Contacts of the helix formed by residues 5009 - 5016 (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 PRO5009 (chain e).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5005e THR* 6.0 5.8 - - + -
5007e GLU 3.2 10.5 - - - +
5008e ARG* 1.4 86.7 - - - +
5010e PHE* 1.3 64.3 + - + +
5011e SER* 4.7 4.9 - - - +
5012e ASP* 3.8 15.0 + - + +
5013e ILE* 3.3 23.3 + - - +
5013f TYR* 3.7 31.6 - - + +
5019f ARG* 4.9 1.6 - - - +
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Residues in contact with PHE5010 (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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5484c UNK 4.7 11.4 - - + -
5027d PHE* 4.2 17.5 - + - -
5009e PRO* 1.3 69.5 - - - +
5011e SER* 1.3 69.9 + - - +
5012e ASP 3.0 1.8 - - - -
5013e ILE* 2.8 16.1 - - + +
5014e ILE* 2.8 39.2 + - + +
5019f ARG* 3.0 53.6 - - - -
5023f VAL* 3.9 19.5 - - + -
5051f HEM 3.7 37.5 - - + -
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Residues in contact with SER5011 (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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5009e PRO* 3.6 3.8 - - - +
5010e PHE* 1.3 79.6 - - - +
5012e ASP* 1.3 65.8 + - - +
5014e ILE* 3.7 7.3 + - - +
5015e THR* 3.1 21.3 + - - -
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Residues in contact with ASP5012 (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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5009e PRO* 3.8 20.1 + - + +
5010e PHE 3.0 0.4 - - - -
5011e SER* 1.3 77.7 - - - +
5013e ILE* 1.3 55.6 + - - +
5015e THR* 2.6 33.3 + - - -
5016e SER* 3.0 11.3 + - - -
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Residues in contact with ILE5013 (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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5008e ARG* 5.2 8.7 - - + -
5009e PRO 3.3 8.8 + - - +
5010e PHE* 2.8 47.9 + - + +
5012e ASP* 1.3 78.5 - - - +
5014e ILE* 1.3 63.5 + - + +
5016e SER* 2.6 30.6 + - - +
5019e TYR* 3.1 19.5 - - + +
5051f HEM 3.0 75.6 - - + +
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Residues in contact with ILE5014 (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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5010e PHE* 2.8 36.3 + - + +
5011e SER* 4.0 6.1 - - - +
5013e ILE* 1.3 79.4 - - + +
5015e THR* 1.3 57.5 + - - +
5019e TYR* 4.7 7.4 - - + -
5020e TRP* 2.6 39.6 + - + -
5051f HEM 5.3 9.2 - - + -
5010j LEU* 6.0 1.3 - - - -
5013j VAL* 3.2 37.7 - - + +
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Residues in contact with THR5015 (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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5011e SER 3.1 13.0 + - - -
5012e ASP* 2.6 18.8 + - - -
5014e ILE* 1.3 75.3 - - - +
5016e SER* 1.3 56.4 + - - -
5017e VAL 3.4 0.9 + - - -
5007j ARG* 3.1 26.1 - - - +
5008j ILE* 2.8 55.2 + - - +
5009j PRO* 4.6 1.2 - - + -
5010j LEU* 4.6 9.7 + - - +
5013j VAL* 4.9 0.2 - - - -
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Residues in contact with SER5016 (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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5012e ASP 3.0 9.5 + - - -
5013e ILE* 2.6 29.9 + - - +
5014e ILE 3.3 0.2 - - - -
5015e THR* 1.3 75.9 - - - +
5017e VAL* 1.3 67.8 + - - +
5018e ARG* 4.2 7.5 - - - +
5019e TYR* 2.9 27.3 + - - +
5020e TRP* 3.1 15.9 - - - -
5051f HEM 5.3 2.1 + - - -
5007j ARG* 4.9 2.0 - - - +
5008j ILE* 3.6 0.4 - - - -
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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