Contacts of the strand formed by residues 5219 - 5227 (chain o) in PDB entry 3A0B
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 THR5219 (chain o).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5173o ASN* 3.7 1.6 - - - -
5174o VAL* 2.7 49.1 + - - +
5217o SER* 5.4 5.6 - - - -
5218o LEU* 1.3 86.9 - - - +
5220o LYS* 1.3 59.9 + - - +
5246o LEU* 4.3 26.2 - - + +
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Residues in contact with LYS5220 (chain o).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5150o ASN* 4.1 14.7 + - - +
5152o VAL* 6.2 1.4 - - - +
5171o GLU* 3.8 40.2 + - + +
5172o PHE 3.1 17.7 - - - +
5173o ASN* 2.8 31.0 - - - +
5174o VAL* 4.1 2.7 - - - -
5218o LEU* 5.6 2.0 - - + -
5219o THR* 1.3 80.4 + - - +
5221o GLY* 1.3 61.9 + - - +
5222o GLN* 4.7 4.3 - - - +
5246o LEU* 5.7 3.8 - - - +
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Residues in contact with GLY5221 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5171o GLU* 3.5 5.9 - - - +
5172o PHE* 2.9 45.9 + - - +
5174o VAL* 3.7 9.5 - - - +
5220o LYS* 1.3 76.4 - - - +
5222o GLN* 1.3 64.9 + - - +
5244o GLU 3.6 16.2 - - - -
5245o GLN* 4.7 0.7 - - - -
5246o LEU* 6.5 0.2 - - - -
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Residues in contact with GLN5222 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5169o LYS 6.3 0.2 - - - -
5170o GLY 3.7 12.8 - - - +
5171o GLU* 4.1 24.3 + - + +
5172o PHE* 3.8 4.2 - - - -
5220o LYS* 4.7 4.0 - - - +
5221o GLY* 1.3 80.2 - - - +
5223o ILE* 1.3 63.9 + - - +
5243o SER* 2.8 25.6 - - - -
5244o GLU* 2.9 17.6 + - + +
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Residues in contact with ILE5223 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5071o LEU* 3.2 35.7 - - + -
5148o VAL* 3.9 15.0 - - + -
5151o LEU* 3.5 26.2 - - + -
5169o LYS* 3.5 8.1 - - - +
5170o GLY 2.9 32.5 + - - +
5172o PHE* 3.5 12.3 - - + -
5222o GLN* 1.3 79.5 - - - +
5224o SER* 1.3 78.9 + - - +
5225o LEU* 3.5 23.1 - - + -
5241o PHE* 4.8 2.0 - - + -
5242o GLU 3.1 17.5 - - - +
5243o SER* 3.9 5.4 - - - +
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Residues in contact with SER5224 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5169o LYS* 3.2 38.4 - - - +
5223o ILE* 1.3 86.5 + - - +
5225o LEU* 1.3 64.0 + - - +
5241o PHE* 3.4 4.5 - - - +
5242o GLU* 3.2 41.7 + - - +
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Residues in contact with LEU5225 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5069o LEU* 4.4 17.9 - - + -
5071o LEU* 5.0 3.6 - - + -
5151o LEU* 5.7 4.3 - - + -
5153o ALA* 6.2 0.7 - - + -
5167o ASP* 3.1 31.2 - - - +
5168o PHE* 4.0 27.8 - - + -
5169o LYS* 3.9 7.1 + - - +
5223o ILE* 3.5 32.1 - - + -
5224o SER* 1.3 84.2 - - - +
5226o ASN* 1.3 60.7 + - - +
5240o THR 3.6 2.7 - - - -
5241o PHE* 4.0 11.7 - - + -
5265o PHE* 3.8 42.4 - - + -
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Residues in contact with ASN5226 (chain o).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5165o SER* 4.0 16.8 + - - +
5166o THR 3.5 10.4 - - - +
5167o ASP* 4.0 13.2 - - - +
5169o LYS* 5.7 1.5 + - - +
5224o SER 4.3 0.2 + - - -
5225o LEU* 1.3 73.9 - - - +
5227o VAL* 1.3 83.1 + - - +
5228o ALA* 5.2 2.4 - - - +
5239o GLY* 3.6 0.2 - - - -
5240o THR* 3.1 32.5 + - - +
5241o PHE* 5.0 0.2 - - - +
5265o PHE* 3.1 16.6 - - - -
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Residues in contact with VAL5227 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5162o ILE* 4.5 7.6 - - + -
5164o THR* 5.0 2.0 - - - -
5165o SER* 3.0 24.2 + - - +
5166o THR* 3.2 30.7 + - - +
5168o PHE* 4.1 20.2 - - + -
5226o ASN* 1.3 88.2 + - - +
5228o ALA* 1.3 68.7 + - - +
5229o LYS 3.7 1.3 - - - +
5230o VAL* 3.7 29.4 - - + -
5237o ILE* 3.7 11.9 - - + -
5238o ALA 3.1 23.3 - - - +
5239o GLY* 4.3 0.2 - - - -
5265o PHE* 4.3 6.7 - - + -
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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