Contacts of the helix formed by residues 388 - 401 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C PHE* 3.8 30.7 - + + -
318C ALA* 4.1 11.9 - - + -
321C TYR* 4.1 15.7 - + - -
322C LYS* 3.4 39.9 - - + -
377C THR* 5.5 11.5 - - + +
383C VAL* 3.6 36.5 + - + +
384C CYS 3.5 11.2 - - - -
385C GLU* 2.7 21.4 + - + +
387C ARG* 1.3 78.8 - - + +
389C ARG* 1.3 53.7 + - - +
390C GLU* 4.0 8.3 - - - +
391C ILE* 2.6 38.6 + - + -
392C ARG* 2.7 17.1 + - - -
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Residues in contact with ARG 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C ARG 3.3 4.9 + - - -
388C TRP* 1.3 69.9 - - - +
390C GLU* 1.3 81.9 + - - +
392C ARG* 3.4 26.6 - - - +
393C ASN* 3.0 42.1 + - - +
452C VAL 4.0 1.1 - - - +
453C ILE 3.0 22.3 + - - -
454C SER* 3.5 18.1 + - - +
455C GLY* 3.6 30.0 - - - +
456C ASP* 3.8 7.8 + - - +
484C GLU* 5.9 1.6 + - - +
485C ASP* 4.8 1.8 + - - -
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Residues in contact with GLU 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322C LYS* 3.7 36.3 + - + +
326C GLY* 5.6 0.9 - - - -
388C TRP* 3.9 5.5 - - - +
389C ARG* 1.3 96.5 + - - +
391C ILE* 1.3 59.9 + - - +
393C ASN* 5.1 0.2 - - - -
394C MET* 3.3 28.9 - - - +
452C VAL 4.7 0.2 - - - -
453C ILE* 3.3 46.5 - - + +
485C ASP* 2.8 28.1 - - - +
487C PHE* 4.5 8.2 - - + -
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Residues in contact with ILE 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C PHE* 5.7 0.4 - - + -
321C TYR* 4.9 6.7 - - + -
322C LYS* 4.3 18.4 - - + +
325C VAL* 3.6 35.2 - - + -
329C LEU* 5.1 0.6 - - + +
338C VAL* 4.1 27.1 - - + -
385C GLU* 3.3 26.7 - - + +
386C HIS* 4.1 5.6 - - - -
388C TRP* 2.6 33.0 + - + +
390C GLU* 1.3 74.6 - - - +
392C ARG* 1.3 67.8 + - - +
393C ASN 3.2 0.2 - - - -
394C MET* 3.1 13.9 + - - +
395C VAL* 3.1 21.0 + - + +
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Residues in contact with ARG 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C TYR* 3.0 32.4 + - + +
35C LYS* 3.8 41.4 - - + +
37C PHE* 4.6 1.1 - - + -
376C THR* 5.1 6.7 + - - -
386C HIS 4.0 7.1 + - - +
387C ARG 4.4 6.3 + - - -
388C TRP 2.7 16.5 + - - +
389C ARG* 3.4 30.7 - - - +
391C ILE* 1.3 72.2 - - - +
393C ASN* 1.3 91.2 + - - +
395C VAL* 2.6 31.3 - - - +
396C TRP* 3.3 5.7 + - - +
456C ASP* 3.2 18.6 + - - -
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Residues in contact with ASN 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C ARG* 3.0 17.2 + - - +
390C GLU 5.1 0.7 - - - +
392C ARG* 1.3 104.8 + - - +
394C MET* 1.3 57.7 + - + +
396C TRP* 3.2 9.7 + - - +
397C PHE* 2.8 25.7 + - - +
452C VAL* 2.6 52.5 + - + +
455C GLY 3.3 8.9 + - - -
456C ASP* 2.9 22.8 + - - +
491C HIS* 4.7 2.1 + - - +
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Residues in contact with MET 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326C GLY* 3.3 35.4 - - - +
329C LEU* 3.6 28.4 - - + +
330C ALA* 3.8 24.5 - - + +
390C GLU 3.3 20.8 + - - +
391C ILE* 3.1 6.4 + - - +
393C ASN* 1.3 76.2 - - - +
395C VAL* 1.3 59.8 + - - +
397C PHE* 3.2 24.9 - - + +
398C ARG 2.9 21.3 + - - -
427C ILE* 4.6 5.4 - - + -
452C VAL* 4.9 0.9 - - - -
453C ILE* 3.6 15.9 - - + -
487C PHE* 4.8 0.7 - - + -
489C ALA* 3.8 27.8 - - - -
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Residues in contact with VAL 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C SER* 4.4 13.6 + - - +
