Contacts of the helix formed by residues 5071 - 5083 (chain e) 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 GLU5071 (chain e).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5068e ASP* 3.3 20.7 - - - +
5069e ARG 2.9 7.7 + - - -
5070e PHE* 1.3 83.2 - - + +
5072e ALA* 1.3 63.9 + - - +
5073e LYS 3.4 2.5 - - - -
5074e GLN* 3.7 27.8 + - + +
5075e GLN* 3.3 21.3 + - - +
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Residues in contact with ALA5072 (chain e).
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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5085d MET* 4.7 2.7 - - - -
5096d GLU* 4.9 3.6 - - + +
5107d LEU* 3.5 25.4 - - + -
5066e VAL* 3.8 16.6 - - + +
5068e ASP 3.0 19.0 + - - +
5069e ARG* 3.9 11.9 - - - -
5070e PHE 3.1 4.7 - - - +
5071e GLU* 1.3 76.9 - - - +
5073e LYS* 1.3 59.8 + - - +
5075e GLN* 3.0 23.6 - - - +
5076e VAL* 3.1 14.9 + - - +
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Residues in contact with LYS5073 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5096d GLU 4.1 13.7 + - - +
5097d ALA 4.0 13.9 + - - +
5098d GLN* 4.3 26.7 + - + +
5100d ASP* 3.3 37.4 + - - +
5103d ARG* 3.5 39.3 - - + +
5107d LEU* 4.5 5.4 - - + +
5070e PHE 4.8 2.2 + - - +
5071e GLU 3.4 0.6 - - - -
5072e ALA* 1.3 73.0 - - - +
5074e GLN* 1.3 67.8 + - - +
5075e GLN 2.9 1.6 - - - -
5076e VAL* 2.7 21.6 + - - +
5077e GLU* 2.9 24.4 + - - +
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Residues in contact with GLN5074 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5071e GLU* 3.7 28.0 + - + +
5072e ALA 3.6 0.6 - - - -
5073e LYS* 1.3 78.2 - - - +
5075e GLN* 1.3 52.2 + - - +
5077e GLU* 3.4 29.7 + - - +
5078e THR* 2.9 44.2 + - + +
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Residues in contact with GLN5075 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5066e VAL* 3.7 5.9 - - + +
5067e THR* 2.7 48.1 + - - +
5068e ASP* 3.1 24.8 + - - +
5071e GLU 3.3 8.5 + - - +
5072e ALA 3.0 15.0 + - - +
5073e LYS 2.8 0.6 + - - -
5074e GLN* 1.3 76.8 - - - +
5076e VAL* 1.3 61.8 + - + +
5078e THR* 2.8 18.8 + - - +
5079e PHE* 3.2 39.6 + - + -
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Residues in contact with VAL5076 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5059d TYR* 3.6 24.9 - - + -
5103d ARG* 4.1 7.0 - - - -
5106d GLN* 3.5 24.5 - - - +
5107d LEU* 3.6 27.4 - - + -
5066e VAL* 3.7 17.9 - - + -
5072e ALA 3.1 15.0 + - - +
5073e LYS* 2.7 13.0 + - - +
5075e GLN* 1.3 73.4 - - - +
5077e GLU* 1.3 57.5 + - - +
5079e PHE* 2.9 28.7 + - - +
5080e LEU* 3.1 15.7 + - + +
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Residues in contact with GLU5077 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5103d ARG* 3.0 35.2 + - - +
5073e LYS* 2.9 29.5 + - - +
5074e GLN* 3.4 32.4 + - - +
5076e VAL* 1.3 72.9 - - - +
5078e THR* 1.3 61.4 + - + +
5080e LEU* 2.9 16.9 + - - +
5081e GLU* 2.9 29.9 + - - +
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Residues in contact with THR5078 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5074e GLN* 2.9 24.3 + - + +
5075e GLN* 2.8 21.3 + - - +
5077e GLU* 1.3 77.8 - - + +
5079e PHE* 1.3 60.5 + - - +
5081e GLU* 3.1 14.5 - - + +
5082e GLN* 2.9 40.9 + - - +
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Residues in contact with PHE5079 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5059d TYR* 4.1 17.3 - + + -
5060e GLN* 5.4 1.4 + - - +
5064e PRO* 3.2 49.5 - - + +
5065e LEU 3.4 27.4 - - - -
5066e VAL* 3.9 5.8 - - - -
5067e THR* 5.2 1.8 - - + -
5075e GLN* 3.2 38.0 + - + -
5076e VAL* 2.9 17.2 + - + +
5078e THR* 1.3 82.9 - - - +
5080e LEU* 1.3 58.3 + - - +
5082e GLN* 3.8 11.4 - - + +
5083e LEU* 3.7 19.2 + - - +
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Residues in contact with LEU5080 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5059d TYR* 3.6 23.3 - - + +
5103d ARG* 3.8 20.6 - - - +
5106d GLN* 4.8 7.9 - - - +
5048e GLY* 5.6 1.6 - - - +
5076e VAL* 3.1 29.1 + - + +
5077e GLU* 2.9 16.8 + - - +
5079e PHE* 1.3 74.3 - - - +
5081e GLU* 1.3 68.0 + - - +
5083e LEU* 2.9 31.5 - - + +
5084e LYS 4.1 0.5 + - - -
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Residues in contact with GLU5081 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5077e GLU* 2.9 12.6 + - - +
5078e THR* 3.1 23.5 - - + +
5080e LEU* 1.3 78.0 - - - +
5082e GLN* 1.3 74.3 + - - +
5083e LEU 2.7 2.1 + - - -
5084e LYS* 2.8 15.4 + - - -
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Residues in contact with GLN5082 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5057e ALA* 3.9 10.5 - - + +
5060e GLN* 4.7 16.2 - - - +
5078e THR* 2.9 30.5 + - - +
5079e PHE* 3.8 13.0 - - + +
5081e GLU* 1.3 86.8 - - - +
5083e LEU* 1.3 54.5 + - - +
5084e LYS* 2.7 17.8 + - - +
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Residues in contact with LEU5083 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5059d TYR* 5.5 2.9 - - - +
5053e ASP 5.5 0.7 - - - +
5054e SER* 3.6 40.2 - - - +
5055e TYR 4.2 4.9 - - - +
5056e TYR* 3.7 10.5 - - - +
5057e ALA* 3.4 39.7 - - - +
5060e GLN* 3.4 11.2 - - - +
5079e PHE 3.7 7.7 + - - +
5080e LEU* 2.9 34.0 + - + +
5081e GLU 2.7 1.2 + - - -
5082e GLN* 1.3 77.9 - - - +
5084e LYS* 1.3 67.4 + - - +
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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