Contacts of the helix formed by residues 2347 - 2358 (chain D) in PDB entry 5X8Q
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 MET2347 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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481C GLU* 3.5 7.5 + - - +
484C GLN* 4.9 0.2 - - - -
2346D ASN* 1.3 73.0 - - - +
2348D GLY* 1.3 59.8 + - - +
2350D GLU* 3.3 35.7 - - - +
2351D ALA* 2.9 32.3 + - + +
2354D ARG* 5.9 1.8 - - - -
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Residues in contact with GLY2348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480C VAL* 5.2 2.2 - - - -
481C GLU* 3.0 22.4 + - - -
484C GLN* 3.2 36.0 + - - -
2346D ASN* 3.1 6.8 + - - -
2347D MET* 1.3 74.7 - - - +
2349D LEU* 1.3 61.8 + - - +
2351D ALA 3.5 0.2 + - - -
2352D ILE* 3.4 24.5 + - - +
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Residues in contact with LEU2349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328C ILE* 4.1 25.6 - - + -
353C LEU 4.9 1.6 - - - +
354C LYS* 4.2 20.2 - - + +
358C MET* 4.2 22.7 - - + +
477C SER* 3.4 35.4 + - - +
480C VAL* 4.6 6.1 - - + -
2346D ASN* 3.2 23.9 + - - +
2348D GLY* 1.3 71.7 - - - +
2350D GLU* 1.4 66.3 + - - +
2351D ALA 3.1 0.5 + - - -
2352D ILE* 3.2 22.6 + - + +
2353D ILE* 2.9 39.9 + - + +
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Residues in contact with GLU2350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C ILE* 3.9 13.5 - - + +
354C LYS* 3.1 47.4 + - + +
2346D ASN 3.0 13.6 + - - +
2347D MET* 3.2 41.0 + - - +
2349D LEU* 1.4 73.8 - - - +
2351D ALA* 1.3 52.5 + - - +
2353D ILE* 3.3 3.1 + - - +
2354D ARG* 2.8 68.0 + - - +
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Residues in contact with ALA2351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484C GLN* 4.1 12.1 - - - +
2347D MET* 2.9 18.9 + - + +
2348D GLY 3.7 6.1 - - - +
2349D LEU 3.1 0.4 - - - -
2350D GLU* 1.3 74.2 - - - +
2352D ILE* 1.4 64.6 + - - +
2354D ARG* 3.5 6.6 + - - +
2355D LYS* 3.1 26.4 + - - +
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Residues in contact with ILE2352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325C THR* 4.1 29.4 - - + +
328C ILE* 3.9 22.2 - - + -
329C GLN* 4.0 24.2 - - + +
480C VAL* 3.8 26.5 - - + -
484C GLN* 4.1 7.2 - - - +
2348D GLY 3.5 16.2 - - - +
2349D LEU* 3.2 21.2 + - + +
2351D ALA* 1.4 77.4 - - - +
2353D ILE* 1.3 57.1 + - - +
2355D LYS* 3.7 4.0 + - - +
2356D ALA* 3.0 27.8 + - + +
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Residues in contact with ILE2353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328C ILE* 4.3 11.9 - - + -
332C VAL* 4.2 17.5 - - + +
350C ILE* 4.3 14.4 - - + -
353C LEU* 3.5 52.5 - - + +
354C LYS* 3.6 13.2 - - + +
357C ALA* 5.3 0.7 - - + -
2349D LEU* 2.9 32.6 + - + +
2350D GLU* 3.7 4.0 - - - +
2352D ILE* 1.3 75.7 - - - +
2354D ARG* 1.4 58.2 + - - +
2356D ALA* 3.2 1.4 + - - +
2357D LEU* 2.8 53.8 + - + +
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Residues in contact with ARG2354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346C GLN* 4.8 11.7 + - - +
350C ILE* 3.6 34.2 - - + +
2347D MET* 5.9 1.5 - - - -
2350D GLU* 2.8 54.1 + - + +
2351D ALA* 4.0 5.4 - - - +
2353D ILE* 1.4 73.3 - - - +
2355D LYS* 1.3 61.8 + - - +
2357D LEU* 3.6 8.3 + - - +
2358D MET* 3.4 39.5 + - + +
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Residues in contact with LYS2355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2351D ALA 3.1 18.7 + - - +
2352D ILE* 3.9 5.2 - - - +
2354D ARG* 1.3 78.2 - - - +
2356D ALA* 1.3 61.3 + - - +
2358D MET* 3.2 37.2 + - - +
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Residues in contact with ALA2356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C GLN* 4.3 22.9 - - + +
332C VAL* 4.0 26.8 - - + +
333C GLU* 5.6 2.1 - - + +
336C LYS* 3.2 20.4 + - - -
2352D ILE 3.0 19.8 + - - +
2353D ILE 4.1 0.7 - - - +
2355D LYS* 1.3 73.6 - - - +
2357D LEU* 1.4 61.7 + - - +
2358D MET 3.2 4.5 - - - +
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Residues in contact with LEU2357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332C VAL* 4.0 17.7 - - + +
336C LYS* 4.1 25.8 + - + +
341C PHE* 4.6 2.2 - - + -
342C MET* 4.6 8.1 - - + +
346C GLN* 5.1 11.7 - - + +
349C GLN* 3.4 31.0 - - + +
350C ILE* 3.6 33.4 - - + -
353C LEU* 4.1 15.0 - - + -
2353D ILE* 2.8 28.7 + - + +
2354D ARG* 3.8 5.4 - - - +
2356D ALA* 1.4 75.4 - - - +
2358D MET* 1.3 61.6 + - - +
2359D GLY* 3.7 1.7 + - - -
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Residues in contact with MET2358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336C LYS* 4.7 2.1 + - - -
346C GLN* 4.5 19.5 - - - +
2354D ARG* 3.4 27.7 + - + +
2355D LYS* 3.2 32.1 + - - +
2356D ALA* 3.7 6.6 - - - +
2357D LEU* 1.3 79.2 - - - +
2359D GLY* 1.3 63.5 + - - +
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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