Contacts of the helix formed by residues 529 - 536 (chain B) in PDB entry 3THY
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 ASN 529 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403B SER* 3.6 24.7 + - - -
404B GLU* 4.8 5.2 + - - -
406B GLU* 5.2 0.7 - - - +
407B THR* 3.2 19.2 + - - -
527B THR* 4.5 6.0 - - + +
528B ILE* 1.3 75.7 - - - +
530B GLY* 1.3 59.0 + - - +
531B THR* 2.8 35.1 + - - +
532B THR* 3.0 20.5 + - - +
533B LEU* 2.8 28.4 + - - +
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Residues in contact with GLY 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406B GLU* 3.9 14.1 - - - +
407B THR* 2.8 37.1 + - - -
410B SER* 4.1 4.7 + - - -
529B ASN* 1.3 72.9 - - - +
531B THR* 1.3 57.5 + - - +
533B LEU* 3.7 8.6 - - - +
534B ARG* 2.9 34.9 + - - -
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Residues in contact with THR 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403B SER* 6.2 0.2 - - - -
406B GLU* 4.3 5.6 + - - -
529B ASN* 2.8 19.8 + - - +
530B GLY* 1.3 78.0 - - - +
532B THR* 1.3 61.3 + - - +
533B LEU 3.3 0.4 - - - -
534B ARG* 2.9 21.3 + - - +
535B ASN* 2.8 51.8 + - - +
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Residues in contact with THR 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528B ILE* 3.8 17.3 - - + -
529B ASN* 3.0 25.1 + - - +
531B THR* 1.3 77.4 - - - +
533B LEU* 1.3 66.7 - - - +
535B ASN* 4.3 6.3 - - + -
536B LEU* 3.1 49.6 + - + +
538B ILE* 4.4 0.2 - - - +
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Residues in contact with LEU 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407B THR* 4.5 2.7 - - + +
410B SER* 4.1 14.8 - - - +
411B SER* 3.9 37.9 - - - +
528B ILE* 3.4 32.4 - - + +
529B ASN 2.8 16.4 + - - +
530B GLY* 3.7 9.4 - - - +
532B THR* 1.3 78.1 - - - +
534B ARG* 1.3 62.5 + - - +
537B GLU* 3.2 1.2 + - - -
538B ILE* 3.1 52.1 + - + -
539B LEU* 4.3 15.7 + - + -
542B GLN* 4.5 0.7 + - - -
572B THR* 5.4 7.9 - - - +
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Residues in contact with ARG 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406B GLU* 3.2 27.8 + - - -
410B SER* 3.9 11.0 - - - -
530B GLY 2.9 15.0 + - - -
531B THR* 2.9 43.2 + - - +
532B THR 3.3 0.2 - - - -
533B LEU* 1.3 77.4 - - - +
535B ASN* 1.3 63.3 + - - +
537B GLU 2.7 21.1 + - - -
540B GLN* 5.6 5.2 - - - +
542B GLN* 3.0 48.4 + - + +
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Residues in contact with ASN 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531B THR* 2.8 43.6 + - - +
532B THR* 4.1 6.1 + - - +
534B ARG* 1.3 77.4 - - - +
536B LEU* 1.3 65.7 + - + +
537B GLU* 3.2 14.2 + - - +
542B GLN* 4.9 2.4 - - - +
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Residues in contact with LEU 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528B ILE* 5.9 2.5 - - + -
532B THR* 3.1 40.6 + - + +
535B ASN* 1.3 79.3 - - + +
537B GLU* 1.3 71.6 + - - +
538B ILE* 3.2 25.0 + - + +
551B LEU* 5.3 1.9 - - - +
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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