Contacts of the helix formed by residues 5410 - 5422 (chain b) in PDB entry 3A0B
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 ASP5410 (chain b).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5408b PHE* 4.7 4.5 - - - +
5409b THR* 1.3 83.3 + - - +
5411b PRO* 1.4 74.7 - - + +
5412b PRO* 2.9 16.6 - - + +
5413b THR* 2.8 42.5 + - - +
5414b VAL 3.5 1.4 + - - -
5038u GLU* 5.8 0.5 - - - +
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Residues in contact with PRO5411 (chain b).
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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5389b PHE* 5.5 0.7 - - + -
5390b GLU* 3.3 47.6 - - + +
5393b GLY* 6.1 0.9 - - - -
5394b VAL 5.8 2.0 - - - +
5409b THR 3.0 10.2 - - - +
5410b ASP* 1.4 80.0 - - + -
5412b PRO* 1.3 72.5 - - + +
5413b THR 3.1 0.3 + - - -
5414b VAL* 3.2 11.2 + - + +
5415b LYS* 2.6 30.4 + - + +
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Residues in contact with PRO5412 (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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5410b ASP* 3.0 18.8 - - + +
5411b PRO* 1.3 96.0 - - + +
5413b THR* 1.3 51.7 + - - +
5415b LYS* 3.0 11.1 + - + +
5416b SER* 2.7 34.2 + - - -
5419b ARG* 5.3 0.3 + - - -
5038u GLU* 5.2 11.0 - - - +
5040u VAL* 5.0 19.5 - - + -
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Residues in contact with THR5413 (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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5408b PHE* 3.7 25.7 - - + -
5410b ASP* 2.8 34.3 + - - -
5412b PRO* 1.3 76.1 - - - +
5414b VAL* 1.3 56.7 + - - +
5416b SER* 2.4 40.8 + - - -
5417b TYR* 2.9 35.3 + - + -
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Residues in contact with VAL5414 (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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5389b PHE* 3.2 11.5 - - + -
5394b VAL* 3.1 29.4 - - + +
5395b THR* 3.3 13.9 - - - -
5396b VAL* 3.1 54.2 - - + +
5408b PHE* 3.9 7.5 - - - +
5409b THR 4.4 4.9 - - - +
5410b ASP 3.5 5.0 + - - +
5411b PRO* 3.2 16.7 + - + +
5413b THR* 1.3 80.4 - - - +
5415b LYS* 1.3 66.1 + - - +
5417b TYR* 3.7 2.1 + - - +
5418b ALA* 3.3 21.7 + - - +
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Residues in contact with LYS5415 (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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5378b ILE* 3.5 38.8 - - + +
5379b PRO* 5.0 5.9 - - - +
5382b ARG* 4.4 8.9 - - - +
5388b SER* 5.3 0.2 + - - -
5389b PHE* 3.8 20.6 - - + -
5390b GLU* 3.5 26.2 + - - -
5411b PRO* 2.6 20.6 + - + +
5412b PRO* 3.1 12.8 - - + +
5414b VAL* 1.3 72.8 - - - +
5416b SER* 1.3 67.1 + - - +
5418b ALA* 3.3 3.5 + - - +
5419b ARG* 3.3 23.7 + - - +
5195o ASP* 4.5 12.5 + - - +
5044u ASP* 2.4 36.8 + - - +
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Residues in contact with SER5416 (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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5412b PRO 2.7 12.4 + - - -
5413b THR* 2.4 30.0 + - - -
5415b LYS* 1.3 68.8 - - - +
5417b TYR* 1.3 71.6 + - - -
5419b ARG* 2.8 42.8 + - - +
5420b LYS* 3.2 10.7 + - - +
5205o GLU* 5.0 6.7 + - - -
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Residues in contact with TYR5417 (chain b).
