Contacts of the helix formed by residues 195 - 199 (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 ASN 195 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189E ARG* 4.8 1.2 + - - -
193E ASP* 3.0 19.1 + - - +
194E TRP* 1.3 76.3 - - - +
196E PRO* 1.3 70.2 - - - +
197E LEU* 2.6 54.4 + - - +
198E HIS* 3.1 27.3 + - + +
199E ILE* 4.4 2.9 + - - +
203E PHE* 3.6 7.5 - - - -
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Residues in contact with PRO 196 (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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194E TRP 3.1 7.6 - - - +
195E ASN* 1.3 91.8 - - - +
197E LEU* 1.3 59.0 + - - +
198E HIS 3.0 0.4 - - - -
199E ILE* 3.0 7.8 + - + -
200E ASP* 2.8 32.3 + - + +
203E PHE* 3.4 39.3 - - + -
48F TYR* 3.2 28.7 - - + +
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Residues in contact with LEU 197 (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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88E LEU* 5.8 8.3 - - + -
195E ASN* 2.6 32.7 + - + +
196E PRO* 1.3 73.0 - - - +
198E HIS* 1.3 65.8 + - + +
199E ILE 3.4 0.2 - - - -
203E PHE* 3.3 13.5 - - + -
204E ALA* 3.9 10.0 - - - +
207E ALA* 3.8 17.5 - - + -
209E PHE* 3.4 37.0 - - + -
212E PRO* 3.5 8.8 - - - +
213E ILE* 3.5 38.7 + - + -
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Residues in contact with HIS 198 (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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185E ALA* 3.3 20.4 - - + +
189E ARG* 5.5 1.8 - - - +
193E ASP* 4.3 6.2 + - - -
195E ASN* 3.1 32.8 + - + +
196E PRO 3.0 1.2 - - - -
197E LEU* 1.3 91.1 - - + +
199E ILE* 1.3 61.4 + - + +
212E PRO* 3.6 9.9 - - - +
213E ILE* 2.7 42.8 + - + +
214E LEU 4.1 0.9 - - - -
215E HIS* 3.3 65.1 + + + +
216E GLY 4.8 2.0 - - - -
252E PRO* 5.4 0.2 - - - +
38F ILE* 5.8 2.3 - - - +
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Residues in contact with ILE 199 (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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186E ALA* 4.5 7.9 - - + +
189E ARG* 3.7 35.9 - - - +
195E ASN 4.6 0.2 - - - +
196E PRO* 3.0 6.7 + - + +
197E LEU 3.4 1.0 - - - -
198E HIS* 1.3 82.3 - - - +
200E ASP* 1.3 69.2 + - - +
201E PRO* 3.3 9.5 - - - +
212E PRO* 3.6 12.3 - - - +
38F ILE* 4.5 12.8 - - + +
44F LEU* 3.9 19.7 - - + +
47F ILE* 4.0 22.4 - - + -
48F TYR* 3.5 45.3 - - + -
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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