Contacts of the helix formed by residues 255 - 259 (chain H) in PDB entry 6X34
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 HIS 255 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221H ARG* 4.4 2.1 + - - -
235H PRO* 6.5 1.1 - - + -
251H SER 4.3 6.9 + - - +
252H VAL* 4.0 22.0 - - + +
253H CYS 3.7 1.0 - - - -
254H THR* 1.3 83.4 + - - +
256H ALA* 1.3 62.6 - - - +
257H ARG* 3.2 8.4 + - + +
258H SER* 2.9 24.4 + - - -
477H LEU* 4.9 2.9 - - - +
480H GLU* 3.7 23.8 - - + +
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Residues in contact with ALA 256 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255H HIS* 1.3 72.9 - - - +
257H ARG* 1.3 63.0 + - - +
258H SER* 3.2 1.5 + - - -
259H LEU* 3.4 20.6 + - - +
285H VAL* 5.1 0.2 - - - +
286H THR* 3.9 14.5 - - + +
401H ALA* 5.4 6.8 - - + +
404H ILE* 4.1 25.1 - - + -
477H LEU* 4.3 34.6 - - + +
480H GLU* 4.2 11.2 - - + +
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Residues in contact with ARG 257 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232H THR* 3.2 29.3 + - - +
233H ILE* 3.8 24.2 + - + +
235H PRO* 6.1 4.3 - - + -
252H VAL* 4.6 9.0 - - + -
255H HIS* 3.2 5.1 - - + +
256H ALA* 1.3 76.9 - - - +
258H SER* 1.3 63.5 + - - +
259H LEU 3.2 8.0 + - - +
260H TRP* 4.5 3.8 - - - -
284H HIS* 4.3 9.7 - - - -
286H THR* 4.8 8.3 - - - +
480H GLU 5.4 4.5 + - - +
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Residues in contact with SER 258 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220H LEU 4.2 0.2 - - - +
221H ARG* 3.0 52.6 + - - +
222H LEU 5.1 1.0 + - - -
223H PHE* 6.2 0.7 - - - -
230H CYS* 5.5 11.8 - - - +
231H LEU 5.2 2.5 - - - +
232H THR* 4.1 7.1 + - - -
252H VAL 3.5 22.5 + - - -
253H CYS 4.3 2.0 + - - -
255H HIS 2.9 15.6 + - - -
257H ARG* 1.3 76.9 - - - +
259H LEU* 1.3 64.6 + - - +
260H TRP* 3.6 7.4 + - - +
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Residues in contact with LEU 259 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219H VAL* 5.2 8.1 - - + -
220H LEU 4.5 4.7 - - - -
221H ARG* 4.9 5.2 - - - +
256H ALA* 3.4 14.0 + - - +
257H ARG 3.2 9.5 - - - +
258H SER* 1.3 83.0 + - - +
260H TRP* 1.3 65.1 + - - +
284H HIS* 4.1 11.6 + - - -
285H VAL* 4.4 15.6 - - + +
393H CYS* 5.1 11.9 - - - -
397H GLU* 5.7 10.1 - - + +
398H SER* 6.0 0.9 - - - -
401H ALA* 5.2 6.7 - - + -
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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