Contacts of the strand formed by residues 5141 - 5147 (chain o) 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 ARG5141 (chain o).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5056a PRO* 3.1 31.7 - - - +
5057a PRO* 2.9 42.4 + - - +
5066a PRO* 4.1 5.0 - - - +
5103a ASP 4.7 1.4 + - - -
5106a LEU* 5.1 0.2 - - - +
5107a TYR* 3.1 50.1 - - + +
5097o VAL* 5.6 0.2 - - + -
5133o THR* 4.4 12.6 - - + -
5134o VAL 3.5 6.1 - - - +
5135o GLN* 2.8 29.3 + - + +
5139o GLY 4.1 2.2 - - - +
5140o GLU* 1.3 78.6 - - - +
5142o ILE* 1.3 62.5 + - - +
5143o PRO* 3.0 14.6 - - + +
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Residues in contact with ILE5142 (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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5078o VAL* 4.5 11.7 - - + -
5133o THR* 3.6 1.3 - - - -
5134o VAL* 2.7 44.1 + - + +
5136o MET* 3.8 23.3 - - + -
5140o GLU* 3.5 32.3 - - + +
5141o ARG* 1.3 78.7 - - - +
5143o PRO* 1.3 63.4 - - + +
5144o LEU* 3.7 4.6 + - + +
5247o SER* 3.8 26.2 - - - -
5257o HIS* 4.0 22.9 - - + +
5259o VAL* 4.4 15.3 - - + -
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Residues in contact with PRO5143 (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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5310d GLU* 5.5 4.7 - - - +
5132o VAL 3.2 6.7 - - - +
5133o THR* 3.4 22.2 - - + +
5141o ARG* 3.0 14.6 - - + +
5142o ILE* 1.3 84.3 - - + +
5144o LEU* 1.3 58.5 + - - +
5177o TYR* 3.7 23.3 - - + +
5247o SER* 3.8 2.4 - - - -
5248o ASP* 3.0 47.9 + - + +
5254o HIS* 6.5 0.9 - - + -
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Residues in contact with LEU5144 (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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5076o PHE* 4.1 16.2 - - + -
5132o VAL* 2.8 62.9 + - + +
5134o VAL* 4.8 6.5 - - + -
5142o ILE* 3.8 12.1 - - + +
5143o PRO* 1.3 75.2 - - - +
5145o LEU* 1.3 60.9 + - - +
5146o PHE* 3.6 8.2 + - + +
5177o TYR* 3.7 11.0 - - - -
5245o GLN* 4.5 6.5 - - - +
5246o LEU 4.3 3.8 - - - +
5247o SER* 4.1 18.8 - - - +
5248o ASP 4.4 1.6 - - - +
5259o VAL* 3.3 39.9 - - + -
5261o ILE* 4.2 9.4 - - + -
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Residues in contact with LEU5145 (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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5332c GLN* 3.8 21.5 - - - +
5336c GLY 4.1 11.9 - - - +
5129o PHE* 3.8 26.9 - - + -
5130o GLN 3.8 1.6 - - - -
5131o PRO* 4.2 8.1 - - + -
5144o LEU* 1.3 75.0 - - - +
5146o PHE* 1.3 64.3 + - - +
5147o THR* 2.8 20.7 + - + +
5174o VAL* 4.9 5.8 - - + -
5175o PRO* 2.8 40.6 - - + -
5176o SER 4.0 8.1 - - - +
5177o TYR* 4.2 26.1 - - + +
5245o GLN* 3.0 13.1 + - - +
5246o LEU 4.7 2.4 + - - -
5247o SER 5.4 0.8 - - - -
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Residues in contact with PHE5146 (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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5071o LEU* 4.4 4.0 - - + -
5073o PRO* 3.9 20.2 - - + -
5076o PHE* 4.7 9.0 - + + -
5102o THR 3.5 22.2 - - - -
5104o LEU* 3.5 36.8 - - + +
5129o PHE* 3.3 2.1 - - - -
5130o GLN* 2.8 41.2 + - + +
5132o VAL* 4.3 12.1 - - + -
5144o LEU* 3.5 7.9 + - + +
5145o LEU* 1.3 68.9 - - - +
5147o THR* 1.3 65.3 + - - +
5148o VAL* 5.4 2.9 - - + -
5241o PHE* 3.7 25.1 - + - -
5243o SER* 4.0 11.7 - - - -
5245o GLN* 3.7 12.5 - - - +
5261o ILE* 3.7 33.7 - - + -
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Residues in contact with THR5147 (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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5104o LEU* 4.2 5.4 - - - -
5128o ASP 2.6 20.7 + - - -
5129o PHE* 3.7 9.4 - - - +
5145o LEU* 2.8 17.6 + - + +
5146o PHE* 1.3 77.9 - - - +
5148o VAL* 1.3 78.9 + - - +
5149o LYS* 2.8 17.4 + - - +
5172o PHE* 3.1 21.9 - - - -
5173o ASN 3.9 7.0 - - - +
5174o VAL* 4.1 13.2 - - + -
5175o PRO* 3.8 25.6 - - + -
5243o SER* 5.4 0.3 + - - -
5245o GLN* 3.5 6.3 + - - +
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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