Contacts of the helix formed by residues 5118 - 5123 (chain E) 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 GLY5118 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2117C ASP 4.5 2.9 - - - -
2118C GLY* 3.9 12.6 - - - -
2160C ASP* 3.4 13.7 - - - -
2179C ARG* 4.9 0.2 + - - -
5117E ASP* 1.3 75.5 - - - +
5119E ALA* 1.3 66.7 + - - +
5120E SER 3.3 2.2 - - - -
5121E LEU* 3.1 25.9 + - - +
5122E HIS* 3.2 16.3 - - - -
5160E ASP* 3.1 8.9 + - - -
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Residues in contact with ALA5119 (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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2160C ASP* 3.2 24.8 + - + +
2161C THR* 4.1 11.4 - - + -
5071E GLY* 4.0 16.4 - - - +
5072E PRO* 4.2 1.6 - - + -
5117E ASP* 3.8 0.4 + - + -
5118E GLY* 1.3 74.1 - - - +
5120E SER* 1.3 59.1 + - - +
5122E HIS* 2.8 30.5 + - - +
5123E PHE* 3.3 8.2 - - - -
5160E ASP* 4.6 0.4 + - - +
5201E THR* 3.1 30.5 - - + +
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Residues in contact with SER5120 (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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5115E ARG* 3.1 24.9 + - - -
5117E ASP* 2.6 36.6 + - - -
5119E ALA* 1.3 75.2 - - - +
5121E LEU* 1.3 59.5 + - - +
5123E PHE* 2.8 25.7 + - - +
5124E ALA 3.0 12.0 + - - +
5126E MET* 6.0 0.2 - - - +
5200E ALA 3.7 6.3 - - - -
5201E THR* 3.5 6.0 + - - +
5204E THR* 3.6 29.4 - - - +
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Residues in contact with LEU5121 (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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2117C ASP 6.0 1.1 - - - +
2121C LEU* 6.2 4.7 - - + -
2177C VAL* 3.7 11.6 - - - +
2179C ARG* 3.6 28.5 - - - +
2180C PHE* 4.4 2.9 - - - -
5115E ARG* 3.5 15.9 - - - +
5117E ASP 4.4 5.8 - - - +
5118E GLY* 3.3 23.3 - - - +
5119E ALA 3.1 0.6 - - - -
5120E SER* 1.3 73.9 + - - +
5122E HIS* 1.3 58.6 + - - +
5123E PHE 2.9 10.1 + - - -
5124E ALA 3.2 15.2 + - - +
5125E PRO* 4.4 2.6 - - + +
5126E MET* 3.7 44.4 - - + +
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Residues in contact with HIS5122 (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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2116C LEU 2.9 26.3 + - - -
2117C ASP* 5.0 0.4 - - - -
2159C SER* 3.0 24.7 - - - -
2160C ASP* 3.4 10.7 - - - +
2161C THR* 2.7 34.5 + - + +
2164C PRO* 3.2 26.9 - - + +
2165C GLY* 3.1 8.0 - - - -
2177C VAL* 3.6 11.3 + - - +
2179C ARG* 4.6 4.3 + - - -
2180C PHE* 3.4 35.5 - + + -
5118E GLY 3.2 18.7 + - - -
5119E ALA* 2.8 14.8 + - - +
5121E LEU* 1.3 75.9 - - - +
5123E PHE* 1.3 59.8 + - + +
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Residues in contact with PHE5123 (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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1190A MET* 4.1 1.0 - - - +
2161C THR* 3.8 20.9 - - + -
2164C PRO* 3.8 24.9 - - + -
2175C ARG* 3.0 34.8 + - - +
2177C VAL* 3.7 8.7 - - - +
5075E SER* 4.2 11.4 - - - -
5079E GLU* 5.3 5.4 - - + -
5119E ALA 3.3 14.8 - - - -
5120E SER* 2.8 9.0 + - - +
5122E HIS* 1.3 82.4 - - - +
5124E ALA* 1.3 61.4 + - - +
5201E THR* 4.9 1.8 - - + -
5204E THR* 4.7 0.9 - - + -
5205E MET* 3.4 43.3 - - + +
5208E SER* 3.9 11.2 - - - +
5209E GLN* 3.3 42.0 - - + -
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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