Contacts of the helix formed by residues 259 - 266 (chain A) in PDB entry 1IZC
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 MET 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A GLY 5.5 1.3 - - - +
254A ALA* 5.3 0.2 - - - -
255A LEU* 3.5 33.4 - - + +
256A SER* 3.0 42.7 + - - +
257A VAL 3.0 1.0 - - - -
258A ASP* 1.3 81.0 - - - +
260A VAL* 1.3 64.8 + - - +
261A PRO 3.4 0.7 - - - -
262A SER* 3.1 11.9 + - - -
263A LEU* 3.0 44.8 + - + +
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Residues in contact with VAL 260 (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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44A MET* 3.7 28.0 - - + -
254A ALA* 4.4 7.6 - - + -
257A VAL* 3.2 24.9 - - + +
259A MET* 1.3 77.6 - - - +
261A PRO* 1.3 72.8 - - + +
263A LEU* 3.1 9.0 + - - +
264A ILE* 2.9 33.4 + - + +
271A ILE* 4.2 9.2 - - + -
273A VAL* 4.1 26.0 - - + -
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Residues in contact with PRO 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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257A VAL 4.5 1.1 - - - +
258A ASP* 3.6 17.5 - - - +
259A MET 3.6 0.2 - - - -
260A VAL* 1.3 94.4 - - + +
262A SER* 1.3 61.1 + - - +
264A ILE* 3.2 9.2 + - + +
265A GLU* 3.0 33.2 + - + +
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Residues in contact with SER 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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258A ASP 5.3 0.6 + - - -
259A MET* 3.1 13.7 + - - -
261A PRO* 1.3 80.0 - - - +
263A LEU* 1.3 64.5 + - - +
265A GLU* 3.2 16.9 + - - +
266A GLN* 3.0 45.9 + - - +
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Residues in contact with LEU 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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253A GLY 3.8 13.5 - - - +
254A ALA* 3.8 30.1 - - + -
259A MET* 3.0 37.3 + - + +
260A VAL* 3.6 5.6 - - - +
262A SER* 1.3 78.4 - - - +
264A ILE* 1.3 62.0 + - - +
266A GLN* 3.1 19.4 + - - +
268A TYR* 2.9 65.7 + - + +
271A ILE* 3.9 18.8 - - + -
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Residues in contact with ILE 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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39A PRO* 3.8 28.3 - - + +
40A SER* 5.8 1.1 - - - -
42A THR* 3.7 29.8 - - + +
44A MET* 4.1 4.7 - - + -
260A VAL* 2.9 35.1 + - + +
261A PRO* 3.6 10.5 - - + +
263A LEU* 1.3 75.6 - - - +
265A GLU* 1.3 65.4 + - + +
267A GLY* 3.0 4.0 + - - -
268A TYR 3.7 10.5 - - - +
269A ARG* 2.8 35.4 + - - +
271A ILE* 4.2 4.0 - - + -
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Residues in contact with GLU 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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244A GLN* 5.0 1.9 + - - -
261A PRO* 3.0 20.9 + - + +
262A SER* 3.2 23.3 + - - +
264A ILE* 1.3 78.4 - - + +
266A GLN* 1.3 62.0 + - + +
267A GLY 3.2 0.9 + - - -
269A ARG* 5.8 0.2 + - - -
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Residues in contact with GLN 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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236A MET* 5.4 4.9 - - - +
240A SER* 4.4 7.0 - - - -
244A GLN* 2.7 29.6 + - - +
250A ILE* 3.7 10.3 - - + +
262A SER* 3.0 40.2 + - - +
263A LEU* 3.1 19.0 + - - +
265A GLU* 1.3 78.9 - - + +
267A GLY* 1.3 56.4 + - - +
268A TYR* 3.9 22.5 + - + -
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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