Contacts of the helix formed by residues 5087 - 5094 (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 SER5087 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5085u TYR* 2.9 6.3 - - - +
5086u GLU* 1.3 86.0 - - - +
5088u VAL* 1.3 69.2 + - - +
5089u GLU* 3.9 13.3 + - - -
5090u ASP* 2.5 44.9 + - - +
5114u VAL* 4.2 12.3 - - - -
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Residues in contact with VAL5088 (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* 4.2 9.0 - - - -
5087u SER* 1.3 70.1 - - - +
5089u GLU* 1.3 77.3 + - - +
5090u ASP 2.9 0.9 + - - -
5091u VAL* 2.8 27.0 + - - +
5109u LEU* 3.8 41.6 - - + +
5112u PHE* 4.0 14.4 - - + +
5113u THR* 4.1 28.0 - - - +
5114u VAL* 4.0 5.8 - - + +
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Residues in contact with GLU5089 (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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5087u SER* 3.9 18.4 + - - -
5088u VAL* 1.3 85.3 + - - +
5090u ASP* 1.3 53.7 + - - +
5091u VAL 2.6 0.2 + - - -
5092u LEU* 2.6 59.9 + - + +
5093u ASN* 4.4 3.2 + - - +
5109u LEU* 4.5 10.8 - - + +
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Residues in contact with ASP5090 (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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5085u TYR* 3.9 24.7 - - + -
5086u GLU* 3.9 22.6 + - - +
5087u SER* 2.5 49.7 + - - +
5089u GLU* 1.3 71.2 - - - +
5091u VAL* 1.3 63.3 + - - +
5093u ASN* 3.0 34.4 + - - +
5094u ILE 4.0 0.5 + - - -
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Residues in contact with VAL5091 (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* 3.3 29.4 - - + -
5079u ILE* 4.4 13.2 - - + -
5085u TYR* 4.1 13.6 - - + -
5088u VAL 2.8 24.6 + - - +
5089u GLU 2.6 5.0 + - - +
5090u ASP* 1.3 74.4 - - - +
5092u LEU* 1.3 54.2 + - - +
5093u ASN 2.6 11.8 + - - -
5094u ILE* 2.8 38.2 + - + +
5097u LEU* 3.6 3.7 - - - +
5105u LEU* 3.5 35.4 - - + -
5109u LEU* 4.5 11.7 - - + -
5112u PHE* 4.6 1.1 - - + -
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Residues in contact with LEU5092 (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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5089u GLU* 2.6 34.5 + - + +
5091u VAL* 1.3 71.6 - - - +
5093u ASN* 1.3 64.7 + - - +
5094u ILE 3.4 1.6 + - - +
5097u LEU* 3.9 12.8 - - - +
5102u LYS* 4.1 22.6 - - + +
5105u LEU* 3.9 24.0 - - + -
5106u ARG* 3.7 38.8 - - + +
5109u LEU* 3.8 25.6 - - + -
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Residues in contact with ASN5093 (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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5089u GLU* 4.4 2.8 + - - +
5090u ASP* 3.0 31.3 + - - +
5091u VAL 2.6 7.1 + - - -
5092u LEU* 1.3 82.7 - - - +
5094u ILE* 1.3 63.7 + - - -
5095u PRO* 3.5 5.2 - - - +
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Residues in contact with ILE5094 (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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5075u LEU* 6.4 0.4 - - + -
5078u LEU* 4.2 12.8 - - + +
5079u ILE* 4.1 12.6 - - + +
5082u ASN* 3.3 25.8 - - + +
5085u TYR* 3.3 33.4 - - + +
5090u ASP 4.6 0.7 - - - +
5091u VAL* 2.8 38.9 + - + +
5092u LEU 3.4 2.1 - - - +
5093u ASN* 1.3 73.0 - - - +
5095u PRO* 1.3 87.6 - - + +
5096u GLY 3.7 0.3 + - - -
5097u LEU* 3.1 35.9 + - + +
5105u LEU* 5.5 1.1 - - + -
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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