Contacts of the helix formed by residues 267 - 271 (chain B) in PDB entry 3CX5
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260B LEU* 3.5 32.5 - - + +
265B SER* 3.1 18.7 - - - +
266B GLU* 1.3 79.5 - - - +
268B SER* 1.3 61.0 + - - +
269B GLY 3.1 2.5 - - - -
270B LEU* 3.0 34.3 + - + +
271B ILE* 3.5 11.2 + - + +
303B LYS* 6.0 2.9 - - + -
304B ILE* 3.6 37.7 - - + +
307B ASP* 4.1 23.3 - - + +
308B LEU* 4.9 2.9 - - + -
312B LYS* 3.9 22.0 - - - +
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Residues in contact with SER 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LYS* 2.8 31.5 + - - -
260B LEU 3.0 27.4 + - - -
261B THR* 3.9 10.7 - - - -
262B SER 3.0 23.6 + - - -
265B SER* 3.1 2.3 + - - -
267B LEU* 1.3 79.5 - - - +
269B GLY* 1.3 58.5 + - - +
270B LEU 3.1 0.7 - - - -
271B ILE* 3.3 22.6 + - - +
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Residues in contact with GLY 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LYS* 4.3 6.5 - - - +
266B GLU 5.0 0.6 - - - -
267B LEU* 3.1 1.6 - - - +
268B SER* 1.3 81.3 + - - +
270B LEU* 1.3 68.3 + - - +
271B ILE 3.5 1.8 - - - -
300B ASN* 4.7 1.6 + - - -
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Residues in contact with LEU 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B GLU 4.4 7.0 - - - +
267B LEU* 3.0 25.1 + - + +
269B GLY* 1.3 87.7 - - - +
271B ILE* 1.3 59.1 + - - +
272B SER 4.3 0.2 + - - -
289B VAL* 3.7 16.8 - - - +
300B ASN* 3.0 45.2 + - + +
303B LYS* 3.9 35.4 - - + +
304B ILE* 3.8 21.1 - - + -
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Residues in contact with ILE 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B LEU* 3.1 43.5 - - + +
261B THR* 4.3 5.8 - - + +
267B LEU* 3.7 12.3 - - + +
268B SER* 3.3 19.8 - - - +
269B GLY 4.8 1.2 - - - -
270B LEU* 1.3 83.4 - - - +
272B SER* 1.3 62.8 + - - +
273B SER* 4.5 4.7 - - - +
274B ALA* 3.9 20.2 - - + -
287B LEU* 4.2 20.9 - - + -
288B PHE 3.8 8.7 - - - +
289B VAL* 4.5 1.8 - - + -
304B ILE* 3.7 22.7 - - + -
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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