Contacts of the helix formed by residues 391 - 408 (chain C) in PDB entry 1XSK
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 ASN 391 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363C LYS 5.2 0.6 + - - -
364C GLY 3.2 27.7 + - - -
365C TYR* 4.2 4.4 - - - -
388C ASP* 3.0 18.9 + - + +
390C THR* 1.3 79.7 + - - +
392C PRO* 1.3 66.9 - - - +
393C ASP* 3.0 22.5 + - - +
394C ALA* 3.3 12.2 + - + -
395C CYS* 3.2 24.1 + - - -
428C PHE* 3.3 40.7 - - + +
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Residues in contact with PRO 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C THR 3.4 9.9 - - - +
391C ASN* 1.3 86.6 - - - +
393C ASP* 1.3 66.8 + - - +
395C CYS* 3.2 10.3 + - + +
396C LYS* 3.2 20.4 + - - +
428C PHE* 3.5 21.8 - - + -
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Residues in contact with ASP 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C TYR* 3.6 27.8 + - + +
391C ASN* 3.0 10.7 + - - +
392C PRO* 1.3 81.4 - - - +
394C ALA* 1.3 58.0 + - - +
396C LYS* 3.4 14.1 + - + +
397C TRP* 3.1 26.7 + - - +
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Residues in contact with ALA 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C TYR* 3.4 43.2 - - + +
387C TYR* 5.1 5.5 - - + -
388C ASP 3.5 24.0 - - - +
389C PHE* 4.8 3.9 - - + -
391C ASN* 3.3 12.4 + - + +
392C PRO 3.3 0.6 - - - -
393C ASP* 1.3 76.7 - - - +
395C CYS* 1.3 63.9 + - - +
397C TRP* 3.9 2.8 - - - +
398C TYR* 3.2 23.4 + - - +
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Residues in contact with CYS 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C PHE* 3.0 37.0 - - - -
391C ASN 3.2 13.1 + - - -
392C PRO* 3.4 11.9 - - + +
393C ASP 3.2 0.4 - - - -
394C ALA* 1.3 76.2 - - - +
396C LYS* 1.3 59.5 + - - +
398C TYR* 3.4 2.3 + - - +
399C ALA* 2.8 31.6 + - - +
443C ILE* 5.5 2.7 - - - -
447C LEU* 3.8 29.8 - - + +
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Residues in contact with LYS 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C PRO 3.2 8.7 + - - +
393C ASP* 3.6 17.5 - - + +
395C CYS* 1.3 79.9 - - - +
397C TRP* 1.3 54.1 + - - +
399C ALA* 3.1 6.7 + - - +
400C ASP* 2.6 70.9 + - - +
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Residues in contact with TRP 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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317C ASP* 5.0 1.6 - - - -
318C PHE* 4.4 9.0 - + - -
356C VAL* 3.2 36.6 - - + -
359C GLU* 2.9 28.0 + - - -
360C LEU* 3.7 15.6 - - + +
363C LYS* 4.6 5.8 - - - -
365C TYR* 3.8 23.3 - + + -
387C TYR* 3.3 34.5 - + - -
393C ASP 3.1 13.3 + - - +
394C ALA 3.9 4.0 - - - +
396C LYS* 1.3 78.0 - - - +
398C TYR* 1.3 70.3 + - - +
400C ASP* 3.2 8.9 + - - +
401C LYS* 3.1 61.1 + - + +
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Residues in contact with TYR 398 (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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318C PHE* 3.3 31.2 - + - -
346C ILE* 3.9 9.5 - - - +
347C ASN 2.9 31.7 + - - -
387C TYR* 3.9 32.8 - + + -
389C PHE* 4.0 26.7 - + + -
394C ALA 3.2 15.8 + - - +
395C CYS 3.8 2.7 - - - +
397C TRP* 1.3 88.3 - - + +
399C ALA* 1.3 61.6 + - - +
401C LYS* 3.3 6.4 + - - +
402C LEU* 3.2 42.7 + - + +
444C TYR* 3.7 11.3 - + - -
447C LEU* 3.9 11.7 - - + -
448C VAL* 4.4 10.5 - - + -
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Residues in contact with ALA 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C CYS 2.8 19.8 + - - +
396C LYS* 3.5 8.1 - - - +
398C TYR* 1.3 77.4 - - - +
400C ASP* 1.3 61.8 + - - +
402C LEU* 3.2 5.0 + - - +
403C LYS* 2.9 36.8 + - - +
447C LEU* 4.2 10.5 - - + -
451C VAL* 3.8 23.7 - - + +
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Residues in contact with ASP 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C LYS* 2.6 58.9 + - - +
397C TRP* 3.2 7.5 + - - +
399C ALA* 1.3 74.0 - - - +
401C LYS* 1.3 64.0 + - - +
