Contacts of the helix formed by residues 388 - 401 (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 TRP 388 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315E PHE* 4.0 21.5 - - + -
318E ALA* 3.7 26.2 - - + -
321E TYR* 3.8 15.9 - + - -
322E LYS* 3.5 37.2 - - + -
377E THR* 5.8 8.7 - - + -
383E VAL* 3.8 34.1 + - + +
384E CYS 3.5 11.9 - - - -
385E GLU* 2.9 21.0 + - + +
387E ARG* 1.3 74.1 - - - +
389E ARG* 1.3 54.5 + - - +
390E GLU* 3.9 9.6 - - - +
391E ILE* 3.1 14.7 + - + -
392E ARG* 2.6 36.2 + - - +
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Residues in contact with ARG 389 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387E ARG 3.2 2.2 + - - -
388E TRP* 1.3 71.4 - - - +
390E GLU* 1.3 70.4 + - - +
392E ARG* 3.6 26.2 - - - +
393E ASN* 2.8 49.0 + - - +
452E VAL 3.9 1.3 - - - +
453E ILE 2.9 22.6 + - - -
454E SER* 3.5 17.4 + - - +
455E GLY* 3.4 34.5 - - - +
456E ASP* 3.8 6.0 + - - +
484E GLU* 5.9 0.4 + - - -
485E ASP* 5.1 1.2 + - - -
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Residues in contact with GLU 390 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322E LYS* 3.5 30.4 + - + +
326E GLY* 5.4 1.4 - - - -
388E TRP* 3.9 6.4 - - - +
389E ARG* 1.3 96.4 + - - +
391E ILE* 1.3 69.0 + - + +
394E MET* 3.2 28.6 + - - +
453E ILE* 3.7 40.2 - - + +
485E ASP* 2.8 32.5 - - - +
487E PHE* 4.6 6.5 - - + -
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Residues in contact with ILE 391 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E PHE* 5.8 0.2 - - + -
321E TYR* 5.4 2.7 - - + -
322E LYS* 3.5 40.4 - - + +
325E VAL* 3.8 23.6 - - + -
326E GLY 6.0 0.2 - - - +
329E LEU* 3.9 2.1 - - + +
338E VAL* 4.2 33.0 - - + -
385E GLU* 3.6 26.2 - - + +
386E HIS* 4.2 5.4 - - - +
388E TRP* 3.1 18.4 + - + +
390E GLU* 1.3 81.4 - - + +
392E ARG* 1.3 67.9 + - - +
393E ASN 3.3 0.2 - - - -
394E MET* 3.3 5.3 + - - +
395E VAL* 3.2 25.7 + - + +
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Residues in contact with ARG 392 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E TYR* 2.7 34.0 + - + +
35E LYS* 3.7 34.1 - - + +
37E PHE* 4.6 3.4 - - + -
376E THR* 5.0 9.5 + - - +
386E HIS 3.9 5.8 - - - +
387E ARG 3.9 7.4 + - - +
388E TRP 2.6 21.9 + - - +
389E ARG* 3.6 27.8 - - - +
391E ILE* 1.3 74.8 - - - +
393E ASN* 1.3 79.4 + - - +
395E VAL* 2.7 30.4 - - - +
396E TRP* 3.6 4.5 + - - +
456E ASP* 2.5 37.0 + - - -
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Residues in contact with ASN 393 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389E ARG* 2.8 23.6 + - - +
390E GLU 5.1 0.7 - - - +
392E ARG* 1.3 98.4 + - - +
394E MET* 1.3 61.9 + - - +
395E VAL 3.4 0.2 - - - -
396E TRP* 3.6 10.4 - - + +
397E PHE* 3.1 21.7 + - - +
452E VAL* 2.9 48.8 + - + +
453E ILE* 5.8 0.2 - - + -
455E GLY 3.3 8.5 + - - -
456E ASP* 2.7 23.6 + - - +
491E HIS* 4.4 3.2 + - - +
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Residues in contact with MET 394 (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* 3.5 33.7 - - - +
329E LEU* 3.3 28.4 - - + +
330E ALA* 3.7 18.8 - - + +
390E GLU 3.2 20.4 + - - +
391E ILE 3.3 0.6 + - - -
392E ARG 3.3 1.0 - - - -
393E ASN* 1.3 77.1 - - - +
395E VAL* 1.3 61.8 + - - +
396E TRP 3.1 1.6 - - - -
397E PHE* 3.0 32.9 - - + +
398E ARG* 2.8 28.4 + - - +
427E ILE* 4.6 6.5 - - + -
452E VAL* 4.5 1.3 - - - -
453E ILE* 3.9 12.3 - - + -
487E PHE* 5.0 0.4 - - - -
489E ALA* 3.8 25.1 - - - -
