Contacts of the strand formed by residues 5064 - 5079 (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 TYR5064 (chain o).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5056o TYR* 3.2 43.1 - + - -
5057o PRO 3.3 8.5 + - - -
5058o ILE* 4.2 6.1 - - + -
5059o ASP* 2.8 46.0 + - + +
5060o SER 4.0 3.6 - - - -
5062o GLN* 3.0 37.5 + - + +
5063o THR* 1.3 82.8 - - - +
5065o ARG* 1.3 61.9 + - - +
5110o GLU* 3.8 2.8 - - - +
5111o LEU* 2.7 46.3 + - + +
5113o VAL* 4.1 14.5 - - + +
5119o LEU* 6.0 0.4 - - + -
5269o ILE* 4.4 6.5 - - + -
5270o GLU 3.4 9.9 - - - +
5271o PRO* 4.2 12.8 - - + -
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Residues in contact with ARG5065 (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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5063o THR* 6.0 1.6 - - + -
5064o TYR* 1.3 74.1 - - - +
5066o ILE* 1.3 80.0 + - - +
5067o ALA* 3.9 3.9 - - - +
5108o GLN* 3.7 33.3 + - - +
5109o GLY* 3.0 22.0 - - - +
5110o GLU* 3.6 23.4 - - + +
5111o LEU* 3.4 8.7 - - - +
5124o GLU* 4.4 7.7 - - - +
5269o ILE* 3.4 6.8 - - - +
5270o GLU* 2.8 35.2 + - + +
5271o PRO 5.1 6.1 - - - +
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Residues in contact with ILE5066 (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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5065o ARG* 1.3 79.5 + - - +
5067o ALA* 1.3 67.5 + - - +
5068o ARG 4.0 21.8 - - - +
5069o LEU* 4.0 17.0 - - + +
5107o ILE 4.8 0.9 - - - +
5108o GLN* 3.3 18.2 - - - +
5109o GLY 2.9 16.1 + - - +
5111o LEU* 4.1 17.0 - - + -
5121o PHE* 3.5 41.5 - - + -
5168o PHE* 5.4 6.3 - - + -
5237o ILE* 6.4 1.1 - - + -
5267o ALA* 4.7 9.2 - - + -
5268o SER 3.6 13.9 - - - +
5269o ILE* 4.2 14.4 - - + -
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Residues in contact with ALA5067 (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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5065o ARG* 3.9 7.3 + - - +
5066o ILE* 1.3 75.1 - - - +
5068o ARG* 1.3 61.3 + - + +
5106o GLN 4.7 1.9 - - - +
5107o ILE 3.7 0.3 - - - +
5108o GLN* 3.3 23.2 - - - +
5268o SER* 2.6 26.1 + - - +
5269o ILE* 4.5 0.2 - - - +
5270o GLU* 3.9 30.8 - - - +
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Residues in contact with ARG5068 (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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5373c ASN* 4.1 19.2 - - - +
5045o CYS* 4.3 0.6 - - - +
5046o PRO* 3.3 39.6 - - - +
5066o ILE* 3.5 2.9 - - - -
5067o ALA* 1.3 79.0 - - + +
5069o LEU* 1.3 63.3 + - - +
5070o CYS* 4.0 2.2 + - - +
5105o ASP* 2.8 43.3 + - - +
5106o GLN* 4.3 9.4 - - - +
5107o ILE 3.5 2.7 - - - -
5266o TYR* 4.3 17.0 - - + -
5267o ALA* 3.2 4.2 + - - -
5268o SER* 2.9 40.8 + - - +
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Residues in contact with LEU5069 (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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5066o ILE* 4.1 17.0 - - + -
5068o ARG* 1.3 73.2 - - - +
5070o CYS* 1.3 69.7 + - - +
5071o LEU* 4.5 11.0 - - + -
5105o ASP* 4.0 3.6 - - - -
5107o ILE* 2.7 54.1 + - + +
5121o PHE* 3.8 31.0 - - + -
5151o LEU* 4.7 9.6 - - + -
5225o LEU* 3.9 30.5 - - + -
5265o PHE* 4.2 3.4 - - + -
5266o TYR 3.3 16.6 - - - +
5267o ALA* 4.2 6.7 - - + +
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Residues in contact with CYS5070 (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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5045o CYS* 2.1 51.4 - - + -
5068o ARG* 4.0 5.9 + - + +
5069o LEU* 1.3 75.8 - - - +
5071o LEU* 1.3 73.7 + - - +
5072o GLN* 4.0 1.1 - - - -
5103o SER* 5.1 4.0 - - - -
5104o LEU 3.3 13.0 - - - -
5105o ASP* 3.2 21.5 - - - +
5265o PHE* 2.9 29.6 - - - +
5266o TYR* 3.1 16.8 + - + +
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Residues in contact with LEU5071 (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* 4.5 12.1 - - + -
5070o CYS* 1.3 78.0 - - - +
5072o GLN* 1.3 59.5 + - - +
5073o PRO* 3.6 3.2 - - - +
5103o SER* 3.5 1.7 - - - -
5104o LEU* 2.7 57.6 + - + +
5107o ILE* 4.3 7.9 - - + -
5146o PHE* 4.7 1.3 - - + -
