Contacts of the helix formed by residues 328 - 339 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A MSE 4.4 1.6 - - - -
327A LEU* 1.3 78.5 - - - +
329A LEU* 1.3 63.2 + - - +
330A SER* 3.2 9.8 + - - +
331A THR* 2.6 44.9 + - - -
332A VAL* 3.3 17.5 + - - +
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Residues in contact with LEU 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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318A ILE* 3.9 22.9 - - + -
322A MSE 3.7 19.2 - - - -
328A ASP* 1.3 74.5 - - - +
330A SER* 1.3 58.5 + - - +
332A VAL* 3.4 2.1 + - - +
333A THR* 2.8 43.6 + - - +
292D PHE* 3.7 29.2 - - + +
295D LEU* 3.9 20.4 - - + +
296D SER* 3.5 37.7 - - - +
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Residues in contact with SER 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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328A ASP* 3.2 10.3 + - - -
329A LEU* 1.3 75.0 - - - +
331A THR* 1.3 61.0 + - - +
333A THR* 3.8 0.5 - - - -
334A GLN* 2.8 35.0 + - - +
292D PHE* 3.9 17.2 - - - -
308D LEU* 4.0 27.3 - - - +
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Residues in contact with THR 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 LEU* 4.0 33.8 - - + +
328A ASP* 2.6 36.5 + - - -
330A SER* 1.3 73.2 - - - +
332A VAL* 1.3 63.2 + - - +
334A GLN* 3.5 7.3 + - - +
335A ALA* 3.0 22.6 + - + +
350A LEU* 4.8 5.4 - - + -
313D LEU* 4.7 13.8 - - + +
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Residues in contact with VAL 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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318A ILE* 4.1 15.5 - - + +
321A LEU* 3.9 25.4 - - + -
322A MSE 3.7 25.4 - - + +
327A LEU* 3.8 24.9 - - + -
328A ASP 3.3 14.0 + - - +
329A LEU 3.8 5.6 - - - +
331A THR* 1.3 76.8 - - - +
333A THR* 1.3 61.1 + - - +
335A ALA* 3.2 7.8 + - - +
336A PHE* 3.1 38.2 + - + -
346A THR* 4.7 0.2 - - - +
350A LEU* 4.6 6.5 - - + -
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Residues in contact with THR 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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318A ILE* 4.6 7.9 - - - +
329A LEU* 2.8 30.0 + - - +
330A SER 3.8 2.9 - - - -
332A VAL* 1.3 77.4 - - - +
334A GLN* 1.3 62.9 + - - +
336A PHE* 3.2 10.6 + - - +
337A LEU* 3.0 22.1 + - + +
288D LEU* 3.8 10.7 - - + +
292D PHE* 3.5 35.4 - - + +
305D PHE* 3.9 26.5 - - + -
308D LEU* 4.2 7.6 - - + -
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Residues in contact with GLN 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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330A SER 2.8 22.5 + - - +
331A THR* 3.9 5.5 - - - +
333A THR* 1.3 73.4 - - - +
335A ALA* 1.3 62.5 + - - +
337A LEU* 3.2 11.0 + - - +
338A LYS* 3.0 42.8 + - - +
308D LEU* 3.1 35.1 + - + +
311D LYS* 3.0 32.9 + - - +
312D ASP 4.0 4.9 + - - +
313D LEU* 3.0 30.5 - - + +
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Residues in contact with ALA 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 THR 3.0 15.4 + - - +
332A VAL 3.4 9.4 - - - +
333A THR 3.2 0.2 - - - -
334A GLN* 1.3 77.2 - - - +
336A PHE* 1.3 62.8 + - - +
338A LYS* 3.2 1.7 + - - -
339A ASN* 2.9 29.1 + - - +
346A THR* 3.9 11.7 - - + -
349A PHE* 4.4 6.5 - - + -
350A LEU* 3.8 25.8 - - + -
313D LEU* 3.6 19.2 - - + +
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Residues in contact with PHE 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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317A ILE* 3.8 9.4 - - + -
318A ILE* 4.2 11.0 - - + -
321A LEU* 3.4 34.8 - - + -
332A VAL* 3.1 29.5 + - + -
333A THR* 3.2 8.0 + - - +
335A ALA* 1.3 76.0 - - - +
337A LEU* 1.3 63.4 + - - +
339A ASN 3.1 1.0 + - - -
340A SER 3.0 4.9 + - - -
341A GLY* 2.8 51.3 + - - -
342A GLU 3.9 6.1 - - - -
343A LEU* 4.0 9.6 - - + -
346A THR* 3.4 24.0 - - + -
283D ILE* 3.8 27.4 - - + -
288D LEU* 3.8 27.8 - - + -
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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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333A THR* 3.0 18.2 + - + +
334A GLN* 3.2 8.7 + - - +
336A PHE* 1.3 79.3 - - - +
338A LYS* 1.3 65.2 + - + +
340A SER 3.6 0.3 + - - -
393A ARG* 2.8 31.6 + - - -
396A PHE* 3.8 15.8 - - + -
285D MSE 4.2 12.3 - - + -
288D LEU* 3.6 13.9 - - + -
305D PHE* 3.7 34.1 - - + +
308D LEU* 3.9 16.8 - - + +
309D ASP* 3.7 45.3 - - + +
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Residues in contact with LYS 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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334A GLN* 3.0 24.7 + - - +
335A ALA 3.2 4.7 + - - +
337A LEU* 1.3 80.8 - - - +
339A ASN* 1.3 58.8 + - - +
340A SER 3.4 2.0 - - - -
355A ARG* 5.8 0.2 + - - -
361A ILE* 3.6 20.8 - - + +
362A TRP* 3.0 56.4 + - - +
363A SER 5.9 0.6 - - - -
364A ARG 5.7 1.8 - - - +
367A ASP* 5.6 2.2 + - - +
393A ARG* 4.2 7.5 - - - +
308D LEU 2.9 19.0 + - - -
309D ASP* 3.0 22.8 + - - +
310D GLN 4.6 0.4 + - - -
311D LYS 2.8 30.9 + - - -
312D ASP* 4.5 3.2 + - - +
313D LEU* 3.8 26.2 - - + +
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Residues in contact with ASN 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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335A ALA* 2.9 21.7 + - - +
336A PHE 3.1 0.8 + - - +
338A LYS* 1.3 77.4 + - - +
340A SER* 1.3 71.4 + - - +
341A GLY 3.2 2.8 + - - -
342A GLU* 3.2 21.6 + - - +
345A ALA* 4.0 8.8 + - + +
346A THR* 3.3 32.6 + - - +
349A PHE* 4.0 14.9 - - - +
355A ARG* 3.2 44.9 - - - +
361A ILE* 3.5 15.9 - - - +
362A TRP* 5.3 1.3 - - - -
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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