Contacts of the helix formed by residues 317 - 331 (chain E) in PDB entry 1KXT
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 317 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267E ARG* 3.2 33.1 + - - -
312E ILE 5.0 0.2 - - - +
313E LEU* 4.2 15.2 - - + +
314E THR* 2.6 22.3 + - - +
316E TRP* 1.3 82.2 - - - +
318E ALA* 1.3 52.4 + - - +
319E ARG 3.4 2.7 - - - -
320E LEU* 3.2 10.8 + - + +
321E TYR* 2.6 33.4 + - - +
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Residues in contact with ALA 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315E PHE 3.3 10.3 + - - +
316E TRP 3.5 1.2 - - - -
317E ASP* 1.3 74.1 - - - +
319E ARG* 1.3 64.1 + - - +
321E TYR* 4.0 5.6 - - - -
322E LYS* 2.8 37.9 + - - +
388E TRP* 3.7 26.9 - - + -
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Residues in contact with ARG 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317E ASP 3.4 1.0 - - - -
318E ALA* 1.3 80.4 - - - +
320E LEU* 1.3 80.9 + - + +
322E LYS* 3.6 13.4 + - - +
323E ILE* 3.3 23.7 + - + +
481E ASN 2.9 25.7 + - - -
482E SER* 4.3 2.2 - - - +
483E ALA 2.9 29.4 + - - -
484E GLU* 3.2 20.0 + - - +
485E ASP* 5.1 1.3 - - - +
486E PRO* 3.5 28.2 - - + +
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Residues in contact with LEU 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266E VAL* 3.9 30.1 - - + +
267E ARG* 4.6 26.2 - - + +
313E LEU* 3.6 17.6 - - + +
317E ASP* 3.2 11.4 + - + +
319E ARG* 1.3 101.1 - - + +
321E TYR* 1.3 67.4 + - - +
323E ILE* 3.2 14.6 + - + +
324E ALA 3.0 18.4 + - - -
431E ASN* 5.5 4.3 - - - +
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Residues in contact with TYR 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296E VAL* 3.7 16.1 - - + +
297E ASP* 2.8 30.7 + - - -
313E LEU* 3.7 15.2 - - - +
314E THR* 3.4 24.5 - - - +
315E PHE 3.7 13.2 - - - -
317E ASP 2.6 23.9 + - - +
318E ALA* 3.6 3.4 - - - +
320E LEU* 1.3 72.3 - - - +
322E LYS* 1.3 56.5 + - - +
324E ALA* 3.2 2.1 + - - +
325E VAL* 2.9 56.2 + - + +
338E VAL* 5.5 1.4 - - - +
339E MET* 3.5 21.0 + - - +
385E GLU* 3.9 28.0 + - + -
388E TRP* 3.8 20.4 - + - -
391E ILE* 5.4 2.7 - - + -
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Residues in contact with LYS 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318E ALA* 2.8 33.8 + - - +
319E ARG* 3.9 9.1 - - - +
321E TYR* 1.3 76.6 - - - +
323E ILE* 1.3 57.0 + - - +
325E VAL* 4.0 0.6 - - - +
326E GLY* 2.9 23.4 + - - -
388E TRP* 3.5 20.9 - - + -
390E GLU* 3.5 31.1 + - + +
391E ILE* 3.5 27.7 - - + +
484E GLU* 4.5 4.9 + - - +
485E ASP* 2.7 36.4 + - - +
487E PHE* 3.4 14.9 - - + -
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Residues in contact with ILE 323 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266E VAL* 4.6 14.3 - - + +
274E MET* 5.0 8.7 - - - -
319E ARG* 3.3 17.9 - - + +
320E LEU* 3.2 20.7 + - + +
322E LYS* 1.3 78.1 - - - +
324E ALA* 1.3 57.5 + - - +
327E PHE* 3.0 25.0 + - + +
429E PHE* 3.5 31.1 - - + -
430E ASN 5.3 2.0 - - - +
431E ASN* 4.6 18.4 - - + +
486E PRO* 3.4 29.8 - - + +
487E PHE* 3.9 23.3 - - + -
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Residues in contact with ALA 324 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E LEU* 3.8 17.5 - - + +
266E VAL* 3.9 17.2 - - + +
296E VAL* 4.1 16.2 - - + -
313E LEU* 3.7 28.9 - - + -
320E LEU 3.0 6.5 + - - +
321E TYR 3.8 2.7 - - - +
323E ILE* 1.3 73.8 - - - +
325E VAL* 1.3 65.7 + - - +
