Contacts of the helix formed by residues 322 - 335 (chain A) in PDB entry 3KMR
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 322 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A ARG* 5.9 0.9 - - - -
321A MET* 1.3 72.6 - - - +
323A ASP* 1.3 59.4 + - - +
324A ALA 3.3 4.3 + - - -
325A GLU* 3.0 29.3 + - - +
326A THR* 2.9 31.2 + - - -
362A TYR* 2.6 25.2 + - - -
366A ARG* 3.2 31.7 + - - +
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Residues in contact with ASP 323 (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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192A ARG* 4.1 12.3 - - + +
195A HIS* 3.5 31.9 + - + +
196A GLN* 3.2 42.3 + - - +
199A PHE* 4.9 7.1 - - - +
201A ALA* 5.7 5.0 - - - +
322A ASP* 1.3 76.2 - - - +
324A ALA* 1.3 57.8 + - - +
326A THR* 4.8 0.2 - - - -
327A GLY* 2.8 28.4 + - - -
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Residues in contact with ALA 324 (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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188A ILE* 4.2 11.0 - - + -
191A VAL* 4.7 0.9 - - - +
192A ARG* 3.7 37.6 - - + +
322A ASP* 3.3 2.7 + - - +
323A ASP* 1.3 77.3 - - - +
325A GLU* 1.3 58.7 + - - +
327A GLY* 3.8 0.3 - - - -
328A LEU* 2.9 38.4 + - + +
362A TYR* 3.6 32.1 - - + +
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Residues in contact with GLU 325 (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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321A MET* 3.2 25.7 - - + +
322A ASP* 3.0 23.4 + - - +
324A ALA* 1.3 73.8 - - - +
326A THR* 1.3 60.2 + - - +
328A LEU* 3.4 1.4 + - - +
329A LEU* 3.0 24.4 + - - +
359A LEU* 4.1 12.4 - - + +
362A TYR* 3.6 17.8 - - + -
363A VAL* 3.8 17.6 - - + +
366A ARG* 2.8 38.6 + - - -
367A ARG* 2.8 35.0 + - - -
377A MET* 4.2 4.0 - - - -
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Residues in contact with THR 326 (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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195A HIS* 3.5 30.7 - - + +
271A LEU* 4.1 18.7 - - + +
272A ARG* 6.0 1.6 - - + -
275A THR* 4.2 27.1 + - + +
321A MET* 3.8 23.5 + - - +
322A ASP 2.9 19.0 + - - -
323A ASP 4.2 0.2 - - - -
325A GLU* 1.3 76.1 - - - +
327A GLY* 1.3 56.4 + - - +
329A LEU* 3.5 2.6 + - - +
330A SER* 3.0 34.2 + - - +
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Residues in contact with GLY 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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191A VAL* 3.4 14.0 - - - +
195A HIS* 3.6 25.2 - - - -
242A PHE* 3.5 9.9 - - - -
323A ASP 2.8 18.6 + - - -
324A ALA 3.8 0.9 - - - -
326A THR* 1.3 77.4 - - - +
328A LEU* 1.3 54.6 + - - +
330A SER* 3.4 4.0 + - - -
331A ALA 2.9 23.4 + - - -
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Residues in contact with LEU 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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187A LEU* 5.3 0.4 - - + +
188A ILE* 4.5 20.2 - - + +
191A VAL* 3.6 22.6 - - + +
324A ALA* 2.9 24.4 + - + +
325A GLU 3.8 3.8 - - - +
326A THR 3.4 0.2 - - - -
327A GLY* 1.3 77.3 - - - +
329A LEU* 1.3 56.3 + - - +
331A ALA* 3.2 3.0 + - - +
332A ILE* 2.8 36.1 + - + +
355A LEU* 4.1 34.1 - - + +
358A ALA* 4.3 13.2 - - + +
359A LEU* 3.8 41.5 - - + +
362A TYR* 4.8 6.1 - - + -
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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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271A LEU* 4.2 24.5 - - + -
316A LEU* 5.3 0.4 - - + -
321A MET* 4.1 17.7 - - + -
325A GLU 3.0 17.6 + - - +
326A THR 3.8 3.8 - - - +
