Contacts of the helix formed by residues 327 - 337 (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 ASP 327 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283F GLU* 5.1 2.1 - - - +
325F PHE* 3.2 2.2 - - - -
326F PRO* 1.3 84.7 - - + +
328F PRO* 1.3 65.1 - - - +
329F GLU* 3.0 21.4 - - - +
330F GLY* 2.9 28.9 + - - -
331F MET* 3.0 18.9 + - - +
333F ARG* 4.8 2.3 + - - -
334F ARG* 4.0 11.5 + - - +
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Residues in contact with PRO 328 (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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320F TRP* 3.4 58.3 - - + +
325F PHE* 3.4 10.9 - - + +
326F PRO 3.8 4.0 - - - +
327F ASP* 1.3 85.0 - - - +
329F GLU* 1.3 74.9 + - - +
331F MET* 3.0 24.8 + - + +
332F ILE* 3.0 19.9 + - - +
408F MET* 3.9 7.4 - - + -
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Residues in contact with GLU 329 (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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327F ASP* 3.0 20.2 - - - +
328F PRO* 1.3 91.1 - - - +
330F GLY* 1.3 61.5 + - - +
332F ILE* 4.0 1.7 - - - +
333F ARG* 3.2 23.8 + - - +
408F MET* 3.8 44.4 - - + +
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Residues in contact with GLY 330 (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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327F ASP* 2.9 26.3 + - - -
328F PRO 3.1 1.0 - - - -
329F GLU* 1.3 76.6 - - - +
331F MET* 1.3 65.9 + - - +
333F ARG* 3.3 22.7 + - - +
334F ARG* 2.8 36.2 + - - +
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Residues in contact with MET 331 (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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283F GLU* 3.6 37.8 - - + +
286F VAL* 5.1 1.1 - - - -
305F PHE* 3.4 34.1 - - + -
320F TRP* 3.7 20.2 - - + -
325F PHE* 3.5 36.3 - - + -
327F ASP 3.0 12.7 + - - +
328F PRO* 3.0 14.2 + - + +
330F GLY* 1.3 75.7 - - - +
332F ILE* 1.3 63.2 - - + +
334F ARG* 3.2 15.6 + - - +
335F LEU* 2.9 38.7 + - + +
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Residues in contact with ILE 332 (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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305F PHE* 4.9 7.9 - - + -
320F TRP* 4.2 20.9 - - + -
328F PRO 3.0 11.7 + - - +
329F GLU 4.1 1.6 - - - +
331F MET* 1.3 82.9 - - + +
333F ARG* 1.3 60.7 + - - +
335F LEU* 3.0 8.6 + - - +
336F LYS* 2.8 57.0 + - + +
342F ILE* 4.1 11.9 - - + -
408F MET* 3.8 42.2 - - + +
409F GLY* 4.0 8.7 - - - +
410F VAL* 4.2 16.6 - - + -
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Residues in contact with ARG 333 (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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327F ASP* 4.8 1.8 + - - -
329F GLU 3.2 15.5 + - - +
330F GLY* 3.5 24.0 - - - +
331F MET 3.3 0.4 - - - -
332F ILE* 1.3 80.2 - - - +
334F ARG* 1.3 64.1 + - - +
336F LYS* 3.3 6.4 + - - +
337F ALA* 3.0 29.5 + - + +
3009F SO4 2.8 44.4 + - - -
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Residues in contact with ARG 334 (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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283F GLU* 2.8 38.8 + - - +
287F ASN* 5.5 9.0 - - - +
327F ASP* 4.0 18.0 + - - +
330F GLY* 2.8 34.2 + - - +
331F MET* 3.2 8.2 + - - +
333F ARG* 1.3 78.3 - - - +
335F LEU* 1.3 63.0 + - + +
337F ALA* 3.7 12.3 + - - +
338F LYS* 3.5 24.4 - - - +
3009F SO4 3.3 45.8 + - - +
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Residues in contact with LEU 335 (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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283F GLU* 5.8 0.2 - - - +
286F VAL* 3.7 13.7 - - + -
287F ASN* 3.8 16.8 - - - +
290F ILE* 3.1 35.4 - - + -
303F PHE* 4.9 4.0 - - + -
305F PHE* 3.7 35.0 - - + -
331F MET* 2.9 31.6 + - + +
332F ILE* 3.0 10.4 + - - +
334F ARG* 1.3 77.9 - - + +
336F LYS* 1.3 61.9 + - - +
337F ALA 3.2 0.2 - - - -
338F LYS* 3.1 25.0 + - + +
340F LEU* 3.3 17.8 - - + +
342F ILE* 4.5 13.0 - - + -
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Residues in contact with LYS 336 (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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332F ILE* 2.8 38.1 + - + +
333F ARG* 4.0 5.6 - - - +
335F LEU* 1.3 72.7 - - - +
337F ALA* 1.3 57.8 + - - +
338F LYS 2.9 5.8 - - - -
339F GLY* 2.8 21.0 + - - -
340F LEU 3.7 17.7 - - - +
341F LYS* 5.0 4.7 - - - +
342F ILE* 3.2 15.0 - - + -
409F GLY* 2.9 26.3 + - - +
411F ASP* 3.1 31.1 + - - -
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Residues in contact with ALA 337 (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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333F ARG* 3.0 18.5 + - + +
334F ARG* 3.7 12.6 - - - +
335F LEU 3.2 0.4 - - - -
336F LYS* 1.3 76.6 - - - +
338F LYS* 1.3 58.9 + - + +
339F GLY 3.2 3.0 + - - -
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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