Contacts of the helix formed by residues 253 - 259 (chain A) in PDB entry 3AA6
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 THR 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A THR* 2.8 19.9 + - + +
252A ASP* 1.3 91.5 + - - +
254A THR* 1.3 67.6 + - - +
255A PHE 3.4 1.1 - - - -
256A LYS* 3.6 1.6 + - - +
257A ALA* 3.0 30.5 + - + +
141B SER* 4.6 16.2 - - - +
142B LYS* 3.2 42.3 + - + +
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Residues in contact with THR 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A MET* 3.3 9.7 + - - -
253A THR* 1.3 77.5 - - - +
255A PHE* 1.3 67.4 + - - +
257A ALA* 3.1 15.5 + - - +
258A LEU* 3.1 19.4 + - + +
138B GLY* 5.4 4.9 - - - -
141B SER 4.4 2.1 + - - -
144B ILE* 3.3 43.7 + - + +
146B GLY* 4.0 18.6 - - - +
177B LEU* 3.5 26.7 - - + -
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Residues in contact with PHE 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A MET 2.8 20.5 + - - +
251A SER 3.7 9.4 - - - +
254A THR* 1.3 74.6 - - - +
256A LYS* 1.3 67.1 + - + +
258A LEU* 3.2 20.5 + - + +
259A ARG* 3.6 7.3 + - - +
148B TRP* 3.8 20.6 - + - -
175B LEU* 3.7 38.1 - - + -
177B LEU* 4.9 2.0 - - + +
225B ARG* 3.5 44.9 - - + -
228B LEU* 4.2 3.1 - - + -
229B ASN* 3.8 33.9 - - + -
233B PHE* 3.6 21.3 - + + -
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Residues in contact with LYS 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A SER 3.1 19.9 + - - +
252A ASP* 3.4 31.0 - - + +
253A THR 3.6 1.5 + - - +
254A THR 3.3 0.2 - - - -
255A PHE* 1.3 80.7 - - + +
257A ALA* 1.3 60.1 + - - +
259A ARG 3.3 21.7 + - - +
260A ARG* 4.3 2.4 + - - +
261A GLN* 3.9 20.2 + - - +
225B ARG* 5.8 2.6 - - - +
229B ASN* 6.1 1.0 - - - +
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Residues in contact with ALA 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A THR* 3.0 20.6 + - + +
254A THR* 3.1 6.5 + - - +
256A LYS* 1.3 72.6 - - - +
258A LEU* 1.3 62.6 + - + +
259A ARG* 3.4 0.4 - - - -
112B PHE 4.8 0.5 - - - +
136B LYS* 3.0 20.8 + - - -
139B ASP* 5.6 11.4 - - - +
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Residues in contact with LEU 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A THR* 3.1 21.2 + - + +
255A PHE* 3.2 13.4 + - + +
257A ALA* 1.3 75.8 - - - +
259A ARG* 1.3 62.4 + - - +
112B PHE* 3.4 19.6 - - - +
136B LYS* 3.4 36.6 + - + +
137B ALA 3.9 1.3 - - - -
138B GLY* 3.5 35.4 - - - +
146B GLY* 4.1 10.3 - - - -
147B CYS 4.1 13.5 - - - +
148B TRP* 4.2 15.9 - - + +
175B LEU* 3.6 31.4 - - + -
177B LEU* 4.9 1.1 - - + -
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Residues in contact with ARG 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A PHE* 3.6 7.3 + - - +
256A LYS* 3.3 15.3 + - - +
257A ALA 3.4 1.1 - - - -
258A LEU* 1.3 83.8 - - - +
260A ARG* 1.3 87.5 + - - +
261A GLN* 4.0 2.1 + - - +
107B TYR* 3.2 12.5 + - - -
111B TYR* 3.4 32.3 - - - +
112B PHE* 3.5 28.0 - - + +
148B TRP* 3.8 29.2 - - + -
218B GLU 4.5 0.4 + - - -
221B GLU* 2.9 42.3 + - - +
222B ASN* 2.9 30.1 + - - -
225B ARG* 3.8 24.7 - - - +
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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