Contacts of the helix formed by residues 256 - 260 (chain G) in PDB entry 3KDO
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 VAL 256 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254G VAL* 3.0 26.8 + - + +
255G ASP* 1.3 70.1 - - - +
257G VAL* 1.3 70.3 + - + +
259G THR* 3.9 2.9 - - - -
260G GLY* 3.1 22.5 + - - +
264G LEU* 3.9 21.1 - - + +
280G GLY* 4.1 8.5 - - - -
281G HIS 3.0 16.4 + - - +
282G ARG* 4.6 0.4 - - - -
305G TYR* 3.6 43.2 + - + -
310G ILE* 4.0 20.0 - - + -
313G LEU* 4.6 8.7 - - + -
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Residues in contact with VAL 257 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B TRP* 5.3 1.2 - - - -
255G ASP 3.4 0.4 - - - -
256G VAL* 1.3 79.1 - - + +
258G ILE* 1.3 64.8 + - - +
260G GLY* 3.4 10.2 + - - -
281G HIS 4.1 0.6 + - - -
282G ARG* 3.6 27.4 - - + +
283G ALA 3.5 16.2 - - - +
284G MET* 4.1 11.1 - - + +
285G HIS* 4.1 15.3 - - + +
288G PHE* 4.0 28.7 - - + -
301G LEU* 4.1 10.5 - - + -
305G TYR* 3.5 20.4 - - + +
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Residues in contact with ILE 258 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B PRO* 3.7 34.8 - - + +
105B LEU* 3.8 7.9 - - + +
106B ALA* 3.3 44.2 - - + +
261B TRP* 3.4 36.7 + - + +
231G THR* 4.8 2.9 - - + -
255G ASP* 3.4 15.1 + - + +
257G VAL* 1.3 76.3 - - - +
259G THR* 1.3 67.4 + - - +
260G GLY* 3.2 0.7 + - - -
283G ALA* 3.7 24.0 + - + +
284G MET* 4.0 19.5 - - + -
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Residues in contact with THR 259 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B PRO* 6.0 0.7 - - - -
259B THR 4.1 1.9 - - - +
260B GLY* 3.8 1.9 - - - -
261B TRP 3.7 1.2 + - - -
262B GLY* 2.7 33.7 + - - +
263B ALA 4.2 0.5 + - - -
231G THR* 4.6 6.8 - - - +
232G ALA 5.4 0.2 + - - -
237G MET* 4.0 29.0 - - + -
254G VAL* 3.4 18.8 - - + +
255G ASP 2.8 24.1 + - - -
256G VAL* 3.9 4.5 - - - -
257G VAL 3.4 0.2 - - - -
258G ILE* 1.3 73.5 - - - +
260G GLY* 1.3 68.5 + - - +
263G ALA* 4.6 12.9 - - + +
264G LEU* 4.2 15.5 - - + +
267G ILE* 5.0 2.9 - - + -
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Residues in contact with GLY 260 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B VAL 5.8 0.2 - - - -
258B ILE 4.6 0.2 - - - -
260B GLY* 3.7 16.4 - - - -
256G VAL 3.1 14.3 + - - +
257G VAL 3.4 10.1 + - - -
258G ILE 3.2 1.8 - - - -
259G THR* 1.3 82.2 - - - +
261G TRP* 1.3 69.1 + - - -
262G GLY 3.4 3.3 + - - -
263G ALA 3.8 0.3 + - - -
264G LEU* 3.4 23.5 + - - +
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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