403C LYS* 3.3 24.8 + - - +
404C GLY* 3.0 17.8 + - - -
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Residues in contact with LYS 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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317C ASP 4.1 11.4 - - - -
318C PHE* 3.6 39.7 - - + +
319C GLU* 5.7 3.4 - - - -
356C VAL* 5.2 4.7 - - - +
359C GLU* 5.4 1.4 + - - -
397C TRP* 3.1 59.4 + - + +
398C TYR 3.3 8.7 + - - +
400C ASP* 1.3 76.3 - - + +
402C LEU* 1.3 57.8 + - - +
404C GLY* 3.1 15.5 + - - -
405C LEU* 3.1 18.1 + - - +
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Residues in contact with LEU 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C PHE* 3.6 26.5 - - + -
346C ILE* 4.0 8.7 - - + -
398C TYR* 3.2 36.2 + - + +
399C ALA 3.6 6.3 - - - +
400C ASP 3.2 0.2 - - - -
401C LYS* 1.3 76.2 - - - +
403C LYS* 1.3 64.3 + - - +
404C GLY 3.0 1.6 - - - -
405C LEU* 3.2 6.5 + - + +
406C VAL* 3.1 26.0 + - - +
413C PHE* 3.6 31.5 - - + -
447C LEU* 4.3 0.9 - - + -
448C VAL* 4.0 30.7 - - + -
451C VAL* 3.9 20.0 - - + -
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Residues in contact with LYS 403 (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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399C ALA* 2.9 19.4 + - - +
400C ASP* 3.6 27.5 + - - +
401C LYS 3.3 0.2 - - - -
402C LEU* 1.3 76.5 - - - +
404C GLY* 1.3 56.5 + - - +
406C VAL* 3.9 6.0 - - - +
407C ALA* 3.0 28.6 + - - +
451C VAL* 3.8 24.0 - - + +
454C ASP* 5.0 16.3 + - - +
455C THR* 4.1 19.2 - - + +
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Residues in contact with GLY 404 (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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400C ASP 3.0 13.3 + - - -
401C LYS* 3.1 5.6 + - - -
402C LEU 3.0 0.4 - - - -
403C LYS* 1.3 77.5 - - - +
405C LEU* 1.3 61.6 + - - +
407C ALA* 3.2 9.1 + - - +
408C MET* 3.1 26.9 + - - +
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Residues in contact with LEU 405 (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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309C TRP* 3.9 23.8 - - + -
318C PHE* 3.8 35.7 - - + +
320C TRP* 3.7 29.8 - - + +
344C VAL* 4.3 4.9 - - + -
346C ILE* 4.9 0.4 - - + -
401C LYS 3.1 10.7 + - - +
402C LEU* 3.2 10.1 + - + +
404C GLY* 1.3 77.7 - - - +
406C VAL* 1.3 60.8 + - - +
408C MET* 3.2 21.1 - - + +
410C VAL* 3.1 30.6 + - + +
413C PHE* 4.0 24.7 - - + -
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Residues in contact with VAL 406 (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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402C LEU 3.1 16.5 + - - +
403C LYS* 3.9 5.8 - - - +
405C LEU* 1.3 71.4 - - - +
407C ALA* 1.3 56.6 + - - +
408C MET 2.8 5.2 - - - -
409C GLY* 2.7 25.3 + - - -
410C VAL 3.6 16.7 + - - +
413C PHE* 3.8 22.4 - - + -
451C VAL* 4.7 2.7 - - + -
452C LEU* 4.3 7.0 - - + -
455C THR* 3.9 35.2 - - + +
456C VAL* 3.9 17.3 - - + -
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Residues in contact with ALA 407 (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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403C LYS 3.0 19.2 + - - +
404C GLY* 3.2 9.2 + - - +
406C VAL* 1.3 77.0 - - - +
408C MET* 1.3 58.0 + - - +
409C GLY 3.3 1.0 + - - -
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Residues in contact with MET 408 (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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320C TRP* 3.2 37.9 - - + +
328C PRO* 4.1 6.1 - - + -
329C GLU* 3.6 47.7 - - + +
332C ILE* 3.3 28.5 - - + +
333C ARG* 6.0 1.0 - - - +
404C GLY 3.1 13.3 + - - +
405C LEU* 3.2 23.1 - - + +
406C VAL 2.8 0.4 - - - -
407C ALA* 1.3 78.7 - - - +
409C GLY* 1.3 55.6 + - - +
410C VAL* 3.6 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
------------------------------------------------------------
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