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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5338b LYS* 4.0 25.2 + - + -
5343b PHE* 4.0 4.9 - - + -
5396b VAL* 4.4 17.5 - - + -
5398b PHE* 3.3 31.4 - + + -
5403b LEU* 3.0 30.2 - - + +
5408b PHE* 4.0 14.1 - + - -
5413b THR* 2.9 42.0 + - + +
5414b VAL 4.3 3.1 - - - +
5416b SER* 1.3 84.4 + - - +
5418b ALA* 1.3 56.9 + - - +
5420b LYS* 3.1 8.3 + - + +
5421b ALA* 2.8 28.8 + - - +
5426b ILE* 4.4 16.8 - - + +
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Residues in contact with ALA5418 (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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5343b PHE* 3.1 32.4 - - + -
5353b VAL* 4.2 1.6 - - + +
5365b VAL* 3.8 13.7 - - + -
5389b PHE* 3.7 20.2 - - + -
5414b VAL 3.3 13.1 + - - +
5415b LYS 3.6 5.2 - - - +
5416b SER 3.2 0.6 - - - -
5417b TYR* 1.3 77.0 - - - +
5419b ARG* 1.3 58.1 + - - +
5421b ALA* 3.1 18.5 + - - +
5422b ILE* 3.2 17.5 - - - +
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Residues in contact with ARG5419 (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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5365b VAL* 4.2 8.5 - - + +
5378b ILE* 4.9 5.2 - - + +
5412b PRO 5.3 0.2 + - - -
5415b LYS* 3.3 10.2 + - - +
5416b SER* 2.8 52.5 + - - +
5418b ALA* 1.3 79.4 - - - +
5420b LYS* 1.3 79.2 + - - +
5421b ALA 3.2 0.9 - - - -
5422b ILE* 3.5 15.5 - - + +
5423b PHE* 3.2 24.4 - - + -
5195o ASP* 3.0 28.3 + - - +
5196o SER* 4.6 13.6 + - - +
5201o PRO 5.4 0.4 - - - -
5205o GLU* 3.7 27.8 + - - -
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Residues in contact with LYS5420 (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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5416b SER* 3.2 8.5 + - - +
5417b TYR* 3.1 11.2 + - + +
5419b ARG* 1.3 106.3 - - - +
5421b ALA* 1.3 56.2 + - - +
5422b ILE 3.4 1.3 - - - -
5423b PHE* 3.5 24.2 - - + +
5424b GLY 4.3 1.0 + - - -
5426b ILE* 2.8 47.6 - - + +
5201o PRO 3.2 20.0 + - - -
5202o GLN* 3.4 29.9 + - - +
5203o ALA 4.7 7.4 + - - -
5205o GLU* 3.4 23.1 + - - +
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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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5341b ALA 5.8 0.7 - - - +
5343b PHE* 3.9 9.4 - - + -
5353b VAL* 3.8 25.8 - - + +
5355b ARG* 4.6 4.2 + - - +
5417b TYR 2.8 12.6 + - - +
5418b ALA* 3.1 18.8 + - - +
5420b LYS* 1.3 76.5 - - - +
5422b ILE* 1.3 53.0 + - - +
5423b PHE 2.9 5.4 - - - -
5424b GLY* 2.6 37.9 + - - +
5426b ILE* 3.7 10.3 - - + -
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Residues in contact with ILE5422 (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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5272b TRP* 4.1 4.0 - - - -
5353b VAL* 4.3 9.4 - - + -
5354b ARG 3.4 19.1 - - - +
5355b ARG* 3.8 11.8 - - - +
5356b MET* 3.4 49.7 + - + +
5363b PHE* 4.0 19.1 - - + +
5365b VAL* 3.3 30.1 - - + +
5366b ILE 4.7 0.2 - - - +
5418b ALA 3.2 17.7 - - - +
5419b ARG* 3.5 20.6 - - + +
5421b ALA* 1.3 77.4 - - - +
5423b PHE* 1.3 62.0 + - + +
5424b GLY 3.2 3.5 + - - -
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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