Contacts of the helix formed by residues 5208 - 5213 (chain o) 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 LEU5208 (chain o).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5306d ALA* 4.1 23.1 - - + +
5307d GLU* 4.0 29.2 - - + +
5197o ALA* 3.5 31.9 - - + -
5200o LEU* 4.2 10.1 - - + -
5203o ALA* 5.5 4.7 - - + -
5204o LYS 4.2 14.4 - - - +
5205o GLU* 2.8 9.4 + - - +
5207o GLU* 1.3 83.8 - - + +
5209o ALA* 1.3 69.3 + - - +
5210o ARG 3.3 2.5 - - - -
5211o ALA* 3.1 9.1 + - + +
5212o ASN* 3.0 32.8 + - - +
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Residues in contact with ALA5209 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5205o GLU 3.0 7.9 + - - +
5206o GLU* 3.5 16.4 - - - +
5207o GLU 3.4 0.8 - - - -
5208o LEU* 1.3 76.1 - - - +
5210o ARG* 1.3 67.1 + - - +
5212o ASN* 2.7 19.4 + - - +
5213o VAL* 3.1 19.6 + - + +
5039u LEU* 3.9 13.9 - - + -
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Residues in contact with ARG5210 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5207o GLU* 4.8 6.0 + - - +
5208o LEU 4.7 1.6 - - - +
5209o ALA* 1.3 79.4 - - - +
5211o ALA* 1.3 59.3 + - + +
5213o VAL 3.4 17.2 - - - +
5214o LYS* 5.9 0.2 - - - +
5215o ARG* 3.1 28.5 + - - +
5251o MET 5.4 0.3 - - - +
5252o GLY 3.0 21.4 + - - +
5253o ALA* 3.0 37.5 + - + +
5254o HIS* 3.5 15.8 + - - +
5255o GLU* 4.3 12.5 + - - +
5039u LEU* 3.5 13.1 - - + +
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Residues in contact with ALA5211 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5306d ALA 3.9 14.4 - - - +
5307d GLU* 3.8 22.0 - - - +
5309d PRO* 4.2 11.2 - - + -
5188o ARG* 3.7 12.4 - - - +
5208o LEU* 3.1 8.8 + - + +
5210o ARG* 1.3 79.4 - - + +
5212o ASN* 1.3 62.7 + - - +
5213o VAL 3.4 0.9 - - - -
5214o LYS* 2.9 31.2 + - - +
5253o ALA* 5.4 4.9 - - + -
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Residues in contact with ASN5212 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5188o ARG* 3.0 39.7 + - - +
5189o GLY 5.5 1.7 - - - +
5194o TYR 4.9 4.2 - - - +
5195o ASP* 3.8 21.6 - - - +
5196o SER* 3.7 15.1 - - - -
5197o ALA* 3.6 14.7 + - - +
5205o GLU* 4.7 9.1 + - - +
5208o LEU* 3.0 35.1 + - - +
5209o ALA* 2.7 11.9 + - - +
5211o ALA* 1.3 74.0 - - - +
5213o VAL* 1.3 64.6 + - + +
5214o LYS* 3.8 6.2 + - - +
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Residues in contact with VAL5213 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5209o ALA* 3.1 15.3 + - + +
5210o ARG 3.4 15.3 - - - +
5212o ASN* 1.3 82.1 - - + +
5214o LYS* 1.3 66.6 + - - +
5215o ARG* 3.4 13.4 + - + -
5251o MET 4.4 1.2 - - - +
5039u LEU* 3.8 24.2 - - + +
5040u VAL 3.6 40.8 - - - +
5041u ASN* 3.7 10.8 - - + +
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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