.2 - - + +
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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