Contacts of the helix formed by residues 5072 - 5082 (chain u) 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 TYR5072 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5320c ARG* 5.4 1.9 + - - -
5324c LEU* 3.7 38.6 - - + +
5062u ILE* 4.1 20.7 - - + +
5063u ALA* 4.5 3.8 - - - +
5065u PHE 3.7 11.4 + - - +
5066u ILE* 3.1 50.5 - - + +
5068u TYR 4.7 0.2 + - - -
5071u LEU* 1.3 84.7 - - - +
5073u PRO* 1.3 101.3 - - + +
5074u THR 2.9 2.5 + - - -
5076u ALA* 3.0 25.7 + - + +
5075v ASN* 5.0 7.3 + - - -
5077v SER* 4.6 9.4 + - - -
5078v LEU* 4.5 13.5 - - + -
5107v THR* 5.6 2.7 - - + -
5108v TYR* 4.4 13.8 - - + -
5552v HEM 5.8 1.3 - - - -
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Residues in contact with PRO5073 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5324c LEU* 4.6 9.2 - - + +
5072u TYR* 1.3 120.1 - - + +
5074u THR* 1.3 62.8 + - - +
5076u ALA* 4.5 1.0 - - - +
5077u LYS* 3.8 17.2 + - - +
5107v THR* 3.2 32.3 - - + -
5108v TYR* 3.6 7.2 - - + +
5109v ASP* 3.0 43.1 - - + +
5112v GLN* 5.7 2.0 - - - +
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Residues in contact with THR5074 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5072u TYR 2.9 2.0 + - - -
5073u PRO* 1.3 74.5 - - - +
5075u LEU* 1.3 64.1 + - - +
5077u LYS* 3.7 7.1 + - - +
5078u LEU* 3.4 24.0 + - + +
5101u GLN* 4.0 21.8 - - - +
5109v ASP* 2.7 18.8 + - - -
5111v GLU* 3.4 30.7 + - - +
5112v GLN* 5.0 7.1 + - - +
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Residues in contact with LEU5075 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5070u GLY 4.4 9.4 - - - +
5071u LEU* 3.1 37.6 + - + +
5072u TYR 3.2 1.8 + - - -
5074u THR* 1.3 76.5 - - - +
5076u ALA* 1.3 55.3 + - - +
5078u LEU* 2.7 27.6 + - + +
5079u ILE* 2.7 42.4 + - + +
5094u ILE* 6.4 0.2 - - + -
5097u LEU* 4.3 1.6 - - + -
5101u GLN* 4.0 38.1 - - + +
5104u ILE* 4.5 11.2 - - + -
5105u LEU* 4.1 28.3 - - + -
5109v ASP* 4.8 0.4 + - - -
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Residues in contact with ALA5076 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5062u ILE* 3.7 15.0 - - + -
5065u PHE* 3.2 43.3 - - + -
5071u LEU 3.2 1.4 + - - -
5072u TYR* 3.0 23.6 + - + +
5073u PRO 4.5 0.4 - - - +
5075u LEU* 1.3 76.4 - - - +
5077u LYS* 1.3 58.1 - - - +
5079u ILE* 3.7 4.1 - - - +
5080u VAL* 2.9 35.9 + - - +
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Residues in contact with LYS5077 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5322c GLN 4.4 3.2 + - - -
5323c LYS* 4.6 4.4 - - - +
5324c LEU* 3.6 36.3 - - + +
5325c GLY* 3.6 20.5 - - - +
5062u ILE* 3.9 11.8 - - + +
5073u PRO 3.8 12.7 + - - +
5074u THR* 3.7 10.7 + - - +
5076u ALA* 1.3 78.2 - - - +
5078u LEU* 1.3 58.7 + - + +
5080u VAL* 4.3 1.1 - - - +
5081u LYS* 2.8 41.9 + - + +
5128u TYR* 5.4 0.6 + - - -
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Residues in contact with LEU5078 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5074u THR* 3.4 14.5 + - + +
5075u LEU* 2.7 29.1 + - + +
5077u LYS* 1.3 74.2 - - + +
5079u ILE* 1.3 68.1 + - - +
5081u LYS* 3.1 10.9 + - + -
5082u ASN* 2.7 37.0 + - - +
5094u ILE* 4.3 11.4 - - + -
5095u PRO 5.2 3.4 - - - +
5096u GLY 5.7 0.9 - - - +
5097u LEU* 3.4 31.6 - - + -
5101u GLN* 4.1 11.9 - - - +
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Residues in contact with ILE5079 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5057u LEU* 3.2 36.3 - - + +
5065u PHE* 3.6 35.2 - - + -
5071u LEU* 5.2 2.7 - - + -
5075u LEU* 2.7 33.3 + - + +
5076u ALA* 3.7 4.3 - - - +
5078u LEU* 1.3 73.2 - - + +
5080u VAL* 1.3 63.1 + - - +
5082u ASN* 3.0 3.1 + - - -
5083u ALA 4.4 0.5 - - - +
5085u TYR* 2.5 42.5 + - + -
5091u VAL* 4.4 12.8 - - + -
5094u ILE* 4.1 4.7 - - + +
5105u LEU* 4.2 21.1 - - + -
5112u PHE* 4.4 4.9 - - + -
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Residues in contact with VAL5080 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5057u LEU 5.2 0.2 - - - -
5062u ILE* 3.9 17.3 - - + -
5065u PHE* 3.7 22.0 - - + -
5076u ALA 2.9 16.7 + - - +
5077u LYS 4.3 1.6 - - - +
5079u ILE* 1.3 76.9 - - - +
5081u LYS* 1.3 58.2 + - - +
5082u ASN* 2.9 6.2 + - - -
5083u ALA* 4.1 6.9 + - - +
5127u ARG* 4.1 49.8 + - + +
5128u TYR* 3.6 33.5 + - + +
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Residues in contact with LYS5081 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5325c GLY* 2.7 39.0 + - - +
5326c ALA 4.8 1.4 + - - -
5327c ASN* 4.1 18.7 + - - +
5077u LYS* 2.8 32.2 + - + +
5078u LEU* 3.1 7.4 + - + +
5080u VAL* 1.3 74.6 - - - +
5082u ASN* 1.3 65.0 + - - +
5083u ALA 3.7 3.3 + - - -
5128u TYR* 3.9 10.3 + - - +
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Residues in contact with ASN5082 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5078u LEU* 2.7 30.5 + - - +
5079u ILE 3.0 0.8 + - - -
5080u VAL 2.9 4.2 + - - -
5081u LYS* 1.3 82.3 - - - +
5083u ALA* 1.3 74.9 + - - +
5084u PRO 3.8 1.0 - - - +
5085u TYR* 2.8 31.4 + - + +
5094u ILE* 3.3 33.2 - - + +
5095u PRO* 4.4 12.3 - - - +
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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