Contacts of the helix formed by residues 260 - 266 (chain A) in PDB entry 3CAA
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 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A PRO* 3.8 23.2 - - + +
256A ASP 4.3 0.6 + - - -
258A ASP* 3.7 1.9 - - - -
259A LYS* 1.3 78.0 - - - +
261A GLU* 1.3 62.0 + - + +
263A VAL* 3.3 2.0 + - - +
264A GLU* 2.9 55.9 + - - +
369B PRO* 3.4 49.1 - - + +
370B PHE* 3.6 13.2 - - - +
371B LEU* 4.0 14.4 - - + -
387B LYS* 3.8 23.3 - - + +
389B THR* 6.3 0.2 - - + -
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Residues in contact with GLU 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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258A ASP 5.2 2.4 - - - +
259A LYS* 3.1 1.0 - - - +
260A MET* 1.3 80.3 - - + +
262A GLU* 1.3 64.5 + - - +
264A GLU* 3.5 17.6 + - - +
265A ALA* 3.0 24.9 + - - +
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Residues in contact with GLU 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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234A GLU 4.3 11.1 - - - +
235A LEU* 4.0 30.3 - - + +
236A SER* 5.5 0.2 - - - -
258A ASP 5.5 0.6 + - - +
259A LYS* 3.1 31.8 + - + +
261A GLU* 1.3 78.3 - - - +
263A VAL* 1.3 63.3 + - - +
265A ALA* 3.5 11.9 + - - +
266A MET* 3.6 22.6 - - - +
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Residues in contact with VAL 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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235A LEU* 3.8 27.3 - - + +
237A CYS* 3.8 23.3 - - + -
253A ILE* 4.6 3.4 - - + -
255A PRO* 3.9 13.5 - - + -
259A LYS 3.0 17.9 + - - +
260A MET 3.6 6.5 - - - +
262A GLU* 1.3 74.5 - - - +
264A GLU* 1.3 69.5 + - - +
266A MET* 2.9 15.4 + - - +
267A LEU* 3.2 11.5 + - + +
275A TRP* 4.2 23.6 - - + -
371B LEU* 4.1 25.1 - - + -
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Residues in contact with GLU 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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38A TYR* 2.7 39.9 + - + +
39A LYS* 3.2 19.8 - - - -
42A VAL* 3.9 13.5 - - - +
260A MET* 2.9 34.4 + - - +
261A GLU* 3.9 19.9 - - - +
263A VAL* 1.3 75.8 - - + +
265A ALA* 1.3 61.4 + - - +
266A MET 3.2 0.9 + - - -
267A LEU* 3.2 22.6 + - + +
371B LEU* 5.2 1.3 - - + -
387B LYS* 2.9 25.3 + - - +
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Residues in contact with ALA 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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39A LYS* 4.6 4.6 - - - +
261A GLU 3.0 19.8 + - - +
262A GLU* 3.6 11.0 - - - +
263A VAL 3.1 0.4 - - - -
264A GLU* 1.3 76.0 - - - +
266A MET* 1.3 64.2 + - + +
267A LEU 3.9 0.5 + - - -
268A LEU* 4.4 10.0 - - - +
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Residues in contact with MET 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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234A GLU* 5.4 6.5 - - - +
235A LEU* 3.8 30.7 - - + -
262A GLU* 3.6 20.0 - - - +
263A VAL 2.9 8.6 + - - +
265A ALA* 1.3 84.2 - - + +
267A LEU* 1.3 58.1 + - - +
268A LEU* 2.9 23.4 + - + +
271A THR* 2.7 41.2 + - - +
274A ARG* 6.3 0.9 - - - +
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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