Contacts of the helix formed by residues 267 - 275 (chain J) in PDB entry 3U3F
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 LEU 267 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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881B TYR* 3.3 32.5 + - + +
884B VAL* 6.3 1.3 - - + -
885B MET* 4.0 21.0 - - + -
988B LYS* 6.2 3.4 - - - -
991B LEU* 6.0 2.9 - - + -
266J GLU* 1.3 76.6 - - - +
268J ASP* 1.3 64.2 + - - +
270J LEU* 3.5 6.1 + - - +
271J MET* 3.1 30.2 + - + +
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Residues in contact with ASP 268 (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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266J GLU 3.1 3.9 - - - +
267J LEU* 1.3 78.8 - - - +
269J GLU* 1.3 60.4 + - - +
271J MET* 3.4 7.6 + - - +
272J ALA* 3.3 22.7 + - - +
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Residues in contact with GLU 269 (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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266J GLU* 3.0 26.4 + - - +
268J ASP* 1.3 77.1 - - - +
270J LEU* 1.3 62.7 + - + +
271J MET 3.2 0.2 + - - -
272J ALA* 3.9 3.5 - - - +
273J SER* 2.9 30.5 + - - -
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Residues in contact with LEU 270 (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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885B MET* 4.1 27.4 - - + +
888B VAL* 4.1 18.5 - - + +
889B ARG* 3.7 50.5 - - + +
892B LEU* 3.7 19.4 - - + +
266J GLU* 3.2 15.3 + - + +
267J LEU* 4.0 6.7 - - - +
268J ASP 3.5 0.2 - - - -
269J GLU* 1.3 79.6 - - + +
271J MET* 1.3 61.5 + - + +
273J SER* 3.5 8.3 - - - -
274J LEU* 3.4 14.6 + - - +
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Residues in contact with MET 271 (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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888B VAL* 4.5 22.7 - - + -
984B ALA* 5.4 4.9 - - + +
985B VAL* 5.0 17.9 - - + +
988B LYS* 4.2 42.8 - - + -
267J LEU* 3.1 22.8 + - + +
268J ASP* 3.5 8.3 - - - +
269J GLU 3.1 0.8 - - - -
270J LEU* 1.3 74.0 - - + +
272J ALA* 1.3 66.8 + - - +
273J SER 3.1 1.1 - - - -
274J LEU* 3.0 26.8 - - + +
275J SER* 3.9 2.8 + - - -
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Residues in contact with ALA 272 (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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268J ASP 3.3 11.5 + - - +
269J GLU* 4.1 3.6 - - - +
271J MET* 1.3 73.9 - - - +
273J SER* 1.3 57.1 + - - +
274J LEU 3.0 2.2 - - - -
275J SER* 2.8 37.5 + - - +
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Residues in contact with SER 273 (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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892B LEU* 4.1 18.8 - - - +
895B LYS* 4.3 4.2 + - - -
269J GLU 2.9 20.3 + - - -
270J LEU* 3.5 15.3 - - - +
272J ALA* 1.3 78.1 - - - +
274J LEU* 1.3 60.4 + - - +
275J SER 3.4 8.4 - - - +
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Residues in contact with LEU 274 (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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888B VAL* 5.6 5.2 - - + -
892B LEU* 3.9 17.5 - - + +
895B LYS* 3.0 24.3 + - - +
981B HIS* 4.2 28.7 - - + +
984B ALA* 5.9 5.2 - - + -
270J LEU 3.4 7.5 + - - +
271J MET* 3.0 23.4 + - + +
273J SER* 1.3 78.1 - - - +
275J SER* 1.3 56.0 + - - +
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Residues in contact with SER 275 (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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895B LYS* 4.2 6.9 + - - +
981B HIS* 3.9 15.6 + - - -
271J MET 3.9 2.0 + - - -
272J ALA* 2.8 19.0 + - - +
273J SER* 3.4 12.5 - - - +
274J LEU* 1.3 78.8 - - - +
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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