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Residues in contact with VAL 395 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E THR* 4.1 0.2 + - - -
12E SER* 4.5 19.9 - - - -
35E LYS 4.2 7.9 - - - +
36E GLY 5.8 0.9 - - - +
37E PHE* 3.9 44.2 - - + +
329E LEU* 4.1 17.3 - - + -
338E VAL* 4.6 11.0 - - + -
391E ILE* 3.2 13.4 + - + +
392E ARG 2.7 28.7 - - - +
394E MET* 1.3 75.7 - - - +
396E TRP* 1.3 69.4 + - - +
398E ARG* 3.0 15.9 + - - +
399E ASN* 3.0 19.1 + - - +
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Residues in contact with TRP 396 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E PRO 3.3 26.5 - - - -
35E LYS* 3.2 31.4 - - + -
36E GLY* 3.8 6.3 - - - -
392E ARG 4.0 8.1 - - - +
393E ASN* 3.6 13.9 - - + +
395E VAL* 1.3 83.5 - - + +
397E PHE* 1.3 56.3 + - - +
399E ASN* 3.0 15.0 + - + +
400E VAL* 2.8 36.8 + - + +
491E HIS* 3.5 27.3 - + - -
493E GLU* 2.8 36.3 + - - +
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Residues in contact with PHE 397 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329E LEU 4.3 0.2 - - - -
330E ALA* 3.8 30.1 - - + -
393E ASN 3.1 17.0 + - - +
394E MET* 3.0 38.6 + - + +
396E TRP* 1.3 77.2 - - - +
398E ARG* 1.3 63.5 + - - +
400E VAL* 3.0 4.3 + - - +
401E VAL* 2.9 47.8 + - + +
419E PHE* 5.9 0.9 - + - -
420E GLY* 6.0 0.2 - - - -
421E ARG* 4.2 7.0 - - + -
425E GLY* 3.9 16.2 - - - -
426E PHE* 3.8 14.4 - - - -
427E ILE* 4.6 2.0 - - + -
452E VAL* 5.3 0.2 - - + -
489E ALA* 4.6 6.7 - - + -
490E ILE 3.6 22.4 - - - -
491E HIS* 3.9 28.3 - + + -
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Residues in contact with ARG 398 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E THR* 3.1 35.9 + - + +
12E SER* 3.8 3.1 - - - +
328E MET 3.1 8.5 + - - -
329E LEU* 2.7 43.7 + - + +
330E ALA 4.2 0.2 - - - -
331E HIS 2.8 27.9 + - - -
332E PRO* 3.5 11.5 + - - +
333E TYR 3.5 4.6 + - - -
334E GLY 2.9 27.1 + - - -
335E PHE* 5.3 0.6 - - - +
336E THR* 3.1 32.0 + - - +
394E MET 2.8 13.9 + - - +
395E VAL* 3.3 10.5 - - - +
397E PHE* 1.3 73.1 - - - +
399E ASN* 1.3 61.4 + - - +
401E VAL* 3.5 7.1 + - - +
402E ASP* 3.1 22.1 + - - +
421E ARG* 4.3 10.5 - - - +
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Residues in contact with ASN 399 (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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9E GLY* 2.9 22.7 + - - +
10E ARG* 3.5 1.8 - - - +
11E THR* 2.6 49.9 + - - +
12E SER* 4.5 1.2 - - - +
36E GLY* 2.9 32.3 + - - +
395E VAL* 3.0 12.5 + - - +
396E TRP* 3.0 18.4 + - + +
398E ARG* 1.3 76.6 - - - +
400E VAL* 1.3 63.3 + - + +
402E ASP* 3.3 17.7 + - - +
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Residues in contact with VAL 400 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396E TRP* 2.8 45.3 + - + +
397E PHE 3.0 6.9 + - - +
399E ASN* 1.3 77.6 - - + +
401E VAL* 1.3 55.3 + - - +
402E ASP 3.3 1.6 + - - +
424E ARG* 2.7 70.4 + - - +
491E HIS* 3.7 24.2 - - + +
492E ALA* 3.8 7.0 - - + -
493E GLU* 4.1 12.3 - - + +
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Residues in contact with VAL 401 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330E ALA 4.8 0.7 - - - +
397E PHE* 2.9 41.9 + - + +
398E ARG* 3.7 9.4 - - + +
400E VAL* 1.3 78.0 - - + +
402E ASP* 1.3 67.7 + - - +
404E GLN* 2.8 24.8 + - - +
421E ARG* 3.0 57.5 + - + +
424E ARG* 3.8 3.8 - - - +
425E GLY* 3.7 22.4 - - - +
491E HIS* 4.9 0.2 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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