Contacts of the helix formed by residues 327 - 337 (chain C) in PDB entry 1XPM
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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8C ILE 4.6 7.3 + - - +
9C ASN* 5.3 2.5 - - - +
61C ASP 5.7 0.3 - - - +
62C ILE* 4.5 16.5 - - - +
290C GLU* 3.6 7.6 + - - -
325C HIS 4.4 7.1 - - - +
326C LEU* 1.3 79.3 - - - +
328C GLN* 1.3 58.3 + - - +
329C ALA 3.3 3.1 - - - +
330C ALA* 3.2 17.2 + - + +
331C HIS* 3.0 40.1 + - + +
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Residues in contact with GLN 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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269C TYR* 4.2 3.2 + - - +
290C GLU* 3.2 58.6 + - + +
291C ASN* 4.3 10.1 + - - +
323C LYS* 5.2 2.9 + - - +
326C LEU* 3.6 5.5 + - + -
327C ASP* 1.3 73.6 - - - +
329C ALA* 1.3 61.2 + - - +
331C HIS* 3.8 0.7 - - - +
332C LYS* 2.9 49.4 + - + +
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Residues in contact with ALA 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* 3.3 1.0 - - - -
328C GLN* 1.3 78.4 - - - +
330C ALA* 1.3 59.2 + - - +
332C LYS* 3.9 6.9 - - - +
333C ALA* 2.9 31.1 + - - +
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Residues in contact with ALA 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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9C ASN* 5.7 0.7 - - - +
327C ASP* 3.2 23.3 + - + +
329C ALA* 1.3 80.0 - - - +
331C HIS* 1.3 60.6 + - + +
333C ALA* 3.3 7.7 + - - +
334C LEU* 2.8 29.0 + - - +
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Residues in contact with HIS 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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8C ILE* 4.2 12.8 - - + -
9C ASN* 2.7 34.1 + - - +
10C PHE* 3.7 28.3 - + + -
269C TYR* 4.2 4.9 - - + +
286C ILE* 3.7 15.2 - - + +
290C GLU* 2.4 44.7 + - - +
326C LEU* 5.7 0.2 - - - -
327C ASP* 3.0 24.7 + - + +
328C GLN 3.8 0.7 - - - +
330C ALA* 1.3 79.6 - - + +
332C LYS* 1.3 66.3 + - - +
334C LEU* 3.2 9.1 + - + +
335C LEU* 3.2 28.5 + - - +
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Residues in contact with LYS 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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269C TYR* 4.3 13.9 + - + +
328C GLN* 2.9 43.8 + - + +
329C ALA* 3.9 5.6 - - - +
331C HIS* 1.3 75.4 - - - +
333C ALA* 1.3 57.7 + - - +
335C LEU* 3.3 6.7 + - - +
336C ASN* 2.8 46.5 + - - +
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Residues in contact with ALA 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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329C ALA 2.9 19.7 + - - +
330C ALA* 3.4 9.0 - - - +
332C LYS* 1.3 77.6 - - - +
334C LEU* 1.3 56.5 + - - +
336C ASN* 4.6 5.2 - - - +
337C ASN* 2.9 49.6 + - - +
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Residues in contact with LEU 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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10C PHE* 3.4 50.5 - - + +
11C TYR* 3.9 31.0 - - + -
12C VAL* 4.0 17.9 - - + +
330C ALA 2.8 14.2 + - - +
331C HIS* 3.2 11.4 + - + +
333C ALA* 1.3 79.7 - - - +
335C LEU* 1.3 61.4 + - - +
337C ASN* 3.8 7.3 + - - +
338C ARG* 3.5 18.3 + - + +
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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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10C PHE* 4.1 18.4 - - + -
12C VAL* 4.2 6.3 - - + -
16C TYR* 5.2 2.3 - - - -
41C GLU* 5.3 0.2 - - - +
269C TYR* 3.9 42.8 - - + +
272C TYR* 4.8 11.2 - - + -
273C VAL* 4.0 20.9 - - + -
331C HIS 3.2 13.4 + - - +
332C LYS* 3.8 8.5 - - - +
334C LEU* 1.3 78.2 - - - +
336C ASN* 1.3 65.1 + - - +
337C ASN 3.6 0.2 + - - -
338C ARG* 3.0 51.6 + - - +
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Residues in contact with ASN 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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16C TYR* 5.9 0.2 - - - -
332C LYS* 2.8 37.4 + - - +
333C ALA* 4.1 4.6 - - - +
335C LEU* 1.3 77.4 - - - +
337C ASN* 1.3 60.5 - - - +
338C ARG 3.1 15.9 + - - +
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Residues in contact with ASN 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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14C LYS* 5.8 1.0 - - - +
333C ALA* 2.9 41.2 + - - +
334C LEU* 3.8 5.7 + - - +
335C LEU 3.4 0.4 - - - -
336C ASN* 1.3 76.8 - - - +
338C ARG* 1.3 63.8 + - - +
339C THR* 4.4 4.2 + - - -
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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