Contacts of the helix formed by residues 327 - 338 (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 ASP 327 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283C GLU* 4.9 5.6 + - - +
325C PHE* 3.2 2.0 - - - -
326C PRO* 1.3 84.9 - - + +
328C PRO* 1.3 53.4 - - - +
329C GLU* 4.3 6.8 - - - +
330C GLY* 3.0 31.5 + - - -
331C MET* 2.9 35.4 + - - +
333C ARG* 4.7 2.6 + - - -
334C ARG* 4.0 16.2 + - - +
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Residues in contact with PRO 328 (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* 3.5 48.9 - - + +
325C PHE 3.3 16.4 - - - +
326C PRO 3.5 5.4 - - - +
327C ASP* 1.3 88.0 - - - +
329C GLU* 1.3 71.1 + - - +
331C MET* 3.4 14.5 + - + +
332C ILE* 2.9 36.4 + - - +
408C MET* 4.1 5.6 - - + -
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Residues in contact with GLU 329 (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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327C ASP* 4.2 6.5 - - - +
328C PRO* 1.3 87.1 - - - +
330C GLY* 1.3 65.4 + - - +
332C ILE* 3.1 2.9 + - - +
333C ARG* 2.9 44.4 + - + +
408C MET* 3.6 51.9 - - + +
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Residues in contact with GLY 330 (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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327C ASP* 3.0 25.4 + - - -
329C GLU* 1.3 78.3 - - - +
331C MET* 1.3 63.2 + - - +
333C ARG* 3.3 26.1 + - - +
334C ARG* 3.1 35.4 + - - +
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Residues in contact with MET 331 (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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283C GLU* 3.4 45.1 - - + +
286C VAL* 5.0 2.5 - - + -
287C ASN* 5.5 0.9 - - - +
305C PHE* 3.6 26.5 - - + -
320C TRP* 3.8 17.7 - - + -
325C PHE* 3.5 40.6 - - + -
327C ASP 2.9 16.1 + - - +
328C PRO* 3.7 15.5 - - + +
330C GLY* 1.3 75.3 - - - +
332C ILE* 1.3 63.7 + - + +
334C ARG* 3.5 7.3 + - - +
335C LEU* 3.2 32.6 + - + +
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Residues in contact with ILE 332 (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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305C PHE* 5.1 2.9 - - + -
320C TRP* 4.2 13.2 - - + -
328C PRO 2.9 21.9 + - - +
329C GLU 3.1 4.7 + - - +
331C MET* 1.3 84.9 - - + +
333C ARG* 1.3 67.0 + - + +
335C LEU* 3.2 8.4 + - - +
336C LYS* 3.0 22.2 + - + +
342C ILE* 4.3 21.5 - - + +
408C MET* 3.3 39.0 - - + +
409C GLY* 3.8 21.3 - - - +
410C VAL* 4.0 21.3 - - + -
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Residues in contact with ARG 333 (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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327C ASP* 4.7 3.2 + - - -
329C GLU* 2.9 42.7 + - + +
330C GLY* 3.5 22.3 - - - +
332C ILE* 1.3 76.6 - - + +
334C ARG* 1.3 57.0 + - + +
336C LYS* 3.2 10.4 + - - +
337C ALA* 3.0 28.1 + - - +
408C MET 6.0 0.7 - - - +
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Residues in contact with ARG 334 (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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283C GLU* 2.6 40.0 + - - +
287C ASN* 5.4 7.6 - - - +
327C ASP* 4.0 16.6 + - - +
330C GLY* 3.1 15.6 + - - +
331C MET 3.7 20.8 - - - +
332C ILE 3.2 0.2 - - - -
333C ARG* 1.3 78.1 - - + +
335C LEU* 1.3 64.7 + - + +
337C ALA* 3.1 17.9 + - - +
338C LYS* 3.2 21.0 + - - +
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Residues in contact with LEU 335 (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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286C VAL* 3.9 13.0 - - + -
287C ASN* 3.6 20.9 - - - +
290C ILE* 3.2 31.4 - - + -
303C PHE* 4.4 6.1 - - + -
305C PHE* 3.8 34.8 - - + -
331C MET* 3.2 18.9 + - + +
332C ILE* 3.2 8.0 + - - +
334C ARG* 1.3 78.2 - - + +
336C LYS* 1.3 62.0 + - - +
338C LYS* 3.0 19.5 + - + +
340C LEU* 3.3 23.6 + - + +
342C ILE* 4.2 16.6 - - + -
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Residues in contact with LYS 336 (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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332C ILE* 3.0 14.8 + - + +
333C ARG* 3.4 13.0 - - + +
334C ARG 3.2 0.2 - - - -
335C LEU* 1.3 73.1 - - - +
337C ALA* 1.3 54.0 + - - +
338C LYS 2.9 4.7 - - - -
339C GLY* 2.7 26.9 + - - -
340C LEU 3.7 17.9 + - - +
341C LYS* 6.2 1.6 - - - +
342C ILE* 4.4 4.2 - - + +
411C ASP* 6.2 0.2 - - - +
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Residues in contact with ALA 337 (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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333C ARG 3.0 13.1 + - - +
334C ARG* 3.1 13.0 + - - +
336C LYS* 1.3 74.9 - - - +
338C LYS* 1.3 58.8 + - + +
339C GLY 3.1 3.8 + - - -
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Residues in contact with LYS 338 (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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287C ASN* 3.0 29.1 + - - +
290C ILE* 3.8 25.4 - - + +
291C ASP* 2.8 33.1 + - - +
300C LEU 5.6 0.3 - - - +
334C ARG* 3.5 19.5 - - - +
335C LEU* 3.0 14.5 + - + +
336C LYS 2.9 1.0 - - - -
337C ALA* 1.3 79.5 - - + +
339C GLY* 1.3 60.2 + - - +
340C LEU* 3.4 10.3 + - + +
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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