Contacts of the helix formed by residues 4133 - 4148 (chain F) in PDB entry 1Y1S
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 ASP4133 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4132F ALA* 1.3 71.9 - - - +
4134F PHE* 1.3 67.7 + - - +
4135F ALA* 2.9 14.0 + - - +
4136F CYS* 2.7 35.9 + - - +
4137F THR* 2.9 25.7 + - - -
4211F LEU 5.2 0.7 - - - +
4212F ARG* 3.8 25.1 - - - +
4213F ALA* 2.8 34.3 + - - +
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Residues in contact with PHE4134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6111B THR* 4.4 10.9 - - + +
6134B PHE* 4.2 12.8 - + - -
6137B THR* 3.5 32.3 - - + -
6138B THR* 3.9 25.4 - - + -
6141B VAL* 3.6 37.7 - - + -
6153B VAL* 4.1 24.2 - - + -
4132F ALA 3.6 3.4 + - - -
4133F ASP* 1.3 75.7 + - - +
4135F ALA* 1.3 65.8 + - + +
4137F THR* 3.3 4.6 + - - -
4138F THR* 2.8 48.3 + - + -
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Residues in contact with ALA4135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4133F ASP* 2.9 12.4 + - - +
4134F PHE* 1.3 83.3 - - + +
4136F CYS* 1.3 62.9 + - - +
4138F THR* 3.7 6.3 - - - -
4139F ALA* 3.1 19.4 + - - +
4212F ARG* 3.6 22.2 - - - +
4252F LEU* 3.6 13.1 - - + +
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Residues in contact with CYS4136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4088F THR* 3.8 18.2 - - - -
4090F LEU* 4.0 7.2 - - + -
4133F ASP* 2.7 28.8 + - - +
4135F ALA* 1.3 75.2 - - - +
4137F THR* 1.3 62.4 + - - +
4139F ALA* 3.5 1.7 + - - +
4140F LEU* 3.0 30.5 + - - +
4212F ARG* 3.7 11.4 - - - -
4213F ALA* 3.6 38.8 - - - +
4214F GLY* 3.7 10.1 - - - +
4252F LEU* 3.9 15.7 - - - +
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Residues in contact with THR4137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6134B PHE* 3.9 24.5 - - + -
4109F VAL* 3.6 20.9 - - + -
4110F THR 4.1 6.4 + - - +
4111F THR* 4.7 7.8 - - + -
4132F ALA* 3.5 21.3 - - - +
4133F ASP 2.9 17.8 + - - -
4134F PHE* 3.8 5.6 - - - -
4136F CYS* 1.3 76.4 - - - +
4138F THR* 1.3 57.7 + - - +
4140F LEU* 3.4 10.9 + - - +
4141F VAL* 3.0 36.7 + - + +
4153F VAL* 4.6 5.2 - - + -
4214F GLY* 5.1 0.5 - - - -
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Residues in contact with THR4138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6134B PHE* 3.9 17.8 - - + -
6138B THR* 6.4 2.0 - - + -
4134F PHE* 2.8 45.6 + - + -
4135F ALA* 3.7 7.6 - - - -
4137F THR* 1.3 77.3 - - - +
4139F ALA* 1.3 53.7 + - - +
4141F VAL* 3.1 4.3 + - - +
4142F GLU* 2.7 52.7 + - + +
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Residues in contact with ALA4139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4135F ALA 3.1 13.9 + - - +
4136F CYS 3.9 3.4 - - - +
4138F THR* 1.3 79.3 - - - +
4140F LEU* 1.3 53.1 + - - +
4142F GLU* 3.5 7.5 - - - +
4143F ALA* 2.6 37.8 + - - +
4248F ALA* 3.7 25.1 - - - +
4251F ARG* 3.8 21.7 - - + +
4252F LEU* 4.0 10.5 - - + -
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Residues in contact with LEU4140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4090F LEU* 4.4 10.8 - - + -
4109F VAL* 4.1 18.1 - - + +
4136F CYS 3.0 26.6 + - - +
4137F THR* 3.6 5.4 - - - +
4138F THR 3.2 0.2 - - - -
4139F ALA* 1.3 76.3 - - - +
4141F VAL* 1.3 61.9 + - - +
4143F ALA* 3.5 0.6 + - - -
