Contacts of the helix formed by residues 391 - 407 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A LYS 4.9 1.0 + - - -
364A GLY 3.0 26.5 + - - -
365A TYR* 3.9 11.9 - - - +
388A ASP* 3.1 16.4 + - + +
389A PHE 3.1 0.6 - - - -
390A THR* 1.3 79.6 + - - +
392A PRO* 1.3 70.7 - - - +
393A ASP* 3.1 20.4 + - - +
394A ALA* 2.8 24.2 + - + +
395A CYS* 3.0 13.6 + - - -
428A PHE* 3.5 39.7 - - + +
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Residues in contact with PRO 392 (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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390A THR 3.2 11.6 - - - +
391A ASN* 1.3 85.4 - - - +
393A ASP* 1.3 66.8 + - - +
395A CYS* 3.1 11.7 + - + +
396A LYS* 3.1 22.0 + - - +
428A PHE* 3.8 17.0 - - + -
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Residues in contact with ASP 393 (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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365A TYR* 3.3 34.0 + - + +
391A ASN* 3.1 8.6 + - - +
392A PRO* 1.3 80.1 - - - +
394A ALA* 1.3 62.0 + - - +
396A LYS* 3.5 12.2 + - - +
397A TRP* 3.1 22.9 + - - +
428A PHE* 6.1 0.5 - - - -
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Residues in contact with ALA 394 (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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365A TYR* 3.7 40.1 - - + +
387A TYR* 5.2 5.3 - - + -
388A ASP 3.3 26.9 - - - +
389A PHE* 4.8 3.6 - - + -
391A ASN* 2.8 12.5 + - + +
393A ASP* 1.3 75.8 - - - +
395A CYS* 1.3 66.1 + - - +
397A TRP* 3.3 3.3 + - - +
398A TYR* 3.0 25.3 + - - +
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Residues in contact with CYS 395 (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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389A PHE* 3.1 41.9 - - - -
391A ASN 3.0 12.1 + - - -
392A PRO* 3.1 11.6 + - + +
394A ALA* 1.3 78.5 - - - +
396A LYS* 1.3 57.0 + - - +
398A TYR* 3.6 2.0 - - - +
399A ALA* 2.9 32.1 + - - +
443A ILE* 5.6 2.0 - - - -
447A LEU* 3.9 26.4 - - + +
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Residues in contact with LYS 396 (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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392A PRO 3.1 11.3 + - - +
393A ASP* 3.9 12.6 - - - +
394A ALA 3.3 0.2 - - - -
395A CYS* 1.3 79.4 - - - +
397A TRP* 1.3 59.1 + - - +
399A ALA* 3.4 5.0 + - - +
400A ASP* 2.8 69.8 + - - +
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Residues in contact with TRP 397 (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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317A ASP 4.9 1.3 - - - -
318A PHE* 4.3 9.4 - + - -
356A VAL* 3.4 35.0 - - + -
359A GLU* 3.5 28.2 + - - -
360A LEU* 3.6 16.1 - - + +
363A LYS* 4.5 6.5 - - - -
365A TYR* 3.8 23.1 - + + -
387A TYR* 3.5 34.5 - + - -
393A ASP 3.1 19.0 + - - +
394A ALA 3.6 4.3 - - - +
395A CYS 3.3 0.2 - - - -
396A LYS* 1.3 78.5 - - - +
398A TYR* 1.3 69.2 + - - +
400A ASP* 3.4 7.3 + - - +
401A LYS* 3.3 58.2 + - + +
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Residues in contact with TYR 398 (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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318A PHE* 3.3 32.1 - + - -
346A ILE* 4.0 5.2 - - - +
347A ASN 2.7 30.8 + - - -
387A TYR* 3.7 40.4 - + + -
389A PHE* 3.7 25.1 - + + -
394A ALA 3.0 16.5 + - - +
395A CYS 3.6 3.6 - - - +
397A TRP* 1.3 86.8 - - + +
399A ALA* 1.3 62.2 + - - +
401A LYS* 3.1 15.6 + - - +
402A LEU* 3.2 32.2 + - + +
444A TYR* 3.7 9.5 - + - -
447A LEU* 3.8 20.6 - - + -
448A VAL* 4.4 8.7 - - + -
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Residues in contact with ALA 399 (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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395A CYS 2.9 18.2 + - - +
396A LYS* 3.7 7.0 - - - +
398A TYR* 1.3 77.7 - - - +
