Contacts of the helix formed by residues 354 - 364 (chain F) 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 SER 354 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314F GLN* 3.8 23.8 - - - +
317F ASP* 3.1 27.0 + - - +
350F ILE* 4.3 3.6 - - - -
351F GLY 3.3 13.3 + - - -
352F GLN 3.0 4.6 + - - +
353F LYS* 1.3 78.2 - - - +
355F PRO* 1.3 65.4 - - - +
356F VAL* 3.1 14.6 + - - +
357F PHE* 2.8 30.0 + - - +
358F LYS* 4.1 0.7 + - - +
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Residues in contact with PRO 355 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A GLU* 6.2 0.4 - - - +
311F LYS* 6.3 0.4 - - - -
314F GLN* 3.6 18.2 - - - +
317F ASP* 4.7 2.2 - - - +
353F LYS 3.7 4.9 - - - +
354F SER* 1.3 89.3 - - - +
356F VAL* 1.3 62.2 + - + +
357F PHE 3.4 0.3 + - - -
358F LYS* 3.7 14.8 + - + +
359F GLU* 3.9 7.3 + - - +
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Residues in contact with VAL 356 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317F ASP* 4.0 23.1 - - + +
319F GLU* 5.1 7.9 - - + +
350F ILE* 3.7 5.6 - - + -
354F SER* 3.0 13.3 + - - +
355F PRO* 1.3 80.4 - - + +
357F PHE* 1.3 67.0 + - - +
359F GLU* 3.0 16.3 + - - +
360F LEU* 2.8 36.9 + - + +
397F TRP* 3.4 35.4 - - + -
401F LYS* 5.2 2.9 - - - -
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Residues in contact with PHE 357 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A GLN* 4.5 11.0 - - + -
350F ILE* 3.8 21.5 - - + +
351F GLY 3.6 10.3 - - - +
352F GLN* 3.3 37.9 - - + +
354F SER 2.8 16.8 + - - +
356F VAL* 1.3 78.8 - - - +
358F LYS* 1.3 54.1 + - - +
360F LEU* 3.2 4.2 + - - +
361F GLN* 2.8 44.6 + - - +
366F LEU* 4.3 3.8 - - + +
374F LEU* 3.5 33.2 - - + -
376F GLN* 3.8 17.3 - - - -
383F GLY 3.6 13.7 - - - -
385F ALA* 3.6 22.7 - - + -
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Residues in contact with LYS 358 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLN* 5.6 6.7 - - - +
354F SER 4.1 0.8 + - - +
355F PRO* 3.7 10.6 + - + +
356F VAL 3.3 0.6 - - - -
357F PHE* 1.3 81.7 - - + +
359F GLU* 1.3 58.0 + - - +
361F GLN* 3.3 12.3 + - - +
362F GLU* 2.8 59.7 + - + +
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Residues in contact with GLU 359 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355F PRO 3.9 3.7 + - - +
356F VAL* 3.0 21.2 + - - +
358F LYS* 1.3 79.1 - - - +
360F LEU* 1.3 57.1 + - - +
362F GLU* 3.2 12.1 + - - +
363F LYS* 2.5 67.4 + - + +
397F TRP* 3.3 33.2 + - - -
401F LYS* 5.3 1.0 + - - -
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Residues in contact with LEU 360 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350F ILE* 3.2 34.8 - - + -
356F VAL* 2.8 21.2 + - + +
357F PHE* 3.6 5.4 - - - +
359F GLU* 1.3 77.8 - - - +
361F GLN* 1.3 59.0 + - - +
363F LYS* 3.3 4.3 + - - -
364F GLY 2.9 24.6 + - - -
365F TYR* 3.1 28.9 + - + -
366F LEU* 3.8 24.2 + - + -
387F TYR* 3.6 22.9 - - + -
397F TRP* 3.7 39.5 - - + +
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Residues in contact with GLN 361 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A GLN* 3.3 31.5 + - - +
74A GLY* 3.6 16.0 + - - -
75A ALA 4.9 2.2 + - - -
357F PHE* 2.8 29.3 + - + +
358F LYS* 3.5 11.5 - - - +
360F LEU* 1.3 77.2 - - - +
362F GLU* 1.3 64.5 + - + +
364F GLY* 3.3 12.6 + - - -
366F LEU* 4.1 8.0 - - - +
368F LYS* 5.8 1.2 - - - -
374F LEU* 3.9 29.2 - - + +
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Residues in contact with GLU 362 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358F LYS* 2.8 57.5 + - + +
359F GLU* 3.2 8.3 + - - +
361F GLN* 1.3 76.0 - - + +
363F LYS* 1.3 62.1 + - + +
364F GLY* 3.5 0.5 + - - -
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Residues in contact with LYS 363 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359F GLU* 2.5 58.9 + - + +
360F LEU 3.9 0.7 - - - +
362F GLU* 1.3 78.3 - - + +
364F GLY* 1.3 60.2 + - - +
365F TYR* 3.6 53.8 - - + +
391F ASN* 5.4 0.5 + - - -
397F TRP* 4.4 6.7 - - - +
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Residues in contact with GLY 364 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360F LEU 2.9 6.0 + - - -
361F GLN* 3.3 8.2 + - - -
362F GLU 3.3 3.4 - - - -
363F LYS* 1.3 80.2 - - - +
365F TYR* 1.3 62.3 + - - +
366F LEU 3.4 9.3 + - - +
368F LYS* 4.3 23.5 + - - -
374F LEU* 6.3 1.6 - - - -
388F ASP* 5.4 0.9 - - - +
391F ASN* 3.3 17.3 + - - -
428F PHE* 5.2 1.6 - - - -
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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