327E PHE* 3.3 6.4 + - - +
328E MET* 3.0 22.9 + - - +
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Residues in contact with VAL 325 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296E VAL* 3.5 23.6 - - + -
321E TYR* 2.9 50.2 + - + +
322E LYS 4.0 2.7 - - - +
324E ALA* 1.3 72.6 - - - +
326E GLY* 1.3 61.3 + - - +
328E MET* 3.3 13.8 + - + +
329E LEU* 2.9 47.4 + - + +
338E VAL* 4.3 9.6 - - + -
391E ILE* 3.8 24.5 - - + -
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Residues in contact with GLY 326 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322E LYS 2.9 18.7 + - - -
323E ILE 3.9 0.7 - - - -
325E VAL* 1.3 75.5 - - - +
327E PHE* 1.3 64.0 + - - +
329E LEU* 3.5 0.6 + - - -
330E ALA* 3.0 25.3 + - - +
390E GLU 5.4 1.6 - - - -
394E MET* 3.5 27.6 - - - +
429E PHE* 4.1 5.8 - - - -
487E PHE* 4.4 8.7 - - - -
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Residues in contact with PHE 327 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E LEU* 3.9 22.4 - - + -
266E VAL* 6.1 0.9 - - + -
274E MET* 5.4 6.3 - - + -
277E LEU* 3.9 37.0 - - + -
280E TRP* 3.6 32.1 - + + -
323E ILE 3.0 18.9 + - - +
324E ALA* 3.5 7.6 - - - +
325E VAL 3.2 0.2 - - - -
326E GLY* 1.3 77.0 - - - +
328E MET* 1.3 58.8 - - - +
330E ALA* 3.0 4.3 + - - +
331E HIS* 2.8 49.6 + + + +
409E TRP* 4.9 5.6 - + - -
417E VAL* 5.5 2.5 - - + -
419E PHE* 3.5 29.6 - + - -
429E PHE* 3.5 24.6 - + + -
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Residues in contact with MET 328 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258E TYR* 3.2 35.9 + - + +
262E LEU* 4.5 0.4 - - + -
294E VAL* 4.0 7.6 - - + -
295E PHE* 3.4 37.0 - - - -
296E VAL* 3.9 15.7 - - + +
324E ALA 3.0 10.9 + - - +
325E VAL* 3.5 17.0 - - + +
327E PHE* 1.3 79.6 - - - +
329E LEU* 1.3 77.1 + - + +
331E HIS* 3.1 12.0 + - - +
333E TYR 5.0 0.7 - - - +
336E THR* 3.4 16.1 - - + +
337E ARG 4.0 16.4 - - - +
338E VAL* 4.4 4.9 - - + -
398E ARG* 3.1 16.1 + - - -
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Residues in contact with LEU 329 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E SER* 3.9 8.7 - - - +
325E VAL* 2.9 33.4 + - + +
326E GLY 3.8 1.3 - - - +
328E MET* 1.3 88.1 - - + +
330E ALA* 1.3 59.9 + - - +
336E THR* 3.8 30.3 - - + +
338E VAL* 4.4 7.9 - - + -
391E ILE* 3.9 9.0 - - - +
394E MET* 3.3 46.9 - - + +
395E VAL* 3.8 15.5 - - + +
397E PHE* 4.3 0.5 - - - -
398E ARG* 2.7 37.1 + - + +
401E VAL* 5.4 0.2 - - - +
421E ARG* 5.1 0.2 + - - -
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Residues in contact with ALA 330 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326E GLY 3.0 17.7 + - - +
327E PHE* 3.6 4.0 - - - +
329E LEU* 1.3 78.5 - - - +
331E HIS* 1.3 60.4 + - - +
394E MET* 3.7 13.2 - - + -
397E PHE* 3.8 18.0 - - + -
419E PHE* 3.7 17.3 - - + -
421E ARG* 2.9 33.3 + - - +
427E ILE* 4.0 15.5 - - + -
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Residues in contact with HIS 331 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258E TYR* 4.7 1.3 - - - +
277E LEU 5.2 0.7 - - - -
278E LYS 5.4 0.8 + - - -
280E TRP* 3.5 52.4 + + + +
327E PHE* 2.8 32.8 + + + +
328E MET* 3.1 8.7 + - - +
330E ALA* 1.3 77.1 - - - +
332E PRO* 1.3 79.7 - - + +
333E TYR* 2.9 41.4 + - + +
398E ARG* 2.8 27.7 + - - -
406E PHE* 4.2 22.3 - + - -
419E PHE* 3.7 8.0 - + + -
421E ARG* 3.8 0.7 - - - -
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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