Contacts of the helix formed by residues 328 - 339 (chain B) in PDB entry 3K6G
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 ASP 328 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365A GLN* 5.4 7.0 - - - +
368A ILE* 3.5 30.6 - - + +
372A LYS* 4.0 15.1 + - - +
322B MSE 4.2 2.9 - - - -
327B LEU* 1.3 77.3 - - - +
329B LEU* 1.3 67.0 + - - +
330B SER* 3.9 15.2 + - - -
331B THR* 2.6 31.0 + - - -
332B VAL* 3.3 19.6 + - - +
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Residues in contact with LEU 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B ILE* 3.8 22.4 - - + -
322B MSE 3.7 18.5 - - - -
328B ASP* 1.3 75.4 - - - +
330B SER* 1.3 59.8 + - - +
332B VAL* 3.4 1.7 + - - +
333B THR* 2.8 44.2 + - - +
292E PHE* 3.8 27.1 - - + +
295E LEU* 3.8 26.2 - - + +
296E SER* 3.6 35.4 - - - +
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Residues in contact with SER 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A LYS* 6.3 0.9 - - - -
328B ASP* 3.3 14.6 + - - -
329B LEU* 1.3 80.7 - - - +
331B THR* 1.3 59.3 + - - +
333B THR* 3.5 0.4 + - - -
334B GLN* 2.9 32.1 + - - +
292E PHE* 4.3 8.1 - - - -
308E LEU* 3.8 34.5 - - - +
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Residues in contact with THR 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A ILE* 4.7 6.1 - - - +
327B LEU* 4.0 25.0 - - + +
328B ASP* 2.6 28.1 + - - -
330B SER* 1.3 75.5 - - - +
332B VAL* 1.3 59.4 + - - +
334B GLN* 3.4 10.1 + - - +
335B ALA* 2.9 27.2 + - - +
350B LEU* 5.1 0.4 - - + -
313E LEU* 4.2 8.9 - - + +
314E VAL 5.0 2.7 + - - +
315E LEU* 3.7 31.2 - - + -
316E PRO* 4.5 6.9 - - + +
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Residues in contact with VAL 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ILE* 4.1 15.9 - - + -
321B LEU* 4.0 20.4 - - + -
322B MSE 3.7 26.7 - - + +
327B LEU* 3.9 22.4 - - + -
328B ASP 3.3 16.3 + - - +
329B LEU 3.9 2.7 - - - +
331B THR* 1.3 72.7 - - - +
333B THR* 1.3 67.0 + - - +
335B ALA* 3.1 8.1 + - - +
336B PHE* 3.0 46.2 + - + -
350B LEU* 4.7 5.2 - - + -
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Residues in contact with THR 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ILE* 4.6 7.8 - - + +
329B LEU* 2.8 30.3 + - - +
330B SER 3.8 4.0 - - - -
332B VAL* 1.3 76.8 - - - +
334B GLN* 1.3 57.6 + - - +
336B PHE* 3.1 11.2 + - - +
337B LEU* 2.9 28.8 + - + +
288E LEU* 3.9 13.4 - - + +
292E PHE* 3.5 29.1 - - + +
305E PHE* 3.8 28.9 - - + -
308E LEU* 4.1 8.1 - - + -
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Residues in contact with GLN 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B SER 2.9 18.4 + - - +
331B THR* 3.6 8.1 - - - +
333B THR* 1.3 75.3 - - - +
335B ALA* 1.3 62.5 + - - +
337B LEU* 3.1 11.7 + - - +
338B LYS* 3.0 44.1 + - - +
308E LEU* 3.2 30.0 + - + +
311E LYS* 2.9 37.0 + - - +
312E ASP 3.7 5.7 + - - +
313E LEU* 3.5 26.5 - - + +
314E VAL 4.7 2.1 + - - +
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Residues in contact with ALA 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B THR 2.9 17.6 + - - +
332B VAL* 3.1 7.2 + - - +
334B GLN* 1.3 76.8 - - - +
336B PHE* 1.3 61.3 + - - +
338B LYS 3.3 1.6 + - - +
339B ASN* 2.8 33.8 + - - +
346B THR* 4.0 12.3 - - + -
349B PHE* 4.8 0.9 - - + -
350B LEU* 3.8 28.3 - - + -
313E LEU* 3.7 20.6 - - + +
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Residues in contact with PHE 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B ILE* 3.8 17.7 - - + -
318B ILE* 4.1 14.8 - - + -
321B LEU* 3.5 33.2 - - + -
332B VAL* 3.0 34.6 + - + -
333B THR 3.5 7.4 - - - +
335B ALA* 1.3 75.5 - - - +
337B LEU* 1.3 62.6 + - - +
339B ASN 3.2 1.2 + - - -
340B SER 3.2 4.0 + - - -
341B GLY* 2.8 45.9 + - - -
343B LEU* 3.9 18.4 - - + -
346B THR* 3.4 24.5 - - + -
396B PHE* 4.3 0.2 - - - -
283E ILE* 3.8 16.4 - - + -
288E LEU* 3.8 27.4 - - + -
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Residues in contact with LEU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B THR* 2.9 17.3 + - + +
334B GLN* 3.1 9.8 + - - +
336B PHE* 1.3 79.6 - - - +
338B LYS* 1.3 59.5 + - + +
339B ASN 3.4 0.2 + - - -
340B SER 3.6 0.3 + - - -
393B ARG* 2.7 38.0 + - - -
396B PHE* 3.9 10.2 - - + -
285E MSE 4.2 16.2 - - + -
288E LEU* 3.6 19.1 - - + -
305E PHE* 3.8 28.0 - - + +
308E LEU* 3.9 16.4 - - + +
309E ASP* 3.8 46.2 - - + +
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Residues in contact with LYS 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334B GLN* 3.0 25.7 + - - +
335B ALA 3.3 3.8 + - - +
336B PHE 3.3 0.4 - - - -
337B LEU* 1.3 80.6 - - - +
339B ASN* 1.3 59.2 + - - +
340B SER 3.4 1.6 - - - -
361B ILE* 3.7 21.7 - - + +
362B TRP* 3.0 57.2 + - - +
363B SER 6.0 0.4 - - - -
364B ARG* 5.7 1.6 - - - +
367B ASP* 5.8 1.8 + - - +
393B ARG* 4.1 7.5 - - - +
308E LEU 2.9 19.0 + - - -
309E ASP* 3.0 22.6 + - - +
310E GLN 4.9 0.2 + - - -
311E LYS 2.8 29.3 + - - -
312E ASP* 4.4 3.3 + - - +
313E LEU* 3.8 23.8 - - + +
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Residues in contact with ASN 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B ALA* 2.8 24.3 + - - +
336B PHE 3.2 0.6 + - - -
338B LYS* 1.3 80.4 - - - +
340B SER* 1.3 68.0 + - - +
341B GLY 3.1 2.8 + - - -
342B GLU* 3.1 24.2 + - - +
345B ALA* 4.3 6.0 - - + +
346B THR* 3.3 35.8 + - - +
349B PHE* 3.9 23.3 - - - +
355B ARG* 3.4 35.2 + - - +
361B ILE* 3.6 11.3 - - - +
362B TRP* 5.3 1.6 - - - -
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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