Contacts of the helix formed by residues 326 - 339 (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 GLU 326 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319G GLY* 4.4 2.5 - - - +
324G GLU* 4.5 13.3 + - + +
325G GLY* 1.3 74.4 - - - +
327G ARG* 1.3 63.4 + - - +
328G ASP* 3.4 2.9 - - + +
329G ILE* 3.4 37.2 + - + +
330G THR* 2.7 30.7 + - - -
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Residues in contact with ARG 327 (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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318G ALA* 3.5 27.5 - - - +
319G GLY* 4.1 1.0 - - - +
326G GLU* 1.3 74.8 - - - +
328G ASP* 1.3 69.1 + - - +
330G THR* 3.2 2.9 + - - -
331G LEU* 3.1 37.2 + - + +
377G PRO 5.3 0.8 + - - -
380G GLU* 4.5 4.9 + - - +
381G ALA* 3.4 43.6 - - + +
382G LEU* 4.9 0.2 - - - +
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Residues in contact with ASP 328 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326G GLU* 3.4 2.1 - - + +
327G ARG* 1.3 85.9 - - - +
329G ILE* 1.3 65.2 + - + +
331G LEU* 3.2 18.3 + - - +
332G GLY* 3.2 9.5 + - - -
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Residues in contact with ILE 329 (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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324G GLU* 5.9 2.2 - - - +
325G GLY* 6.3 0.9 - - - -
326G GLU* 3.4 39.6 + - + +
327G ARG 3.3 1.0 - - - -
328G ASP* 1.3 76.7 - - + +
330G THR* 1.3 65.3 + - - +
332G GLY* 3.2 10.9 + - - -
333G PHE* 3.4 41.8 + - + -
351G HIS* 6.4 2.0 - - + -
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Residues in contact with THR 330 (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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315G VAL* 3.7 26.8 + - + +
316G GLY 4.1 4.5 - - - +
317G THR 4.6 0.7 + - - -
318G ALA* 3.4 24.7 + - - +
325G GLY* 4.0 9.0 - - - -
326G GLU 2.7 22.4 + - - -
327G ARG 3.6 4.0 - - - -
329G ILE* 1.3 74.7 - - - +
331G LEU* 1.3 66.1 + - - +
333G PHE* 3.0 22.9 + - - +
334G VAL* 3.0 12.0 + - - +
382G LEU* 3.8 26.9 - - + -
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Residues in contact with LEU 331 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327G ARG* 3.1 28.5 + - - +
328G ASP* 3.2 13.2 + - - +
330G THR* 1.3 77.0 - - - +
332G GLY* 1.3 62.8 + - - +
334G VAL* 3.5 5.9 + - + +
335G ASP* 3.0 43.1 + - - +
338G ARG* 5.3 1.6 - - - +
381G ALA* 3.4 24.7 - - + +
382G LEU* 3.9 16.1 - - + +
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Residues in contact with GLY 332 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299G PHE* 4.1 14.3 - - - -
328G ASP 3.2 6.3 + - - -
329G ILE* 3.2 9.0 + - - -
330G THR 3.1 1.0 - - - -
331G LEU* 1.3 76.4 - - - +
333G PHE* 1.3 66.8 + - - +
335G ASP* 3.3 7.7 + - - +
336G LEU* 3.0 23.7 + - - +
342G TYR* 4.4 6.4 - - - -
351G HIS* 6.1 2.5 - - - -
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Residues in contact with PHE 333 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282G ARG* 4.9 1.6 - - - -
297G SER* 4.6 2.7 - - - -
298G MET* 3.6 34.1 - - + -
299G PHE* 3.5 45.1 - + + -
302G ALA* 4.7 6.7 - - + +
315G VAL* 3.5 39.9 - - + -
329G ILE* 3.4 40.4 - - + -
330G THR* 3.0 11.3 + - - +
332G GLY* 1.3 74.8 - - - +
334G VAL* 1.3 63.0 + - - +
336G LEU* 3.1 8.1 + - - +
337G LEU* 3.1 27.9 + - - +
351G HIS* 5.7 1.6 - + - -
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Residues in contact with VAL 334 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315G VAL* 4.0 21.8 - - + -
330G THR 3.0 12.8 + - - +
331G LEU* 3.7 10.5 - - + +
332G GLY 3.3 0.2 - - - -
333G PHE* 1.3 76.3 - - - +
335G ASP* 1.3 62.8 + - - +
337G LEU* 3.1 3.7 + - - +
338G ARG* 3.0 68.4 + - - +
364G PRO* 4.0 18.4 - - + -
382G LEU* 3.8 28.7 - - + +
386G ILE* 5.1 0.4 - - + -
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Residues in contact with ASP 335 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331G LEU* 3.0 41.4 + - - +
332G GLY* 3.7 5.9 - - - +
333G PHE 3.3 0.2 - - - -
334G VAL* 1.3 76.6 - - - +
336G LEU* 1.3 63.3 + - - +
338G ARG* 4.3 12.0 + - - +
339G GLU* 3.1 58.6 + - - +
342G TYR* 4.2 11.7 - - + -
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Residues in contact with LEU 336 (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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299G PHE* 3.3 61.5 - - + +
302G ALA* 4.3 4.0 - - + -
303G LYS* 3.9 27.8 - - + +
306G ARG* 2.8 19.3 + - - -
332G GLY 3.0 17.3 + - - +
333G PHE* 3.1 6.7 + - - +
335G ASP* 1.3 76.9 - - - +
337G LEU* 1.3 58.1 + - - +
342G TYR* 4.2 17.0 - - + -
356G PHE* 2.9 32.5 - - + -
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Residues in contact with LEU 337 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302G ALA* 3.2 37.9 - - + +
306G ARG* 3.0 31.1 + - + +
313G LEU* 4.2 17.9 - - + -
315G VAL* 3.5 31.6 - - + -
333G PHE 3.1 12.8 + - - +
334G VAL 3.7 6.5 - - - +
335G ASP 3.1 0.6 - - - -
336G LEU* 1.3 82.0 - - - +
338G ARG* 1.3 60.1 + - - +
361G ALA* 3.2 0.3 - - - -
362G ALA* 2.9 41.8 + - + +
364G PRO* 4.2 19.3 - - + -
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Residues in contact with ARG 338 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143G ILE* 3.5 25.8 - - + -
306G ARG* 4.1 0.9 + - - -
331G LEU* 5.3 2.2 - - - +
334G VAL* 3.0 35.4 + - - +
335G ASP* 4.3 10.9 + - - -
337G LEU* 1.3 79.5 - - - +
339G GLU* 1.3 65.9 + - + +
340G SER* 3.9 2.3 + - - -
361G ALA* 3.3 20.0 - - + +
362G ALA 3.8 1.8 - - - +
364G PRO* 3.7 13.2 - - + -
382G LEU 3.0 29.1 + - - -
383G GLY* 4.6 2.6 - - - -
385G ASP* 3.0 48.6 + - - +
386G ILE* 3.9 1.6 - - - +
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Residues in contact with GLU 339 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306G ARG* 2.8 30.4 + - - -
335G ASP* 3.1 39.9 + - - +
338G ARG* 1.3 81.0 - - + +
340G SER* 1.3 62.0 + - - +
341G HIS 3.7 14.0 - - - +
342G TYR* 3.5 29.9 - - + +
343G LYS* 4.3 2.8 + - - +
356G PHE* 3.6 3.7 - - - -
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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