Contacts of the helix formed by residues 255 - 260 (chain J) in PDB entry 5AYZ
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 255 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250J GLY 3.3 20.4 + - - -
251J ILE* 3.6 5.0 - - - +
252J THR* 2.8 35.2 + - - +
254J ASP* 1.3 75.6 - - - +
256J LEU* 1.3 60.4 + - - +
257J PRO* 3.3 3.4 - - - -
258J GLN* 2.8 49.6 + - - +
259J PHE* 3.3 22.9 - - + -
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Residues in contact with LEU 256 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121J ALA* 3.1 46.2 - - + +
124J ALA* 4.1 7.2 - - + -
125J ALA* 4.2 9.0 - - + +
134J VAL* 4.7 3.6 - - + -
251J ILE* 3.6 13.5 - - + -
252J THR 3.1 14.0 + - - +
253J LEU* 3.8 5.4 - - - +
254J ASP 3.5 0.2 - - - -
255J ASN* 1.3 80.8 + - - +
257J PRO* 1.3 70.3 - - + +
259J PHE* 3.1 11.1 + - - -
260J CYS* 3.3 20.8 + - - -
267J ILE* 3.6 41.3 - - + -
269J MET* 4.2 8.3 - - + -
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Residues in contact with PRO 257 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124J ALA* 4.4 19.5 - - + +
128J ALA* 4.2 15.0 - - + +
253J LEU 4.0 6.1 - - - +
254J ASP 3.9 11.7 - - - +
255J ASN 3.5 3.6 - - - -
256J LEU* 1.3 93.8 - - + +
258J GLN* 1.3 62.3 + - + +
259J PHE 3.4 0.5 + - - -
260J CYS* 3.5 25.5 + - - +
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Residues in contact with GLN 258 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226J PRO* 3.3 34.2 - - + +
227J GLU* 5.0 4.5 - - - +
230J HIS* 3.1 18.8 + - - -
254J ASP 4.7 3.0 + - - -
255J ASN* 2.8 41.2 + - - +
257J PRO* 1.3 74.9 - - + +
259J PHE* 1.3 57.6 + - + +
260J CYS 3.5 1.1 - - - +
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Residues in contact with PHE 259 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224J PHE* 3.5 23.3 - - + -
226J PRO* 3.8 26.7 - - + -
229J LEU* 3.8 20.2 - - + +
230J HIS* 3.3 14.2 - - - -
247J ALA* 4.8 1.6 - - + -
248J SER 6.1 0.7 - - - -
249J GLY 4.8 8.1 - - - -
250J GLY 5.1 0.9 - - - -
251J ILE* 3.6 46.4 - - + -
255J ASN* 3.3 41.5 - - + -
256J LEU 3.1 7.1 + - - +
258J GLN* 1.3 75.8 - - - +
260J CYS* 1.3 64.9 + - - +
261J GLY 3.5 0.9 + - - -
264J ILE* 3.7 12.8 - - - +
267J ILE* 3.9 14.6 - - + +
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Residues in contact with CYS 260 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125J ALA* 4.0 23.1 - - - -
128J ALA* 4.3 10.8 - - + +
130J TRP* 3.6 37.2 - - + -
230J HIS* 3.2 12.0 + - - -
256J LEU* 3.3 17.9 + - - -
257J PRO* 3.5 20.9 + - - +
258J GLN 4.3 0.5 - - - +
259J PHE* 1.3 77.4 - - - +
261J GLY* 1.3 58.7 + - - +
267J ILE* 4.1 10.3 - - - -
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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