Contacts of the helix formed by residues 326 - 339 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319I GLY* 4.5 3.4 - - - +
324I GLU* 4.5 5.3 + - - +
325I GLY* 1.3 72.8 - - - +
327I ARG* 1.3 62.5 + - - +
328I ASP* 3.6 2.5 - - + +
329I ILE* 3.4 24.9 + - + +
330I THR* 2.8 31.3 + - - -
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Residues in contact with ARG 327 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318I ALA* 3.6 26.6 - - + +
319I GLY* 4.9 1.0 - - - -
326I GLU* 1.3 72.2 - - - +
328I ASP* 1.3 80.1 + - - +
330I THR* 3.1 5.0 + - - -
331I LEU* 3.0 32.9 + - + +
377I PRO 5.2 1.4 + - - -
380I GLU* 4.2 19.4 + - - +
381I ALA* 3.5 43.6 - - + +
382I LEU* 5.0 0.3 - - - +
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Residues in contact with ASP 328 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326I GLU* 3.6 2.1 - - + +
327I ARG* 1.3 95.1 + - - +
329I ILE* 1.3 62.9 + - + +
331I LEU* 3.3 11.4 + - - +
332I GLY* 3.0 22.2 + - - -
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Residues in contact with ILE 329 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324I GLU* 6.1 0.9 - - - +
325I GLY* 6.3 1.1 - - - -
326I GLU* 3.4 25.9 + - + +
327I ARG 3.2 0.8 - - - -
328I ASP* 1.3 75.7 - - + +
330I THR* 1.3 65.9 + - - +
332I GLY* 3.0 12.4 + - - +
333I PHE* 3.2 43.4 + - + -
351I HIS* 6.2 5.8 - - + -
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Residues in contact with THR 330 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315I VAL* 3.8 23.8 + - + +
316I GLY 4.0 4.3 - - - +
317I THR 4.6 0.3 + - - -
318I ALA* 3.1 27.8 + - - +
325I GLY* 3.9 8.3 + - - -
326I GLU 2.8 23.0 + - - -
327I ARG 3.1 4.7 + - - -
329I ILE* 1.3 76.2 - - - +
331I LEU* 1.3 61.4 + - - +
333I PHE* 3.2 15.0 + - - +
334I VAL* 3.0 21.0 + - - +
382I LEU* 3.7 28.3 - - + -
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Residues in contact with LEU 331 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327I ARG* 3.0 23.5 + - + +
328I ASP* 3.5 13.5 - - - +
330I THR* 1.3 73.6 - - - +
332I GLY* 1.3 65.1 + - - +
334I VAL* 4.2 6.7 - - + -
335I ASP* 2.9 46.6 + - - +
338I ARG* 5.2 1.8 - - - +
381I ALA* 3.3 27.1 - - + +
382I LEU* 3.8 19.0 - - + +
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Residues in contact with GLY 332 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299I PHE* 4.1 14.9 - - - -
328I ASP 3.0 10.0 + - - -
329I ILE* 3.0 10.5 + - - -
331I LEU* 1.3 77.7 - - - +
333I PHE* 1.3 64.3 + - - +
335I ASP* 3.3 6.7 + - - +
336I LEU* 3.1 22.3 + - - +
342I TYR* 4.5 6.3 - - - -
351I HIS* 5.9 3.6 - - - -
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Residues in contact with PHE 333 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282I ARG* 5.0 1.8 - - - -
297I SER* 4.6 3.1 - - - -
298I MET* 3.6 32.8 - - + -
299I PHE* 3.6 44.0 - + + -
302I ALA* 4.7 7.2 - - + -
315I VAL* 3.5 40.4 - - + -
329I ILE* 3.2 39.5 + - + -
330I THR* 3.2 9.3 + - - +
332I GLY* 1.3 73.3 - - - +
334I VAL* 1.3 64.3 + - - +
336I LEU* 3.0 18.0 + - - +
337I LEU* 3.0 19.7 + - - +
351I HIS* 5.8 1.1 - + - -
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Residues in contact with VAL 334 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315I VAL* 4.0 12.5 - - + +
330I THR 3.0 17.4 + - - +
331I LEU* 3.6 13.9 - - + +
332I GLY 3.3 0.2 - - - -
333I PHE* 1.3 75.9 - - - +
335I ASP* 1.3 65.1 + - - +
337I LEU* 3.3 2.1 + - - +
338I ARG* 3.2 66.3 + - - +
364I PRO* 4.0 27.4 - - + -
382I LEU* 3.6 28.3 - - + +
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Residues in contact with ASP 335 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331I LEU* 2.9 43.2 + - - +
332I GLY* 3.7 5.6 - - - +
334I VAL* 1.3 78.7 - - - +
336I LEU* 1.3 58.8 + - - +
338I ARG* 4.7 7.4 + - - +
339I GLU* 3.0 63.9 + - - +
342I TYR* 4.2 13.1 - - + -
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Residues in contact with LEU 336 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299I PHE* 3.3 57.4 - - + +
302I ALA* 4.2 6.1 - - + -
303I LYS* 4.0 28.7 - - + +
306I ARG* 2.6 28.4 + - - -
332I GLY 3.1 11.2 + - - +
333I PHE 3.0 10.8 + - - +
335I ASP* 1.3 76.8 - - - +
337I LEU* 1.3 53.8 + - - +
342I TYR* 3.9 25.1 - - + -
354I GLN* 5.1 0.2 - - + -
356I PHE* 3.5 31.1 - - + -
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Residues in contact with LEU 337 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302I ALA* 3.2 39.0 - - + +
306I ARG* 3.2 29.2 - - + +
313I LEU* 4.2 18.8 - - + +
315I VAL* 3.5 31.9 - - + -
333I PHE 3.0 15.9 + - - +
334I VAL 3.9 3.8 - - - +
335I ASP 3.2 0.2 - - - -
336I LEU* 1.3 79.9 - - - +
338I ARG* 1.3 58.6 + - - +
361I ALA* 3.2 0.5 - - - -
362I ALA* 2.9 42.3 + - + +
364I PRO* 4.2 20.4 - - + -
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Residues in contact with ARG 338 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143I ILE* 3.5 24.9 - - + -
306I ARG* 4.4 0.3 + - - -
331I LEU* 5.2 2.8 - - - +
334I VAL* 3.2 34.2 + - - +
335I ASP* 4.5 9.5 + - - +
337I LEU* 1.3 80.7 - - - +
339I GLU* 1.3 65.3 + - + +
340I SER 3.7 1.6 + - - -
361I ALA* 3.4 18.5 - - - +
364I PRO* 3.7 13.0 - - + -
382I LEU 2.8 31.1 + - - -
383I GLY* 4.6 2.8 - - - -
385I ASP* 2.9 50.0 + - - +
386I ILE* 3.7 1.8 - - - +
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Residues in contact with GLU 339 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306I ARG* 2.8 28.2 + - - -
335I ASP* 3.0 44.0 + - - +
338I ARG* 1.3 80.6 - - + +
340I SER* 1.3 62.7 + - - +
341I HIS 3.5 14.6 - - - +
342I TYR* 3.2 32.9 - - + +
343I LYS 3.8 4.2 + - - +
356I PHE* 3.5 6.1 - - - -
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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
------------------------------------------------------------
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