Contacts of the helix formed by residues 5271 - 5277 (chain b) in PDB entry 2AXT
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 THR5271 (chain b).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5257b TRP 3.6 13.2 + - - -
5258b TYR 3.7 15.1 + - - -
5265b ILE* 4.6 0.6 - - - +
5270b PRO* 1.3 78.0 - - - +
5272b ARG* 1.3 62.2 + - - +
5273b TYR* 2.8 39.0 + - + +
5274b GLN* 2.8 42.2 + - + +
5275b TRP* 4.0 4.7 + - - +
5318b ASN* 4.7 0.7 - - - +
5319b PRO* 4.1 2.7 - - - +
5448b ARG* 4.0 11.7 + - - +
5062h TRP* 3.9 11.5 - - - +
5208h DGD 4.4 6.5 - - - +
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Residues in contact with ARG5272 (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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5257b TRP* 3.8 26.4 + - + -
5271b THR* 1.3 73.9 - - - +
5273b TYR* 1.3 84.0 + - + +
5274b GLN 3.3 0.2 - - - -
5275b TRP* 3.6 5.4 + - - +
5276b ASP* 2.8 58.5 + - - +
5318b ASN* 3.2 27.4 + - - +
5319b PRO* 4.0 5.5 - - + +
5320b ALA* 3.9 19.1 - - + +
5361b ALA* 3.8 16.8 + - - +
5362b PHE* 4.6 3.0 - - - -
5448b ARG* 5.1 0.4 - - - +
5163d GLY 3.8 9.4 + - - -
5164d GLN* 3.4 45.0 - - - +
5165d SER* 4.2 13.0 - - - +
5169d PHE* 6.3 0.2 - - - -
5290d ALA 4.7 1.6 + - - -
5291d LEU* 6.1 0.4 - - - +
5292d ASN* 4.1 8.5 - - - +
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Residues in contact with TYR5273 (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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5257b TRP* 2.9 30.1 + + - -
5258b TYR* 3.6 21.5 - + - -
5271b THR* 2.8 18.5 - - + +
5272b ARG* 1.3 89.0 - - + +
5274b GLN* 1.3 60.1 + - - +
5275b TRP 3.1 1.8 - - - -
5276b ASP* 3.3 19.9 - - + +
5277b SER* 2.9 28.6 + - - -
5087d HIS* 4.3 6.1 - + - -
5162d LEU 3.5 4.7 + - - -
5163d GLY 2.8 18.4 + - - -
5164d GLN 2.7 33.2 + - - -
5165d SER* 4.1 7.2 - - - -
5208h DGD 3.1 45.1 + - - +
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Residues in contact with GLN5274 (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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5265b ILE* 3.8 16.6 - - - +
5270b PRO* 3.5 11.3 - - + +
5271b THR* 2.8 45.9 + - + +
5273b TYR* 1.3 78.8 - - - +
5275b TRP* 1.3 56.8 + - - +
5278b SER* 3.6 0.5 - - - -
5279b TYR* 2.7 68.8 + - + +
5280b PHE* 3.6 34.5 + - + -
5062h TRP* 3.5 23.6 + - - +
5208h DGD 3.9 4.9 - - - -
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Residues in contact with TRP5275 (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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5271b THR 4.0 2.9 + - - +
5272b ARG 3.6 7.7 + - - +
5273b TYR 3.1 0.4 - - - -
5274b GLN* 1.3 77.3 - - - +
5276b ASP* 1.3 76.7 + - - +
5277b SER 3.2 0.2 - - - -
5278b SER* 3.0 15.9 + - - +
5280b PHE* 6.0 0.7 - - - -
5312b TYR 5.3 2.9 - - - +
5313b ASP* 4.1 9.6 - - - -
5314b TYR 4.1 7.2 - - - -
5315b ILE* 3.4 39.0 - - + +
5318b ASN* 3.4 30.7 - - + +
5358b ARG* 3.5 52.6 + - + -
5359b MET 3.2 29.7 + - - -
5360b PRO* 4.6 1.4 - - + +
5361b ALA* 3.9 12.2 - - + +
5425b ILE 4.2 0.7 - - - -
5426b PHE 3.6 22.0 - - - -
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Residues in contact with ASP5276 (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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5272b ARG* 2.8 55.3 + - - +
5273b TYR* 3.3 26.6 + - + +
5275b TRP* 1.3 89.2 - - - +
5277b SER* 1.3 57.6 + - - +
5278b SER* 3.3 3.7 + - - -
5361b ALA* 4.8 4.2 + - - +
5165d SER* 4.7 9.7 - - - -
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Residues in contact with SER5277 (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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5273b TYR 2.9 16.2 + - - -
5275b TRP 3.2 0.2 - - - -
5276b ASP* 1.3 77.5 - - - +
5278b SER* 1.3 69.6 + - - +
5279b TYR* 2.9 7.1 + - - +
5282b GLN* 2.7 26.8 + - - -
5208h DGD 3.1 17.9 + - - -
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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