Contacts of the helix formed by residues 5041 - 5047 (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 GLY5041 (chain e).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5038e VAL* 2.6 23.3 + - - -
5039e SER 3.2 0.6 - - - -
5040e THR* 1.3 73.9 - - - +
5042e LEU* 1.3 65.5 + - - +
5043e ALA 3.4 1.6 - - - -
5044e TYR* 3.5 25.1 - - - +
5045e ASP* 3.1 17.8 - - - +
5051e ARG* 3.4 13.0 + - - -
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Residues in contact with LEU5042 (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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5037e PHE* 3.1 37.1 + - + +
5040e THR* 3.2 18.3 - - + -
5041e GLY* 1.3 76.1 - - - +
5043e ALA* 1.3 69.2 + - - +
5045e ASP* 2.9 25.9 + - + +
5046e VAL* 3.0 22.0 + - + +
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Residues in contact with ALA5043 (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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5054d PHE* 4.1 19.7 - - + -
5068d LEU* 4.3 10.5 - - + -
5037e PHE* 2.9 52.5 + - + +
5038e VAL* 4.3 7.6 - - + -
5041e GLY 5.1 0.2 - - - -
5042e LEU* 1.3 76.2 - - - +
5044e TYR* 1.3 67.6 + - + +
5046e VAL* 3.0 10.7 + - - +
5047e PHE* 3.0 17.3 + - - +
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Residues in contact with TYR5044 (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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5068d LEU* 3.3 44.4 + - + +
5038e VAL 5.0 4.9 - - - -
5041e GLY* 3.5 23.8 + - - +
5042e LEU 3.0 1.2 + - - -
5043e ALA* 1.3 82.0 - - + +
5045e ASP* 1.3 64.2 + - - +
5046e VAL 3.1 0.3 + - - -
5047e PHE 3.1 2.3 + - - -
5048e GLY* 3.1 19.8 + - - -
5049e THR* 3.4 26.4 + - + +
5050e PRO 4.3 10.3 - - - -
5051e ARG* 3.2 53.6 - - + +
5052e PRO* 4.0 9.5 - - + +
5043f ILE* 3.5 34.4 - - + +
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Residues in contact with ASP5045 (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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5102d THR* 3.6 9.4 + - - +
5041e GLY 3.1 16.1 - - - +
5042e LEU* 2.9 15.4 + - + +
5044e TYR* 1.3 72.4 - - - +
5046e VAL* 1.3 64.1 + - - +
5048e GLY* 3.9 4.4 + - - +
5051e ARG* 2.7 30.4 + - - -
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Residues in contact with VAL5046 (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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5101d PHE* 4.0 15.4 - - + -
5102d THR* 2.4 29.7 + - - -
5037e PHE* 3.8 24.2 - - + -
5042e LEU* 3.0 27.5 + - + +
5043e ALA 3.0 6.1 + - - +
5045e ASP* 1.3 76.3 - - - +
5047e PHE* 1.3 81.3 + - + +
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Residues in contact with PHE5047 (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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5050d THR* 4.0 25.4 - - + -
5054d PHE* 3.2 36.1 - + + +
5055d VAL* 3.4 37.2 - - + +
5056d THR* 4.7 0.9 + - - +
5101d PHE* 3.6 27.4 - + - -
5102d THR* 3.8 2.5 - - - -
5105d CYS* 3.9 15.9 - - - -
5106d GLN* 4.6 2.9 - - - +
5037e PHE* 3.9 21.8 - + - -
5043e ALA 3.0 18.3 + - - +
5044e TYR 3.4 0.2 - - - -
5046e VAL* 1.3 84.0 - - + +
5048e GLY* 1.3 51.2 + - - +
5049e THR* 2.5 33.4 + - - +
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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