Contacts of the helix formed by residues 359 - 366 (chain D) in PDB entry 1XS2
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 359 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332D ARG* 3.1 26.3 + - - -
333D ASP 5.0 1.5 - - - +
334D LEU 2.8 22.6 + - - +
335D ILE 4.2 11.9 - - - +
336D GLN* 4.2 15.3 - - + +
357D THR 3.4 1.8 + - - -
358D LEU* 1.3 68.7 - - - +
360D ARG* 1.3 58.7 + - - +
361D GLU* 3.7 8.5 + - - +
362D PHE* 3.0 27.4 + - + +
363D LEU* 2.9 29.8 + - - +
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Residues in contact with ARG 360 (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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14D GLU* 2.9 37.8 + - - -
16D VAL* 4.9 5.1 - - - +
42D ILE* 3.6 21.9 - - - +
44D HIS* 4.6 0.4 - - - -
49D GLN* 4.3 18.6 + - - +
336D GLN* 5.7 0.2 - - - +
358D LEU* 3.3 20.2 + - + +
359D ASP* 1.3 71.2 + - - +
361D GLU* 1.3 66.5 + - - +
363D LEU* 3.7 22.8 - - - +
364D ALA* 2.9 25.2 + - - +
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Residues in contact with GLU 361 (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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332D ARG* 5.9 1.5 + - - +
359D ASP* 3.8 7.1 - - - +
360D ARG* 1.3 78.1 - - - +
362D PHE* 1.3 63.6 + - - +
364D ALA* 3.2 20.0 - - - +
365D THR* 3.5 12.3 - - - +
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Residues in contact with PHE 362 (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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20D LEU* 4.0 6.5 - - + -
21D PRO* 5.5 5.2 - - + -
332D ARG* 3.6 64.1 - - + +
333D ASP 3.5 17.9 - - - -
334D LEU* 3.8 22.2 - - + -
359D ASP* 3.0 26.8 + - - +
361D GLU* 1.3 76.1 - - - +
363D LEU* 1.3 67.3 + - - +
365D THR* 2.9 37.1 + - + -
366D VAL* 3.5 20.1 - - + +
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Residues in contact with LEU 363 (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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16D VAL* 4.1 18.4 - - + -
18D ALA* 3.8 26.0 - - + -
40D LEU* 4.0 18.6 - - + -
42D ILE* 5.5 0.7 - - + -
334D LEU* 3.9 27.8 - - + +
358D LEU* 4.3 18.8 - - + -
359D ASP 2.9 18.2 + - - +
360D ARG* 3.7 23.8 - - - +
361D GLU 3.4 0.2 - - - -
362D PHE* 1.3 76.7 - - - +
364D ALA* 1.3 58.1 + - - +
366D VAL* 3.1 10.0 + - - +
367D THR* 2.9 37.5 + - - +
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Residues in contact with ALA 364 (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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360D ARG 2.9 14.4 + - - +
361D GLU* 3.2 17.3 - - - +
362D PHE 3.1 0.2 - - - -
363D LEU* 1.3 78.0 - - - +
365D THR* 1.3 59.2 + - + +
366D VAL 3.4 1.0 + - - -
367D THR* 3.5 19.7 + - - +
370D GLN* 6.0 2.7 - - - +
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Residues in contact with THR 365 (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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361D GLU 3.5 16.4 - - - +
362D PHE* 2.9 29.3 + - + +
364D ALA* 1.3 75.8 - - + +
366D VAL* 1.3 64.5 + - - +
367D THR 5.1 1.1 - - - +
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Residues in contact with VAL 366 (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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18D ALA* 3.4 5.9 - - + -
19D ARG* 3.0 46.2 + - - +
20D LEU* 4.2 5.6 - - + -
21D PRO* 4.5 11.7 - - + -
334D LEU* 4.1 17.9 - - + -
362D PHE* 3.5 25.1 - - + +
363D LEU* 3.3 17.5 - - - +
365D THR* 1.3 88.6 - - - +
367D THR* 1.3 65.6 + - - +
368D GLU* 3.5 0.7 + - - +
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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