Contacts of the helix formed by residues 259 - 266 (chain A) in PDB entry 1A8H
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 LYS 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A TYR* 3.5 38.8 - - + -
258A GLY* 1.3 70.8 - - - -
260A ASP* 1.3 62.3 + - - +
261A ILE 3.2 1.0 + - - -
262A LEU* 3.5 19.9 + - + +
286A VAL* 3.6 9.8 - - - +
287A GLY 3.2 13.6 + - - +
288A GLY* 4.3 2.9 - - - -
289A PHE* 3.4 35.8 - - + -
333A ASP* 2.8 41.3 + - - -
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Residues in contact with ASP 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A GLY* 3.3 19.9 + - - +
259A LYS* 1.3 77.0 + - - +
261A ILE* 1.3 75.6 + - - +
262A LEU 3.5 1.3 + - - -
264A PRO* 4.9 2.8 - - - +
289A PHE* 4.1 26.7 - - + -
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Residues in contact with ILE 261 (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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10A PRO* 3.7 33.4 - - + -
257A ILE* 3.7 10.2 - - + +
258A GLY 3.4 15.9 - - - +
260A ASP* 1.3 97.1 - - - +
262A LEU* 1.3 59.1 + - - +
264A PRO* 3.4 21.0 - - + +
265A HIS* 3.0 46.3 + - + +
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Residues in contact with LEU 262 (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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181A ILE* 4.7 3.1 - - + -
186A TYR* 4.2 26.2 - - + +
189A GLU* 4.6 20.0 - - + +
190A VAL* 4.1 19.5 - - + -
193A MET* 4.6 5.6 - - + -
257A ILE* 3.7 8.5 - - + -
259A LYS* 3.5 20.6 + - + +
260A ASP 3.5 2.2 - - - -
261A ILE* 1.3 77.0 - - - +
263A LYS* 1.3 64.3 + - - +
265A HIS* 3.3 0.7 + - - -
266A ALA* 2.8 48.3 + - + +
284A LEU* 4.1 7.9 - - + -
286A VAL* 4.0 24.9 - - + -
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Residues in contact with LYS 263 (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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193A MET* 4.1 40.1 - - + +
198A ILE* 5.5 12.8 + - - +
262A LEU* 1.3 76.2 - - - +
264A PRO* 1.3 67.7 - - + +
266A ALA 4.6 0.2 - - - +
267A VAL* 2.8 43.9 + - + +
268A PHE* 3.4 32.8 + - + -
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Residues in contact with PRO 264 (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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227A TRP* 3.4 39.0 - - + -
231A LEU* 4.0 6.8 - - + +
260A ASP 4.9 2.0 - - - +
261A ILE* 3.4 30.7 - - + +
262A LEU 3.7 0.2 - - - +
263A LYS* 1.3 97.4 - - + +
265A HIS* 1.3 64.3 + - + +
268A PHE* 3.4 16.4 - - + +
269A TRP* 2.8 30.1 + - - +
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Residues in contact with HIS 265 (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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10A PRO* 5.2 1.3 - - + -
231A LEU* 4.0 16.8 - - + +
234A TYR* 2.4 45.2 + + - -
255A HIS* 4.8 5.2 - - + -
257A ILE* 3.6 16.3 - - + +
261A ILE* 3.0 47.2 + - + +
262A LEU 3.3 1.9 + - - +
263A LYS 3.2 0.2 - - - -
264A PRO* 1.3 83.7 - - + +
266A ALA* 1.3 54.3 + - - +
267A VAL 3.6 0.4 - - - -
269A TRP* 3.5 14.4 - + + +
270A PRO* 3.3 11.2 - - - +
281A TYR* 2.6 28.4 + - + -
284A LEU* 3.9 21.8 - - + -
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Residues in contact with ALA 266 (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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170A LEU* 3.6 13.5 - - - +
174A ILE* 4.5 2.3 - - - +
180A LEU* 6.3 0.2 - - - -
181A ILE* 4.3 5.6 - - + -
190A VAL* 3.4 38.8 - - + +
193A MET* 4.9 0.4 - - + -
262A LEU* 2.8 21.6 + - + +
265A HIS* 1.3 74.7 - - - +
267A VAL* 1.3 62.4 + - + +
270A PRO* 3.2 13.9 - - - +
281A TYR* 3.7 7.1 + - - -
284A LEU* 3.8 13.2 - - + -
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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