Contacts of the helix formed by residues 5063 - 5068 (chain v) 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 CYS5063 (chain v).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5058v LEU 4.3 0.9 - - - -
5059v PHE* 2.6 67.2 + - + +
5060v GLN 4.3 0.2 + - - -
5061v TYR 3.9 0.4 - - - -
5062v ALA* 1.3 74.3 - - - +
5064v ALA* 1.3 69.2 + - - +
5065v SER* 2.5 8.0 + - - -
5066v CYS* 2.6 16.5 + - - +
5067v HIS* 3.0 11.0 + - + -
5141v ILE* 3.8 6.7 - - - -
5552v HEM 3.2 41.7 - - + +
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Residues in contact with ALA5064 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5416c SER* 4.1 11.9 - - - +
5417c VAL* 4.2 9.2 - - + -
5059v PHE* 3.0 12.5 + - + -
5060v GLN* 3.7 28.4 - - + +
5063v CYS* 1.3 74.1 - - - +
5065v SER* 1.3 54.2 + - - +
5066v CYS* 2.5 13.7 + - - -
5067v HIS 3.0 1.3 + - - -
5068v VAL* 2.6 51.5 + - + +
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Residues in contact with SER5065 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5394c GLU* 5.5 0.7 + - - -
5397c THR* 3.6 35.5 + - - +
5398c HIS* 3.7 20.9 + - - -
5417c VAL* 4.3 19.2 - - - +
5060v GLN 4.6 4.1 + - - -
5062v ALA 5.2 2.7 - - - -
5063v CYS 2.5 7.6 + - - -
5064v ALA* 1.3 73.8 - - - +
5066v CYS* 1.3 59.0 + - - +
5068v VAL* 4.8 0.2 - - - -
5073v LYS* 4.3 11.6 + - - +
5129v LYS* 4.9 13.0 - - - -
5552v HEM 4.7 10.1 - - - +
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Residues in contact with CYS5066 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5397c THR* 4.6 3.6 - - + +
5063v CYS 2.6 7.3 + - - +
5064v ALA 2.5 5.2 + - - -
5065v SER* 1.3 75.6 - - - +
5067v HIS* 1.3 56.9 + - - +
5068v VAL 3.6 1.1 - - - -
5071v ILE 4.2 0.2 - - - -
5072v THR* 3.4 8.1 - - - -
5073v LYS* 3.0 36.5 + - - +
5074v THR* 3.6 32.8 - - - -
5552v HEM 3.5 58.6 - - + -
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Residues in contact with HIS5067 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5059v PHE* 3.8 24.1 - - + -
5063v CYS* 3.0 7.9 + - + +
5064v ALA* 3.0 5.5 + - - -
5066v CYS* 1.3 78.0 + - - +
5068v VAL* 1.3 69.1 + - - +
5069v GLY 3.3 0.2 + - - -
5070v GLY* 2.8 15.0 + - - -
5071v ILE 2.7 23.8 + - - +
5072v THR* 3.2 17.9 + - + -
5080v LEU* 3.8 17.0 - - + +
5552v HEM 2.1 96.2 + + + -
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Residues in contact with VAL5068 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5413c GLU* 4.1 17.7 - - - +
5414c ILE* 4.7 6.1 - - + -
5416c SER* 3.6 23.3 - - - +
5417c VAL* 3.8 14.8 - - + -
5059v PHE* 5.1 1.8 - - - -
5064v ALA* 2.6 41.1 + - + +
5065v SER 4.8 0.4 - - - -
5066v CYS 3.6 0.2 - - - -
5067v HIS* 1.3 76.1 - - - +
5069v GLY* 1.3 59.9 + - - +
5070v GLY 2.9 6.1 + - - -
5071v ILE* 3.1 20.5 - - + +
5073v LYS* 3.6 35.2 - - - +
5163v TYR* 5.0 1.6 + - - +
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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