Contacts of the helix formed by residues 326 - 339 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319F GLY* 4.7 2.9 - - - +
324F GLU* 4.5 14.1 + - - +
325F GLY* 1.3 70.9 - - - +
327F ARG* 1.3 58.6 + - - +
328F ASP* 3.0 30.6 - - - +
329F ILE* 3.8 27.2 - - + +
330F THR* 2.7 37.6 + - - -
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Residues in contact with ARG 327 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318F ALA* 3.5 30.1 + - + +
319F GLY* 4.8 0.6 - - - -
326F GLU* 1.3 71.7 - - - +
328F ASP* 1.3 69.2 + - - +
330F THR* 3.2 3.1 + - - -
331F LEU* 3.0 31.7 + - + +
377F PRO 4.9 3.5 + - - -
380F GLU* 4.7 5.5 + - - +
381F ALA* 3.2 42.5 - - + +
382F LEU* 5.1 0.5 - - - +
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Residues in contact with ASP 328 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326F GLU* 3.0 35.3 - - - +
327F ARG* 1.3 80.1 + - - +
329F ILE* 1.3 75.7 + - + +
331F LEU* 3.1 18.5 + - - +
332F GLY* 3.3 9.4 + - - -
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Residues in contact with ILE 329 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324F GLU* 5.8 2.5 - - - +
325F GLY* 6.3 1.1 - - - -
326F GLU* 3.5 35.6 + - + +
327F ARG 3.4 0.6 - - - -
328F ASP* 1.3 90.5 - - + +
330F THR* 1.3 62.3 + - - +
332F GLY* 3.2 10.4 + - - +
333F PHE* 3.2 45.7 + - + -
351F HIS* 6.4 4.5 - - + -
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Residues in contact with THR 330 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315F VAL* 4.0 24.3 + - + +
316F GLY 4.0 5.5 - - - +
318F ALA* 3.4 29.4 + - + +
325F GLY* 3.6 9.7 + - - -
326F GLU 2.7 22.5 + - - -
327F ARG 3.6 3.8 - - - -
329F ILE* 1.3 77.5 - - - +
331F LEU* 1.3 62.9 + - - +
333F PHE* 3.2 14.1 + - - +
334F VAL* 3.1 20.8 + - - +
382F LEU* 3.9 23.3 - - + -
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Residues in contact with LEU 331 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327F ARG* 3.0 21.1 + - + +
328F ASP* 3.4 12.3 - - - +
330F THR* 1.3 72.9 - - - +
332F GLY* 1.3 66.1 + - - +
334F VAL* 3.4 12.6 + - + +
335F ASP* 3.1 41.9 + - - +
338F ARG* 5.2 2.5 - - - +
381F ALA* 3.4 28.7 - - + +
382F LEU* 4.7 7.4 - - + +
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Residues in contact with GLY 332 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299F PHE* 4.2 14.4 - - - -
328F ASP 3.3 6.1 + - - -
329F ILE* 3.2 8.1 + - - -
330F THR 3.2 0.6 - - - -
331F LEU* 1.3 77.2 - - - +
333F PHE* 1.3 66.9 + - - +
335F ASP* 3.1 8.8 + - - +
336F LEU* 2.9 24.3 + - - +
342F TYR* 4.5 6.5 - - - -
351F HIS* 6.1 2.0 - - - -
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Residues in contact with PHE 333 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282F ARG* 5.0 1.3 - - - -
297F SER* 4.6 3.1 - - - -
298F MET* 3.4 37.2 - - + -
299F PHE* 3.5 44.6 - + + -
302F ALA* 4.8 6.9 - - + +
315F VAL* 3.6 37.9 - - + -
325F GLY* 6.5 0.7 - - - -
329F ILE* 3.2 39.3 - - + -
330F THR* 3.2 11.1 + - - +
332F GLY* 1.3 74.9 - - - +
334F VAL* 1.3 63.9 + - - +
336F LEU* 3.2 7.3 + - - +
337F LEU* 3.0 28.9 + - - +
351F HIS* 5.6 0.9 - + - -
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Residues in contact with VAL 334 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315F VAL* 4.3 9.6 - - + -
330F THR 3.1 13.3 + - - +
331F LEU* 3.6 11.2 - - + +
332F GLY 3.2 0.2 - - - -
333F PHE* 1.3 76.7 - - - +
335F ASP* 1.3 63.7 + - - +
337F LEU* 3.2 3.1 + - - +
338F ARG* 2.8 74.0 + - - +
364F PRO* 4.0 24.9 - - + -
382F LEU* 3.8 28.7 - - + +
386F ILE* 5.0 0.4 - - + -
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Residues in contact with ASP 335 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331F LEU* 3.1 38.0 + - - +
332F GLY* 3.6 8.6 - - - +
334F VAL* 1.3 77.6 - - - +
336F LEU* 1.3 58.4 + - - +
338F ARG* 4.4 12.0 + - - +
339F GLU* 2.9 64.6 + - - +
342F TYR* 4.2 13.4 - - + -
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Residues in contact with LEU 336 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299F PHE* 3.1 65.5 - - + +
302F ALA* 4.0 6.5 - - + -
303F LYS* 3.8 29.8 - - + +
306F ARG* 2.7 27.9 + - - -
332F GLY 2.9 16.5 + - - +
333F PHE 3.5 5.6 - - - +
335F ASP* 1.3 76.6 - - - +
337F LEU* 1.3 52.0 + - - +
342F TYR* 4.0 20.8 - - + -
354F GLN* 5.1 0.2 - - + -
356F PHE* 3.6 33.8 - - + -
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Residues in contact with LEU 337 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302F ALA* 3.3 38.1 - - + +
306F ARG* 3.2 22.5 + - + +
313F LEU* 4.2 20.2 - - + -
315F VAL* 3.5 32.1 - - + -
333F PHE 3.0 16.0 + - - +
334F VAL 3.7 4.3 - - - +
335F ASP 3.1 0.2 - - - -
336F LEU* 1.3 79.0 - - - +
338F ARG* 1.3 56.9 + - - +
361F ALA* 3.4 0.2 - - - -
362F ALA* 2.8 51.1 + - + +
364F PRO* 4.2 17.0 - - + -
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Residues in contact with ARG 338 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F ILE* 3.8 16.2 - - + -
306F ARG* 4.1 1.9 + - - -
331F LEU* 5.2 2.8 - - - +
334F VAL* 2.8 37.8 + - - +
335F ASP* 4.3 11.3 + - - +
337F LEU* 1.3 81.7 - - - +
339F GLU* 1.3 66.4 + - + +
340F SER 3.7 1.6 + - - -
361F ALA* 3.5 19.1 - - - +
362F ALA 3.8 2.7 - - - +
364F PRO* 3.6 17.9 - - + -
382F LEU* 2.8 31.1 + - - +
383F GLY* 4.5 3.2 - - - -
385F ASP* 2.7 56.2 + - - +
386F ILE* 3.7 0.8 - - - +
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Residues in contact with GLU 339 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306F ARG* 2.9 25.3 + - - -
335F ASP* 2.9 39.1 + - - +
338F ARG* 1.3 78.7 - - + +
340F SER* 1.3 63.3 + - - +
341F HIS 3.8 15.4 - - - +
342F TYR* 3.3 32.5 - - + +
343F LYS 3.8 5.2 + - - +
356F PHE* 3.4 7.4 - - - -
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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