Contacts of the helix formed by residues 256 - 260 (chain C) in PDB entry 5DO7
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 256 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C THR* 4.8 4.7 - - + -
228C ALA* 5.9 0.2 - - + -
229C ASN* 4.0 20.6 - - - +
232C VAL* 3.5 35.2 - - + -
249C ILE* 5.5 5.2 - - + -
251C GLN* 5.2 2.0 - - + +
253C ARG* 3.4 38.8 - - + +
254C SER 3.2 0.2 - - - -
255C GLU* 1.3 80.2 - - + +
257C PHE* 1.3 67.0 + - - +
258C GLN 3.1 2.5 - - - -
259C LEU* 2.8 37.2 + - + +
260C PHE* 3.5 30.5 - - + -
298C PHE* 4.3 11.0 - - + -
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Residues in contact with PHE 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C ARG 3.9 6.3 + - - -
254C SER* 3.9 12.3 + - - +
256C LEU* 1.3 77.0 - - - +
258C GLN* 1.3 74.9 + - + +
259C LEU 3.2 3.3 + - - -
260C PHE* 3.9 8.8 + - - -
263C ILE* 4.0 7.9 - - + -
277C PRO* 3.4 49.5 - - + +
280C MET* 3.5 32.1 - - + -
281C LEU* 4.1 19.1 - - + -
296C ASN* 5.2 0.2 - - - +
297C PRO* 4.0 28.7 - - + -
298C PHE* 3.6 43.1 - + + +
311D CYS* 6.4 0.7 - - - -
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Residues in contact with GLN 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C SER 5.1 2.4 + - - +
255C GLU 4.9 4.2 + - - +
256C LEU* 3.0 2.2 + - - +
257C PHE* 1.3 95.1 - - + +
259C LEU* 1.3 69.3 + - + +
260C PHE 3.5 2.4 + - - -
277C PRO* 4.7 13.5 - - - +
278C ALA 5.6 1.0 + - - -
281C LEU* 6.3 0.6 - - - +
311D CYS* 5.7 7.3 - - - +
312D PRO* 6.0 5.6 - - + +
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Residues in contact with LEU 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C ILE* 3.2 22.9 - - - +
229C ASN* 6.1 2.2 - - - +
232C VAL* 4.5 15.0 - - + -
233C VAL* 6.1 4.3 - - + +
236C VAL* 4.6 12.0 - - + +
255C GLU 4.3 7.9 - - - +
256C LEU* 2.8 40.9 + - + +
258C GLN* 1.3 87.7 - - + +
260C PHE* 1.3 63.0 + - + +
261C ASP 4.1 0.4 + - - -
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Residues in contact with PHE 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C ILE* 3.7 22.2 - - + -
83C CYS* 3.6 41.3 - - + -
232C VAL* 4.9 17.9 - - + -
236C VAL* 6.0 0.9 - - + -
247C LEU* 3.5 31.0 - - + -
249C ILE* 4.9 4.3 - - + -
256C LEU* 3.5 45.8 - - + -
257C PHE* 3.9 12.5 + - - +
258C GLN 3.5 2.8 - - - -
259C LEU* 1.3 80.5 - - + +
261C ASP* 1.3 64.8 + - - +
262C LYS 4.4 7.0 - - - +
263C ILE* 4.7 4.9 - - + +
276C THR* 5.0 0.5 - - - +
277C PRO* 2.9 29.3 - - + +
298C PHE* 4.5 4.9 - + - -
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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