Contacts of the helix formed by residues 332 - 337 (chain A) in PDB entry 5XOU
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 332 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327A VAL* 3.6 17.4 - - + -
328A SER* 3.2 17.7 + - - -
329A LYS* 2.8 52.5 + - - +
330A PRO 3.0 0.6 + - - -
331A ALA* 1.3 74.2 - - - +
333A ALA* 1.3 61.4 + - - +
335A ARG* 2.9 38.4 + - - +
336A VAL* 3.0 18.5 + - + +
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Residues in contact with ALA 333 (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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323A GLY* 4.5 2.0 - - - -
327A VAL* 4.0 3.7 - - + +
330A PRO 3.0 15.6 + - - +
332A ASP* 1.3 79.4 - - - +
334A LEU* 1.3 54.3 + - - +
336A VAL* 4.0 4.0 - - - -
337A GLY* 2.7 49.1 + - - +
338A PHE* 3.9 11.8 + - + -
368A ALA* 4.7 0.3 - - - +
452A LEU* 5.3 0.4 - - + -
462A VAL* 3.6 32.3 - - + +
463A VAL* 4.2 6.7 - - + -
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Residues in contact with LEU 334 (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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331A ALA* 3.0 18.5 + - - +
333A ALA* 1.3 78.4 - - - +
335A ARG* 1.3 62.0 + - + +
338A PHE* 4.2 11.7 - - + -
364A ALA* 4.5 10.5 - - + +
365A LEU* 5.7 1.6 - - + -
367A ARG* 4.3 8.4 + - - +
368A ALA* 3.4 42.3 + - + +
447A TRP* 5.6 1.3 - - + -
448A GLU* 3.7 48.5 - - + +
451A LEU* 4.7 16.4 - - + -
452A LEU* 4.3 14.6 - - + -
455A LEU* 4.2 14.4 - - + -
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Residues in contact with ARG 335 (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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329A LYS* 4.2 13.0 - - - +
331A ALA* 3.8 14.2 + - - +
332A ASP* 2.9 29.9 + - - +
334A LEU* 1.3 82.3 - - - +
336A VAL* 1.3 66.0 + - + +
337A GLY 3.4 0.4 - - - -
367A ARG* 3.9 36.1 + - - +
371A ALA* 3.7 12.7 - - - +
444A ARG* 3.4 23.8 - - - +
448A GLU* 2.9 40.3 + - - -
647A PHE* 4.9 0.2 - - - -
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Residues in contact with VAL 336 (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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324A ARG* 3.3 19.1 - - - +
325A ARG* 3.6 57.0 - - + +
326A ALA 4.9 3.4 - - - +
327A VAL* 3.8 20.9 - - + -
332A ASP* 3.0 20.5 + - + +
333A ALA* 4.0 0.4 - - - -
335A ARG* 1.3 84.3 - - + +
337A GLY* 1.3 71.7 + - - +
371A ALA* 3.5 10.4 - - - +
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Residues in contact with GLY 337 (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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323A GLY* 3.5 3.8 - - - -
324A ARG* 2.7 27.3 + - - -
333A ALA* 2.7 21.4 + - - +
335A ARG 3.4 1.8 - - - -
336A VAL* 1.3 85.1 - - - +
338A PHE* 1.3 58.2 + - - -
368A ALA 4.0 2.7 - - - -
371A ALA* 3.7 11.3 - - - +
372A SER* 3.1 13.0 - - - -
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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