Contacts of the helix formed by residues 5413 - 5425 (chain b) 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 ASP5413 (chain b).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5411b PHE* 3.6 2.8 - - + -
5412b THR* 1.3 78.0 + - - +
5414b PRO* 1.3 74.9 - - - +
5415b PRO* 3.1 20.7 - - - +
5416b THR* 2.9 40.3 + - - +
5417b VAL* 3.1 10.1 + - - +
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Residues in contact with PRO5414 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5392b PHE* 5.5 4.5 - - + -
5393b GLU* 3.4 45.5 - - + +
5397b VAL 5.9 0.7 - - - +
5412b THR 3.3 11.0 - - - +
5413b ASP* 1.3 87.2 - - - +
5415b PRO* 1.3 73.0 - - + +
5417b VAL* 3.0 8.3 + - + +
5418b LYS* 2.8 31.1 + - + +
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Residues in contact with PRO5415 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5413b ASP* 3.0 21.7 - - - +
5414b PRO* 1.3 89.8 - - + +
5416b THR* 1.3 58.9 + - - +
5418b LYS* 3.0 19.1 + - - +
5419b SER* 2.8 30.6 + - - -
5422b ARG* 5.1 1.0 + - - -
5038u GLU* 6.0 2.5 - - - +
5040u VAL* 6.5 0.4 - - + -
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Residues in contact with THR5416 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5411b PHE* 3.7 27.8 - - + -
5413b ASP* 2.9 29.5 + - - -
5415b PRO* 1.3 75.5 - - - +
5417b VAL* 1.3 63.5 + - - +
5419b SER* 3.6 6.9 - - - -
5420b TYR* 3.0 56.8 + - + -
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Residues in contact with VAL5417 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5346b PHE* 3.8 6.9 - - + -
5392b PHE* 3.9 22.7 - - + -
5397b VAL* 4.0 9.2 - - + +
5398b THR* 3.9 20.4 - - - +
5399b VAL* 3.8 22.0 - - + -
5411b PHE 3.7 21.3 - - - +
5412b THR 3.9 5.2 - - - -
5413b ASP 3.1 24.6 + - - +
5414b PRO* 3.0 7.3 + - + +
5416b THR* 1.3 77.9 - - - +
5418b LYS* 1.3 65.4 + - - +
5420b TYR* 3.3 2.8 + - - +
5421b ALA* 2.9 20.8 + - - +
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Residues in contact with LYS5418 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5381b ILE* 3.9 31.6 - - + -
5392b PHE* 3.5 30.5 - - + -
5393b GLU* 2.7 27.9 + - - +
5414b PRO* 2.8 26.5 + - - +
5415b PRO* 3.4 16.2 - - + +
5417b VAL* 1.3 74.3 - - - +
5419b SER* 1.3 69.4 + - - +
5421b ALA* 2.7 15.3 + - - +
5422b ARG* 2.9 21.2 + - - +
5195o ASP* 4.6 11.6 + - - +
5044u ASP* 4.0 22.2 + - - +
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Residues in contact with SER5419 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5415b PRO 2.8 19.0 + - - -
5416b THR* 3.6 9.2 - - - -
5418b LYS* 1.3 74.9 - - - +
5420b TYR* 1.3 67.2 + - - +
5422b ARG* 3.1 34.4 + - - +
5423b LYS* 3.3 18.8 + - - +
5205o GLU* 3.4 21.1 + - - -
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Residues in contact with TYR5420 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5341b LYS* 3.3 32.0 + - - -
5346b PHE* 3.7 12.0 - - + -
5399b VAL* 4.7 5.8 - - + -
5401b PHE* 3.3 36.1 - + + -
5406b LEU* 3.3 24.6 - - + +
5411b PHE* 4.3 13.5 - + - -
5416b THR* 3.0 45.7 + - + +
5417b VAL* 3.6 5.2 - - - +
5419b SER* 1.3 84.3 - - - +
5421b ALA* 1.3 60.7 + - - +
5423b LYS* 3.5 5.3 + - + +
5424b ALA* 3.2 17.3 + - - +
5429b ILE* 3.3 24.4 - - + +
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Residues in contact with ALA5421 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5346b PHE* 3.6 21.1 - - + -
5356b VAL* 3.8 11.6 - - + +
5368b VAL* 4.0 13.8 - - + +
5370b LEU* 5.2 0.4 - - + -
5381b ILE* 5.1 0.7 - - + -
5392b PHE* 3.9 23.8 - - + -
5417b VAL 2.9 12.9 + - - +
5418b LYS* 2.7 16.0 + - - +
5420b TYR* 1.3 69.9 - - - +
5422b ARG* 1.3 58.5 + - - +
5424b ALA* 3.0 21.1 + - - +
5425b ILE* 3.3 5.2 + - - +
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Residues in contact with ARG5422 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5368b VAL* 4.4 12.6 - - + -
5381b ILE* 4.1 20.3 - - + +
5415b PRO 5.1 0.6 + - - -
5418b LYS* 2.9 11.8 + - - +
5419b SER* 3.4 30.4 - - - +
5421b ALA* 1.3 76.0 - - - +
5423b LYS* 1.3 71.4 + - - +
5424b ALA 3.5 0.3 + - - -
5425b ILE* 3.6 22.5 - - + +
5426b PHE* 4.0 12.1 - - - -
5195o ASP* 3.5 29.8 + - - +
5196o SER* 4.3 22.2 + - - -
5205o GLU* 2.8 30.1 + - - -
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Residues in contact with LYS5423 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5314b TYR* 5.9 0.2 - - - -
5419b SER* 3.3 17.1 + - - +
5420b TYR* 3.9 9.0 - - + +
5421b ALA 3.2 0.6 - - - -
5422b ARG* 1.3 88.3 - - - +
5424b ALA* 1.3 62.5 + - - +
5425b ILE 3.3 0.2 - - - -
5426b PHE* 3.5 24.7 + - + +
5427b GLY 3.9 2.3 - - - +
5428b GLU 5.0 0.5 - - - +
5429b ILE* 3.6 28.3 - - + +
5201o PRO 3.7 14.5 + - - -
5202o GLN* 3.0 33.9 - - - +
5203o ALA 4.8 8.2 + - - -
5205o GLU* 3.3 27.9 + - - +
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Residues in contact with ALA5424 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5344b ALA* 5.8 0.4 - - + -
5346b PHE* 4.0 9.9 - - + -
5356b VAL* 3.7 25.7 - - + +
5358b ARG* 4.8 3.3 + - - +
5420b TYR 3.2 13.9 + - - +
5421b ALA 3.0 14.5 + - - +
5423b LYS* 1.3 74.8 - - - +
5425b ILE* 1.3 54.6 + - - +
5426b PHE 2.9 2.2 - - - -
5427b GLY* 2.5 39.0 + - - +
5429b ILE* 4.0 7.6 - - + -
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Residues in contact with ILE5425 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5275b TRP* 4.2 1.2 - - - -
5356b VAL* 3.9 16.0 - - + +
5357b ARG 3.7 16.6 - - - +
5358b ARG* 3.5 9.8 - - - +
5359b MET* 3.1 45.4 + - + +
5366b PHE* 3.6 22.2 - - + +
5367b PRO 3.3 28.5 - - - +
5368b VAL* 3.9 8.7 - - + -
5421b ALA 3.3 4.3 + - - +
5422b ARG* 3.6 16.6 - - + +
5424b ALA* 1.3 77.5 - - - +
5426b PHE* 1.3 70.3 + - + +
5427b GLY 3.2 4.3 + - - -
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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