35C LYS 4.4 5.4 - - - +
36C GLY 5.8 1.3 - - - +
37C PHE* 3.7 40.8 - - + -
329C LEU* 4.2 15.3 - - + -
338C VAL* 4.1 26.2 - - + -
391C ILE* 3.1 12.6 + - + +
392C ARG 2.6 28.9 - - - +
394C MET* 1.3 75.9 - - - +
396C TRP* 1.3 63.1 + - - +
398C ARG* 3.3 7.1 + - - +
399C ASN* 3.2 26.9 + - - -
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Residues in contact with TRP 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C PRO 3.7 12.1 - - - -
35C LYS* 3.2 42.8 - - + -
36C GLY* 3.6 9.9 - - - -
392C ARG 3.9 7.4 - - - +
393C ASN* 3.2 13.6 + - - +
394C MET 3.2 0.4 - - - -
395C VAL* 1.3 81.7 - - - +
397C PHE* 1.3 64.5 + - - +
399C ASN* 3.0 16.7 + - + +
400C VAL* 2.9 31.6 + - + +
491C HIS* 4.1 14.1 - + - -
493C GLU* 2.8 31.5 + - - +
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Residues in contact with PHE 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C LEU 4.3 3.1 - - - -
330C ALA* 4.0 20.6 - - + -
393C ASN 2.8 14.9 + - - +
394C MET* 3.2 34.3 - - + +
396C TRP* 1.3 76.4 - - - +
398C ARG* 1.3 66.4 + - - +
400C VAL* 3.1 4.4 + - - +
401C VAL* 2.9 47.2 + - + +
419C PHE* 6.3 0.4 - + - -
420C GLY* 6.1 0.4 - - - -
421C ARG* 4.7 4.9 - - + -
425C GLY* 4.1 4.7 - - - -
426C PHE* 3.9 23.6 - - - -
427C ILE* 4.6 7.9 - - + -
452C VAL* 5.3 0.2 - - + -
489C ALA* 4.3 10.5 - - + -
490C ILE 3.5 22.4 - - - -
491C HIS* 3.5 32.3 - + + -
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Residues in contact with ARG 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C THR* 3.2 30.6 + - + +
12C SER* 3.7 4.9 - - - +
328C MET 3.4 0.4 + - - -
329C LEU* 2.8 45.9 + - - +
331C HIS 2.7 29.5 + - - -
332C PRO* 3.9 7.3 + - - +
333C TYR 3.9 2.6 + - - -
334C GLY 3.0 27.9 + - - -
335C PHE* 4.9 0.6 - - - +
336C THR* 3.2 39.0 + - - +
394C MET 2.9 11.1 + - - +
395C VAL* 3.5 9.9 - - - +
396C TRP 3.2 0.2 - - - -
397C PHE* 1.3 76.7 - - - +
399C ASN* 1.3 62.3 + - - +
401C VAL* 3.6 9.0 - - - +
402C ASP* 3.2 21.3 + - - +
421C ARG* 3.6 13.6 + - - +
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Residues in contact with ASN 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C GLY* 2.8 21.9 + - - +
10C ARG* 3.5 1.6 - - - +
11C THR* 2.7 40.5 + - - +
12C SER* 4.7 0.8 - - - +
36C GLY* 2.9 32.8 + - - +
395C VAL 3.2 12.3 + - - +
396C TRP* 3.0 20.4 + - + +
398C ARG* 1.3 75.1 - - - +
400C VAL* 1.3 61.1 + - + +
402C ASP* 3.0 25.4 - - - +
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Residues in contact with VAL 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C TRP* 2.9 41.4 + - + +
397C PHE* 3.5 8.5 - - - +
399C ASN* 1.3 79.3 - - + +
401C VAL* 1.3 58.5 + - - +
402C ASP 3.2 2.0 + - - +
424C ARG* 2.8 54.6 + - - +
491C HIS* 3.9 30.5 - - + +
492C ALA* 4.1 5.2 - - + +
493C GLU* 3.7 20.6 - - + +
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Residues in contact with VAL 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397C PHE* 2.9 44.2 + - + +
398C ARG* 3.6 6.1 - - - +
400C VAL* 1.3 77.5 - - + +
402C ASP* 1.3 65.4 + - - +
403C GLY 3.1 0.5 + - - -
404C GLN* 2.8 26.2 + - - +
421C ARG* 3.2 46.6 + - + +
424C ARG* 3.7 9.4 - - - +
425C GLY* 3.7 33.2 - - - +
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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
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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