Contacts of the helix formed by residues 355 - 364 (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 PRO 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311A LYS* 6.2 0.7 - - - -
314A GLN* 3.7 19.7 - - - +
317A ASP* 4.2 1.6 - - - +
353A LYS 3.8 5.8 - - - +
354A SER* 1.3 90.5 - - - +
356A VAL* 1.3 60.7 + - + +
357A PHE 3.3 0.6 + - - -
358A LYS* 4.1 10.7 + - - +
359A GLU* 4.3 6.1 + - - +
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Residues in contact with VAL 356 (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* 4.2 17.0 - - + +
319A GLU* 5.5 5.8 - - + -
350A ILE* 3.8 7.2 - - + -
354A SER* 3.0 12.2 + - - +
355A PRO* 1.3 80.4 - - + +
357A PHE* 1.3 66.0 + - - +
358A LYS 3.4 0.2 - - - -
359A GLU* 3.1 20.3 + - - +
360A LEU* 3.0 30.9 + - + +
397A TRP* 3.4 36.8 - - + -
401A LYS* 5.0 6.1 - - - +
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Residues in contact with PHE 357 (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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350A ILE* 3.6 24.7 - - + +
351A GLY 3.5 9.9 - - - +
352A GLN* 3.4 35.0 - - + +
354A SER* 3.2 18.0 + - - +
356A VAL* 1.3 77.7 - - - +
358A LYS* 1.3 65.6 + - - +
360A LEU* 3.0 7.1 + - - +
361A GLN* 2.8 36.5 + - - +
366A LEU* 4.0 4.4 - - + +
374A LEU* 3.7 29.2 - - + -
376A GLN* 3.5 23.3 - - - -
383A GLY 3.7 7.6 - - - -
385A ALA* 3.6 24.2 - - + -
73B GLN* 4.3 11.4 - - + +
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Residues in contact with LYS 358 (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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354A SER 4.5 0.4 + - - -
355A PRO 4.1 8.8 + - - +
356A VAL 3.4 0.6 - - - -
357A PHE* 1.3 79.4 - - - +
359A GLU* 1.3 58.2 + - - +
361A GLN* 3.2 15.0 + - - +
362A GLU* 2.8 61.9 + - + +
73B GLN* 5.6 4.5 + - - +
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Residues in contact with GLU 359 (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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355A PRO 4.3 3.0 + - - +
356A VAL* 3.1 30.7 + - - +
358A LYS* 1.3 80.2 - - - +
360A LEU* 1.3 62.9 + - + +
362A GLU* 3.4 10.9 + - - +
363A LYS* 3.1 59.0 + - + +
397A TRP* 3.5 24.3 + - - +
401A LYS* 5.4 1.4 + - - -
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Residues in contact with LEU 360 (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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350A ILE* 3.5 33.9 - - + -
356A VAL* 3.0 20.6 + - + +
357A PHE* 3.5 6.3 - - - +
359A GLU* 1.3 74.7 - - + +
361A GLN* 1.3 65.1 + - - +
363A LYS* 3.3 2.6 + - - -
364A GLY 3.0 17.2 + - - -
365A TYR* 3.0 33.9 + - + -
366A LEU* 3.9 24.1 + - + -
387A TYR* 3.6 21.3 - - + -
397A TRP* 3.6 39.5 - - + +
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Residues in contact with GLN 361 (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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357A PHE* 2.8 23.5 + - + +
358A LYS* 3.5 15.4 - - - +
360A LEU* 1.3 77.6 - - - +
362A GLU* 1.3 65.8 + - + +
364A GLY* 3.0 15.6 + - - +
366A LEU* 4.1 8.4 - - + +
368A LYS* 5.8 0.7 - - - -
374A LEU* 3.8 29.3 - - + +
73B GLN* 3.1 33.0 + - - +
74B GLY* 3.5 16.8 + - - -
75B ALA 4.8 2.6 + - - -
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Residues in contact with GLU 362 (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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358A LYS* 2.8 58.6 + - + +
359A GLU* 3.7 9.7 + - - +
361A GLN* 1.3 75.8 - - + +
363A LYS* 1.3 61.0 + - + +
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Residues in contact with LYS 363 (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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359A GLU* 3.1 46.7 + - + +
360A LEU 3.9 2.7 - - - +
362A GLU* 1.3 79.6 - - + +
364A GLY* 1.3 62.5 + - - +
365A TYR* 3.4 49.7 + - + +
391A ASN* 4.9 0.9 + - - -
397A TRP* 4.5 10.1 - - + -
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Residues in contact with GLY 364 (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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360A LEU 3.0 0.6 + - - -
361A GLN* 3.0 16.1 + - - -
362A GLU 3.4 0.8 + - - -
363A LYS* 1.3 79.2 - - - +
365A TYR* 1.3 62.6 + - - +
366A LEU 3.3 5.8 + - - +
368A LYS* 3.8 30.9 + - - -
374A LEU* 6.2 1.6 - - - -
388A ASP* 5.3 1.6 - - - +
391A ASN* 3.0 18.2 + - - -
428A PHE* 5.1 0.9 - - - -
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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