Contacts of the helix formed by residues 326 - 339 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A ALA* 3.7 0.8 - - - -
319A GLY* 4.9 1.8 - - - -
324A GLU* 3.8 7.2 + - - +
325A GLY* 1.3 78.2 - - - +
327A ARG* 1.3 62.2 + - - +
328A ASP* 4.8 1.3 - - + +
329A ILE* 4.2 29.3 - - + +
330A THR* 2.9 23.6 + - - -
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Residues in contact with ARG 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A ALA* 3.9 22.9 - - + +
319A GLY* 4.9 0.6 - - - -
326A GLU* 1.3 71.9 - - - +
328A ASP* 1.3 73.3 + - - +
330A THR* 3.0 15.4 + - - -
331A LEU* 3.2 22.7 + - + +
377A PRO 5.1 1.8 + - - -
380A GLU* 4.7 5.7 + - - +
381A ALA* 3.3 42.5 - - + +
382A LEU* 5.0 0.7 - - - +
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Residues in contact with ASP 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A GLU* 4.8 1.2 - - + +
327A ARG* 1.3 82.6 - - - +
329A ILE* 1.3 66.7 + - + +
331A LEU* 3.0 16.2 + - - +
332A GLY* 2.9 17.0 + - - -
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Residues in contact with ILE 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ARG* 6.2 2.2 - - - +
326A GLU* 4.2 25.9 + - + +
327A ARG 3.2 0.6 - - - -
328A ASP* 1.3 78.8 - - + +
330A THR* 1.3 55.7 + - - +
332A GLY* 2.6 23.5 + - - +
333A PHE* 2.9 49.8 + - + -
351A HIS* 6.2 8.3 - - + +
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Residues in contact with THR 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A VAL* 4.2 18.4 + - + -
316A GLY* 4.2 12.2 - - - +
318A ALA* 3.5 21.3 + - - +
325A GLY* 4.1 6.2 + - - -
326A GLU 2.9 18.0 + - - -
327A ARG 3.0 9.9 + - - -
329A ILE* 1.3 78.9 - - - +
331A LEU* 1.3 56.9 + - - +
333A PHE* 3.2 12.6 + - - +
334A VAL* 2.9 31.9 + - - +
382A LEU* 3.3 32.5 - - + -
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Residues in contact with LEU 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A ARG* 3.2 18.8 + - + +
328A ASP* 3.0 17.6 + - - +
330A THR* 1.3 79.2 - - - +
332A GLY* 1.3 61.3 + - - +
334A VAL* 3.3 10.1 + - + +
335A ASP* 2.9 48.7 + - - +
338A ARG* 5.0 2.5 - - - +
381A ALA* 3.2 26.9 - - + +
382A LEU* 4.2 9.5 - - - +
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Residues in contact with GLY 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A PHE* 4.4 11.4 - - - -
328A ASP 2.9 8.7 + - - -
329A ILE* 2.6 17.0 + - - -
331A LEU* 1.3 69.8 - - - +
333A PHE* 1.3 63.8 + - - -
335A ASP* 3.0 10.4 + - - +
336A LEU* 2.8 23.5 + - - +
342A TYR* 4.7 5.4 - - - -
351A HIS* 5.8 4.5 - - - -
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Residues in contact with PHE 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A ARG* 5.8 0.7 - - - -
297A SER* 4.8 2.9 - - - -
298A MET* 3.5 34.5 - - + -
299A PHE* 3.5 44.9 - + + -
302A ALA* 4.7 7.2 - - + -
315A VAL* 3.7 39.9 - - + -
329A ILE* 2.9 43.3 + - + -
330A THR* 3.6 12.1 - - - +
332A GLY* 1.3 73.2 - - - +
334A VAL* 1.3 63.7 + - - +
336A LEU* 3.2 7.4 + - - +
337A LEU* 3.0 29.2 + - - +
351A HIS* 5.5 0.9 - - - -
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Residues in contact with VAL 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A VAL* 4.4 3.6 - - + -
330A THR* 2.9 22.1 + - + +
331A LEU* 3.4 9.9 - - + +
333A PHE* 1.3 75.9 - - - +
335A ASP* 1.3 63.3 + - - +
337A LEU* 3.2 2.3 + - - +
338A ARG* 2.5 76.4 + - - +
364A PRO* 4.1 23.8 - - + -
382A LEU* 3.5 34.3 - - + +
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Residues in contact with ASP 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A LEU* 2.9 42.1 + - - +
332A GLY* 3.5 7.9 - - - +
334A VAL* 1.3 76.3 - - - +
336A LEU* 1.3 63.3 + - - +
338A ARG* 4.5 8.8 + - - +
339A GLU* 3.1 62.2 + - - +
342A TYR* 4.4 11.0 - - + -
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Residues in contact with LEU 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A PHE* 3.3 57.7 - - + +
302A ALA* 4.0 13.2 - - + -
303A LYS* 4.0 22.6 - - + +
306A ARG* 3.1 20.8 + - - -
332A GLY 2.8 16.3 + - - +
333A PHE* 3.2 7.2 + - - +
335A ASP* 1.3 77.0 - - - +
337A LEU* 1.3 58.0 + - - +
342A TYR* 4.0 27.3 - - + -
354A GLN* 5.4 0.2 - - + -
356A PHE* 3.6 27.5 - - + -
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Residues in contact with LEU 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A ALA* 3.2 37.5 - - + +
306A ARG* 3.3 18.8 + - + +
313A LEU* 4.3 20.4 - - + -
315A VAL* 3.5 31.6 - - + -
333A PHE 3.0 14.3 + - - +
334A VAL 3.7 4.0 - - - +
335A ASP 3.0 0.2 - - - -
336A LEU* 1.3 80.5 - - - +
338A ARG* 1.3 57.2 + - - +
339A GLU 3.6 0.4 - - - -
361A ALA* 3.3 1.0 - - - -
362A ALA* 2.7 57.4 + - + +
364A PRO* 4.3 17.0 - - + -
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Residues in contact with ARG 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ILE* 3.5 20.4 - - + -
331A LEU* 5.0 3.0 - - - +
334A VAL* 2.5 43.6 + - - +
335A ASP* 4.5 9.2 + - - +
337A LEU* 1.3 77.1 - - - +
339A GLU* 1.3 65.4 + - + +
340A SER 4.1 0.5 + - - -
361A ALA* 3.7 18.3 - - - +
362A ALA 3.7 0.7 - - - +
364A PRO* 3.6 14.8 - - + -
382A LEU* 2.7 26.1 + - - +
383A GLY* 4.4 3.2 - - - -
385A ASP* 2.7 64.1 + - - +
386A ILE* 3.9 0.2 - - - +
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Residues in contact with GLU 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A ARG* 2.8 29.6 + - - -
335A ASP* 3.1 47.7 + - - +
338A ARG* 1.3 83.4 - - + +
340A SER* 1.3 63.9 + - - +
341A HIS 3.9 14.7 - - - +
342A TYR* 3.7 21.7 - - - +
343A LYS 4.3 2.6 + - - +
356A PHE* 3.5 6.4 - - - -
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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