400A ASP* 1.3 58.8 + - - +
402A LEU* 3.1 6.1 + - - +
403A LYS* 2.9 40.0 + - - +
447A LEU* 4.2 10.8 - - + -
451A VAL* 3.6 25.0 - - + +
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Residues in contact with ASP 400 (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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396A LYS* 2.8 60.1 + - - +
397A TRP* 3.7 8.0 - - - +
398A TYR 3.3 0.2 - - - -
399A ALA* 1.3 74.7 - - - +
401A LYS* 1.3 62.3 + - + +
403A LYS* 3.4 25.1 + - - +
404A GLY* 3.1 17.7 + - - -
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Residues in contact with LYS 401 (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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317A ASP 4.1 13.9 - - - -
318A PHE* 3.5 38.2 - - + +
319A GLU* 4.1 13.5 - - - +
356A VAL* 5.0 6.3 - - - +
359A GLU* 5.4 1.4 + - - -
397A TRP* 3.3 47.0 + - + +
398A TYR 3.1 10.4 + - - +
400A ASP* 1.3 77.8 - - + +
402A LEU* 1.3 65.8 + - - +
404A GLY* 2.9 12.8 + - - -
405A LEU* 3.2 15.8 + - - +
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Residues in contact with LEU 402 (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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318A PHE* 3.4 30.5 - - + -
346A ILE* 4.0 11.7 - - + -
398A TYR* 3.2 32.3 + - + +
399A ALA 3.1 7.5 + - - +
401A LYS* 1.3 77.0 - - - +
403A LYS* 1.3 62.4 + - - +
405A LEU* 3.0 8.1 + - + +
406A VAL* 3.0 23.4 + - - +
413A PHE* 3.7 26.2 - - + -
447A LEU* 4.3 0.9 - - + -
448A VAL* 3.9 35.4 - - + -
451A VAL* 4.0 21.1 - - + -
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Residues in contact with LYS 403 (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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399A ALA* 2.9 22.5 + - - +
400A ASP* 3.6 26.8 + - - +
401A LYS 3.2 0.2 - - - -
402A LEU* 1.3 76.0 - - - +
404A GLY* 1.3 57.1 + - - +
406A VAL* 3.8 8.2 - - - +
407A ALA* 3.0 30.5 + - - +
451A VAL* 3.6 28.0 - - + +
454A ASP* 5.1 10.8 + - - +
455A THR* 4.0 19.2 - - + +
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Residues in contact with GLY 404 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400A ASP 3.1 10.0 + - - -
401A LYS* 2.9 10.6 + - - -
403A LYS* 1.3 78.5 - - - +
405A LEU* 1.3 61.6 + - - +
407A ALA* 3.5 7.2 + - - +
408A MET* 3.3 24.8 + - - +
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Residues in contact with LEU 405 (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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309A TRP* 3.8 26.5 - - + -
318A PHE* 3.9 27.4 - - + +
320A TRP* 3.5 36.6 - - + +
344A VAL* 4.1 8.3 - - + -
346A ILE* 4.8 0.7 - - + -
401A LYS 3.2 9.1 + - - +
402A LEU* 3.0 8.0 + - + +
404A GLY* 1.3 75.2 - - - +
406A VAL* 1.3 64.8 + - - +
408A MET* 2.9 24.8 + - + +
410A VAL* 3.0 26.7 + - + +
413A PHE* 3.8 23.1 - - + -
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Residues in contact with VAL 406 (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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402A LEU 3.0 18.7 + - - +
403A LYS* 3.8 10.3 - - - +
404A GLY 3.4 0.2 - - - -
405A LEU* 1.3 72.1 - - - +
407A ALA* 1.3 55.0 + - - +
408A MET 2.8 4.9 - - - -
409A GLY* 2.7 26.2 + - - -
410A VAL* 3.6 17.9 + - - +
413A PHE* 3.9 22.7 - - + -
451A VAL* 4.7 2.7 - - + -
452A LEU* 4.2 9.0 - - + -
455A THR* 3.8 33.7 - - + +
456A VAL* 4.0 16.2 - - + -
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Residues in contact with ALA 407 (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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329A GLU* 3.5 12.5 - - - +
403A LYS 3.0 18.4 + - - +
404A GLY* 3.8 8.1 - - - +
406A VAL* 1.3 77.2 - - - +
408A MET* 1.3 57.8 + - - +
409A GLY 3.3 0.4 - - - -
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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