Contacts of the helix formed by residues 200 - 206 (chain E) in PDB entry 1S9C
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 ASP 200 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196E PRO 2.8 19.8 + - - +
199E ILE* 1.3 73.7 - - - +
201E PRO* 1.3 78.6 - - - +
202E ASN* 3.3 16.0 + - - +
203E PHE* 3.5 22.0 + - + +
204E ALA* 3.0 21.5 + - - +
212E PRO* 3.6 1.0 - - - +
44F LEU* 5.2 1.0 - - - +
48F TYR* 3.0 40.4 + - + +
50F GLY 5.3 0.3 - - - +
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Residues in contact with PRO 201 (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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199E ILE 3.3 8.9 - - - +
200E ASP* 1.3 93.2 - - - +
202E ASN* 1.3 62.7 + - + +
204E ALA* 3.2 12.0 + - - +
205E SER* 3.2 13.7 + - - -
209E PHE 5.2 0.2 - - - +
210E ASP 5.9 0.3 - - - -
211E LYS* 5.2 3.1 - - - -
212E PRO* 3.7 19.1 - - + +
44F LEU* 3.8 23.1 - - + -
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Residues in contact with ASN 202 (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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200E ASP* 3.3 11.0 + - - +
201E PRO* 1.3 74.6 - - - +
203E PHE* 1.3 64.0 + - - +
204E ALA 2.9 4.3 - - - -
205E SER* 2.8 30.2 + - - -
206E LEU* 3.0 33.0 + - - +
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Residues in contact with PHE 203 (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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195E ASN* 3.6 13.5 - - - -
196E PRO* 3.4 22.2 - - + -
197E LEU* 3.3 38.6 - - + -
200E ASP* 3.5 27.4 + - + +
201E PRO 3.4 0.4 - - - -
202E ASN* 1.3 79.1 - - - +
204E ALA* 1.3 59.5 + - - +
206E LEU* 3.6 23.2 + - + +
207E ALA* 3.6 13.2 + - + +
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Residues in contact with ALA 204 (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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197E LEU* 3.9 17.5 - - + +
200E ASP 3.0 12.8 + - - +
201E PRO 3.3 10.1 - - - +
202E ASN 2.9 1.2 - - - -
203E PHE* 1.3 79.0 - - - +
205E SER* 1.3 57.7 + - - +
206E LEU 3.1 0.4 - - - -
207E ALA* 3.0 7.1 + - - +
208E GLY 3.0 19.4 + - - -
209E PHE* 3.1 14.0 + - + +
211E LYS 3.8 30.5 - - - +
212E PRO* 3.8 8.1 - - + -
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Residues in contact with SER 205 (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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201E PRO 3.2 8.0 + - - -
202E ASN* 2.8 29.2 + - - -
204E ALA* 1.3 72.7 - - - +
206E LEU* 1.3 61.1 + - - +
207E ALA 3.0 5.8 - - - -
208E GLY* 3.2 13.9 + - - +
209E PHE 3.5 16.8 - - - +
210E ASP* 5.8 0.9 - - - -
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Residues in contact with LEU 206 (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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202E ASN* 3.0 36.1 + - - +
203E PHE* 3.9 17.5 - - + +
204E ALA 3.1 0.6 - - - -
205E SER* 1.3 82.1 - - - +
207E ALA* 1.3 56.7 + - - +
208E GLY 3.3 2.2 - - - -
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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