Contacts of the helix formed by residues 252 - 260 (chain C) in PDB entry 5HVO
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 ASP 252 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46C SER* 5.1 7.7 + - - +
48C LEU* 6.6 0.2 - - - -
251C ILE* 1.3 74.5 - - - +
253C PRO* 1.3 67.1 - - - +
254C ASP* 3.1 24.7 + - - +
255C LYS* 3.2 31.1 + - + +
256C PHE* 3.6 7.4 - - - -
462C THR* 5.0 1.6 - - - -
463C SER* 3.8 10.4 + - - +
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Residues in contact with PRO 253 (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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251C ILE* 3.3 23.1 - - + +
252C ASP* 1.3 86.4 - - - +
254C ASP* 1.3 66.4 + - - +
255C LYS 3.2 0.2 - - - -
256C PHE* 3.1 16.3 + - + +
257C THR* 3.1 16.2 + - - +
397C ALA* 4.4 13.5 - - + +
455C TYR* 5.0 8.7 - - - +
458C ILE* 3.9 27.4 - - + +
459C SER* 3.9 16.8 - - - +
462C THR* 4.0 13.9 - - + -
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Residues in contact with ASP 254 (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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252C ASP* 3.1 14.0 + - - +
253C PRO* 1.3 82.2 - - - +
255C LYS* 1.3 54.3 + - - +
257C THR* 3.0 11.4 + - - -
258C ASP* 2.7 49.7 + - - +
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Residues in contact with LYS 255 (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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44C GLY 5.9 3.0 - - - +
252C ASP* 3.2 27.4 + - + +
253C PRO 3.2 0.4 - - - -
254C ASP* 1.3 78.5 - - - +
256C PHE* 1.3 66.4 + - + +
258C ASP* 3.9 6.0 - - - +
259C GLY* 3.0 24.3 + - - -
366C PHE* 3.3 45.9 - - + -
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Residues in contact with PHE 256 (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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251C ILE* 3.9 25.4 - - + -
252C ASP 3.6 18.2 - - - -
253C PRO 3.1 7.4 + - - +
255C LYS* 1.3 89.3 - - + +
257C THR* 1.3 63.7 + - - +
260C LEU* 3.1 30.6 + - - +
366C PHE* 4.0 24.9 - + - -
369C LEU* 4.8 3.8 - - + -
370C ILE* 3.2 12.3 - - + +
373C TYR* 4.4 7.2 - + - -
394C GLU* 3.3 48.0 - - + -
397C ALA* 3.8 19.1 - - + +
398C THR* 4.0 21.1 - - + -
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Residues in contact with THR 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 PRO 3.1 8.7 + - - +
254C ASP* 3.0 30.7 + - - +
256C PHE* 1.3 74.3 - - - +
258C ASP* 1.3 64.5 + - - +
260C LEU* 3.5 18.6 + - + +
261C LYS* 3.7 20.1 + - - +
397C ALA 4.2 10.5 - - - +
400C GLN* 3.8 13.0 - - - +
455C TYR* 3.6 23.8 - - - +
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Residues in contact with ASP 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 ASP* 2.7 33.8 + - - +
255C LYS* 3.9 6.4 + - - +
257C THR* 1.3 73.6 + - - +
259C GLY* 1.3 65.3 + - - +
261C LYS* 3.2 42.7 + - - +
262C SER* 4.1 2.1 + - - -
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Residues in contact with GLY 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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255C LYS 3.0 14.9 + - - -
256C PHE 3.4 0.4 + - - -
258C ASP* 1.3 76.3 - - - +
260C LEU* 1.3 60.9 + - - +
261C LYS 3.3 0.7 + - - -
262C SER* 3.4 12.3 + - - -
265C VAL* 3.4 20.6 - - - +
366C PHE* 4.4 8.1 - - - -
367C ASP* 5.3 2.9 - - - -
370C ILE* 3.6 20.2 - - - -
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Residues in contact with LEU 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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256C PHE 3.1 20.7 + - - +
257C THR* 3.7 13.9 - - + +
258C ASP 3.1 0.8 - - - -
259C GLY* 1.3 76.9 - - - +
261C LYS* 1.3 61.3 + - - +
262C SER 3.3 1.3 + - - +
265C VAL* 4.2 6.4 - - + +
266C GLN* 2.3 38.8 + - - +
269C ILE* 4.0 13.7 - - + -
370C ILE* 4.0 19.7 - - + +
374C ALA* 4.0 22.9 - - + -
397C ALA 4.5 3.8 - - - +
398C THR* 3.9 31.4 - - - +
400C GLN* 6.4 1.6 - - + -
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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