4144F ALA* 3.1 22.5 + - - +
4214F GLY* 3.8 9.9 - - - -
4215F MET 3.4 41.3 - - - +
4216F VAL* 3.8 26.5 - - + -
4244F ILE* 3.7 9.7 - - + +
4245F VAL* 4.5 7.9 - - + -
4248F ALA* 3.5 23.8 - - + -
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Residues in contact with VAL4141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6134B PHE* 4.1 27.6 - - + -
4109F VAL* 4.1 15.3 - - + -
4137F THR* 3.0 22.1 + - + +
4138F THR 3.5 3.8 - - - +
4140F LEU* 1.3 75.3 - - - +
4142F GLU* 1.3 66.9 + - - +
4144F ALA* 3.3 15.7 + - - +
4145F LYS* 3.3 28.2 + - + +
4151F THR* 5.5 3.1 - - + -
4153F VAL* 3.7 32.3 - - + -
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Residues in contact with GLU4142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6134B PHE* 5.9 1.9 - - - -
4138F THR* 2.7 39.1 + - + +
4139F ALA* 3.6 6.3 - - - +
4141F VAL* 1.3 74.4 - - - +
4143F ALA* 1.3 64.6 + - - +
4145F LYS* 3.0 50.2 + - - +
4146F SER* 3.2 13.9 + - - -
4251F ARG* 3.6 30.1 + - - +
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Residues in contact with ALA4143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4139F ALA 2.6 21.2 + - - +
4140F LEU 3.7 4.9 - - - +
4142F GLU* 1.3 71.6 - - - +
4144F ALA* 1.3 56.9 + - - +
4146F SER* 3.2 3.0 + - - -
4147F ILE* 3.0 33.8 + - - +
4244F ILE* 3.2 29.8 - - + +
4247F GLU* 3.6 17.0 - - + -
4248F ALA* 3.6 14.6 - - - +
4251F ARG* 4.0 3.5 - - - +
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Residues in contact with ALA4144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4107F VAL* 5.2 1.1 - - + -
4109F VAL* 5.5 0.7 - - + -
4140F LEU 3.1 14.4 + - - +
4141F VAL 3.4 10.5 - - - +
4142F GLU 3.1 0.4 - - - -
4143F ALA* 1.3 76.2 - - - +
4145F LYS* 1.3 60.0 + - + +
4148F GLY* 2.8 27.5 + - - -
4149F ALA* 3.5 7.1 + - - +
4151F THR* 3.3 34.5 + - + +
4244F ILE* 4.0 22.9 - - + -
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Residues in contact with LYS4145 (chain F).
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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4141F VAL* 3.5 23.3 - - + +
4142F GLU* 3.0 43.4 + - - +
4144F ALA* 1.3 76.2 - - - +
4146F SER* 1.3 66.1 + - - +
4148F GLY* 3.4 10.9 + - - -
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Residues in contact with SER4146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4142F GLU 3.2 4.7 + - - -
4143F ALA* 3.4 11.0 - - - -
4145F LYS* 1.3 81.8 - - - +
4147F ILE* 1.3 68.4 + - - +
4148F GLY* 4.2 0.5 - - - -
4247F GLU* 4.4 15.6 + - - -
4251F ARG* 3.5 24.1 + - - -
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Residues in contact with ILE4147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4143F ALA 3.0 16.6 + - - +
4146F SER* 1.3 77.4 - - - +
4148F GLY* 1.3 63.9 + - - +
4240F HIS* 3.9 27.7 + - + -
4243F LYS* 3.8 38.4 - - + +
4244F ILE* 3.7 28.7 - - + -
4247F GLU* 4.2 14.8 - - + +
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Residues in contact with GLY4148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4144F ALA 2.8 12.7 + - - -
4145F LYS* 3.7 9.0 - - - -
4146F SER 3.1 3.4 - - - -
4147F ILE* 1.3 81.6 - - - +
4149F ALA* 1.3 61.2 + - - -
4240F HIS* 2.9 21.8 + - - -
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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