Contacts of the helix formed by residues 367 - 372 (chain A) in PDB entry 1XPU
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 LYS 367 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A LEU* 3.5 33.9 - - + +
141A ALA* 3.8 19.8 - - + +
365A THR 3.7 0.8 + - - -
366A ARG* 1.3 87.0 - - + +
368A GLU* 1.3 64.1 + - - +
369A GLU* 3.2 31.3 + - + +
370A LEU* 3.7 14.4 + - + -
371A LEU* 4.1 3.1 - - - +
186B MET* 5.7 5.7 - - - +
215B GLU* 4.2 10.3 + - - +
218B GLU* 3.4 30.1 + - - -
2600B AGS 4.3 37.4 + - - +
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Residues in contact with GLU 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A PRO* 4.7 5.3 - - + +
364A GLY* 4.8 0.3 - - - -
365A THR* 3.1 45.1 + - + +
367A LYS* 1.3 73.6 - - - +
369A GLU* 1.3 66.0 + - - +
371A LEU* 3.0 17.9 + - - +
372A THR* 3.3 10.4 + - - -
377A LEU* 3.5 21.3 - - + +
380A MET* 5.2 5.7 - - + +
381A TRP* 4.0 17.8 + - - -
384A ARG* 2.7 44.5 + - - -
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Residues in contact with GLU 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A LYS* 3.3 32.3 - - - +
368A GLU* 1.3 90.1 + - - +
370A LEU* 1.3 75.0 + - + +
372A THR 2.8 20.3 + - - +
377A LEU* 3.8 25.3 - - + +
2600B AGS 4.2 19.6 + - - -
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Residues in contact with LEU 370 (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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139A LEU* 5.1 16.2 - - + -
141A ALA* 2.8 42.6 - - + +
142A ASN* 3.5 25.4 - - + +
367A LYS* 3.7 12.7 + - + +
368A GLU 3.3 0.6 - - - -
369A GLU* 1.3 99.7 - - + +
371A LEU* 1.3 55.4 + - - +
372A THR 3.3 0.6 + - - -
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Residues in contact with LEU 371 (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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140A HIS* 4.7 0.9 - - + -
141A ALA* 3.3 28.9 - - + +
142A ASN 5.2 0.2 - - - -
144A ARG* 3.3 38.6 - - + +
146A ARG* 4.9 1.2 + - - -
167A PRO* 3.5 31.2 - - + +
168A ILE 3.4 8.5 - - - +
169A GLY* 3.4 29.6 - - - -
172A GLN* 4.3 8.5 - - - +
365A THR* 3.9 16.6 - - + +
366A ARG 4.7 0.4 - - - +
367A LYS 4.1 11.4 - - - +
368A GLU* 3.0 8.6 + - - +
370A LEU* 1.3 77.7 - - - +
372A THR* 1.3 66.6 + - - +
376A GLU* 4.6 0.2 - - - +
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Residues in contact with THR 372 (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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144A ARG* 2.9 24.3 + - - -
146A ARG* 5.4 0.4 - - - +
167A PRO* 4.9 1.7 - - - +
368A GLU 3.3 10.2 + - - -
369A GLU* 2.8 22.4 - - - +
370A LEU 3.3 2.2 - - - -
371A LEU* 1.3 88.1 + - - +
373A THR* 1.3 63.3 + - - +
374A GLN 3.8 0.2 + - - -
376A GLU* 3.0 30.1 + - - +
377A LEU* 3.3 39.4 - - - +
380A MET* 3.8 7.6 - - + +
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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