328A LEU* 1.3 75.4 - - - +
330A SER* 1.3 57.3 + - - +
332A ILE* 3.3 5.7 + - + +
333A CYS* 2.9 36.1 + - - -
359A LEU* 4.4 18.0 - - + +
377A MET* 3.5 28.7 - - + +
378A LEU* 4.7 1.6 - - + -
380A LYS* 4.1 23.3 - - + -
381A ILE* 3.7 27.1 - - + +
384A LEU* 5.2 3.4 - - + -
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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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195A HIS* 4.7 6.1 + - - -
242A PHE* 3.7 20.9 - - - -
268A ILE* 4.1 23.4 - - - +
271A LEU* 3.4 18.8 - - - +
272A ARG* 5.3 3.6 + - - +
326A THR* 3.0 18.1 + - - +
327A GLY* 3.5 9.8 - - - -
329A LEU* 1.3 76.6 - - - +
331A ALA* 1.3 57.6 + - - +
333A CYS* 3.3 7.7 + - - +
334A LEU* 3.0 28.4 + - - +
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Residues in contact with ALA 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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191A VAL* 4.4 1.8 - - + -
242A PHE* 4.0 0.6 - - + -
246A LEU* 3.9 35.9 - - + -
327A GLY 2.9 17.5 + - - +
328A LEU* 3.2 6.3 + - - +
330A SER* 1.3 72.9 - - - +
332A ILE* 1.3 60.0 + - - +
334A LEU* 4.5 0.4 - - - -
335A ILE* 2.9 35.5 + - - +
355A LEU* 3.8 25.5 - - + +
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Residues in contact with ILE 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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328A LEU 2.8 21.0 + - - +
329A LEU* 3.8 5.2 - - - +
331A ALA* 1.3 75.7 - - - +
333A CYS* 1.3 62.0 + - - +
335A ILE 3.5 7.1 - - - +
336A CYS* 4.2 2.4 - - - +
352A GLN* 3.1 38.8 + - + +
355A LEU* 3.8 35.7 - - + +
356A LEU* 3.8 31.4 - - + -
359A LEU* 3.8 28.7 - - + -
378A LEU* 5.1 1.6 - - + -
381A ILE* 3.4 22.9 - - + -
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Residues in contact with CYS 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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264A ALA* 4.3 0.9 - - - -
267A ASP* 4.8 16.8 - - + -
268A ILE* 4.9 5.4 - - + -
271A LEU* 5.5 0.9 - - - -
329A LEU* 2.9 25.8 + - - +
330A SER* 3.5 8.5 - - - +
332A ILE* 1.3 77.7 - - - +
334A LEU* 1.3 61.2 + - - +
336A CYS* 3.7 7.5 - - - +
339A ARG* 3.1 25.8 + - - +
381A ILE* 3.4 39.0 - - - -
384A LEU* 4.2 23.1 - - - -
385A ARG* 5.3 0.5 + - - -
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Residues in contact with LEU 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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242A PHE* 5.1 3.1 - - + -
243A ALA* 3.5 29.8 - - + -
246A LEU* 3.8 20.4 - - + -
249A PHE* 3.9 14.8 - - + -
260A LEU* 3.4 52.3 - - + +
261A LEU* 3.9 18.4 - - + +
264A ALA* 3.8 12.9 - - + +
268A ILE* 4.2 12.8 - - + -
330A SER 3.0 16.0 + - - +
331A ALA* 3.7 3.8 - - - +
332A ILE 3.3 0.2 - - - -
333A CYS* 1.3 80.4 - - - +
335A ILE* 1.3 60.3 + - + +
336A CYS* 3.0 7.6 + - - +
339A ARG* 4.9 1.2 + - - -
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Residues in contact with ILE 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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246A LEU* 3.9 30.1 - - + -
247A PRO 5.0 2.0 - - - +
249A PHE* 4.3 13.9 - - + -
260A LEU* 4.4 4.3 - - + -
331A ALA 2.9 16.6 + - - +
332A ILE 3.5 1.4 - - - +
333A CYS 3.6 0.2 - - - -
334A LEU* 1.3 82.4 - - + +
336A CYS* 1.3 57.9 + - - +
348A VAL* 3.6 30.5 - - + +
351A LEU* 3.9 30.3 - - + -
352A GLN* 3.0 43.2 + - - +
355A LEU* 4.0 19.1 - - + -
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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
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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