5148o VAL* 3.4 39.5 - - + -
5151o LEU* 5.4 1.1 - - + -
5223o ILE* 5.2 4.7 - - + -
5225o LEU* 4.4 13.5 - - + -
5241o PHE* 3.5 42.0 - - + -
5264o VAL 3.5 2.2 - - - -
5265o PHE* 3.8 12.8 - - + -
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Residues in contact with GLN5072 (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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5043o ASN* 4.2 3.1 + - - +
5044o LYS* 3.1 42.7 + - - +
5045o CYS* 2.6 47.0 + - - +
5070o CYS* 4.0 0.4 - - - -
5071o LEU* 1.3 71.8 - - - +
5073o PRO* 1.3 76.4 - - - +
5074o THR* 3.9 6.8 + - - +
5103o SER* 3.5 14.4 - - - +
5241o PHE* 3.8 2.2 - - - -
5263o GLY* 3.1 1.4 - - - -
5264o VAL* 2.7 52.3 + - + +
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Residues in contact with PRO5073 (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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5043o ASN* 5.6 0.5 + - - -
5071o LEU 3.6 4.0 - - - +
5072o GLN* 1.3 94.8 - - - +
5074o THR* 1.3 61.2 + - - +
5076o PHE* 3.6 24.7 - - + -
5102o THR* 2.9 43.8 + - - +
5103o SER* 3.5 24.0 - - - +
5146o PHE* 3.9 15.5 - - + -
5241o PHE* 4.2 5.8 - - + -
5261o ILE* 4.1 5.6 - - + -
5263o GLY* 4.2 4.3 - - - -
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Residues in contact with THR5074 (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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5072o GLN* 3.6 7.0 + - - +
5073o PRO* 1.3 76.4 + - - +
5075o THR* 1.3 71.8 + - - +
5076o PHE* 5.0 5.2 - - - -
5262o GLN* 3.0 16.9 + - + +
5263o GLY* 3.7 13.0 - - - -
5264o VAL* 4.3 8.8 + - - +
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Residues in contact with THR5075 (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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5074o THR* 1.3 90.8 + - - +
5076o PHE* 1.3 67.8 + - - +
5077o LEU* 3.2 26.5 - - + -
5093o PRO* 5.6 6.7 - - + -
5260o LYS 3.9 0.5 - - - +
5261o ILE* 3.5 6.8 - - - +
5262o GLN* 2.8 49.4 + - - +
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Residues in contact with PHE5076 (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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5073o PRO* 3.6 32.8 - - + -
5074o THR 4.9 3.4 - - - -
5075o THR* 1.3 83.2 - - - +
5077o LEU* 1.3 64.7 + - - +
5078o VAL* 5.8 0.4 - - + -
5093o PRO* 3.9 1.0 - - - +
5094o THR* 3.2 40.7 + - - +
5096o LEU* 5.1 11.0 - - + -
5102o THR* 4.2 9.9 - - + -
5132o VAL* 3.9 32.3 - - + -
5134o VAL* 4.2 17.9 - - + -
5144o LEU* 4.1 16.6 - - + -
5146o PHE* 4.7 5.6 - + + -
5259o VAL* 4.7 3.6 - - + -
5260o LYS 3.5 3.6 - - - +
5261o ILE* 3.6 29.4 - - + -
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Residues in contact with LEU5077 (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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5075o THR* 3.2 28.9 - - + +
5076o PHE* 1.3 82.4 - - - +
5078o VAL* 1.3 69.1 + - - +
5079o LYS 4.2 0.2 - - - -
5091o PHE* 3.6 37.7 - - + +
5092o VAL 3.1 15.5 - - - +
5093o PRO* 4.4 4.5 - - + -
5094o THR* 4.8 0.2 - - - -
5259o VAL* 3.3 4.2 - - - +
5260o LYS* 2.9 41.8 + - + +
5262o GLN* 4.3 22.9 - - + +
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Residues in contact with VAL5078 (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* 5.8 0.2 - - + -
5077o LEU* 1.3 81.9 - - - +
5079o LYS* 1.3 67.2 + - - +
5080o GLU* 3.0 5.7 + - - -
5092o VAL* 2.9 24.2 + - - +
5094o THR* 3.8 22.7 - - + +
5134o VAL* 4.6 7.2 - - + -
5136o MET* 4.0 15.9 - - + +
5142o ILE* 4.5 14.8 - - + -
5257o HIS* 3.7 32.8 - - + +
5258o GLU 3.3 15.7 - - - +
5259o VAL* 4.2 13.0 - - + -
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Residues in contact with LYS5079 (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* 1.3 76.4 - - - +
5080o GLU* 1.3 69.0 + - - +
5081o GLU* 3.0 6.2 + - - +
5089o ALA* 5.1 7.2 - - + +
5090o GLU 3.0 14.1 - - - +
5091o PHE* 3.4 36.0 - - + +
5257o HIS* 4.9 2.6 + - - +
5258o GLU* 3.3 27.5 + - + +
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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