Contacts of the helix formed by residues 200 - 206 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196K PRO* 2.8 25.8 + - + +
199K ILE* 1.3 73.6 - - - +
201K PRO* 1.3 73.8 - - - +
202K ASN* 3.0 31.6 + - - +
203K PHE* 3.9 13.3 - - + +
204K ALA* 3.1 19.4 + - - +
212K PRO* 3.8 0.6 - - - +
44L LEU* 5.5 1.1 - - - +
48L TYR* 3.1 41.2 + - + +
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Residues in contact with PRO 201 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199K ILE 3.0 12.5 - - - +
200K ASP* 1.3 84.3 - - - +
202K ASN* 1.3 59.8 + - - +
204K ALA* 2.9 20.3 - - - +
205K SER* 3.5 5.7 + - - -
209K PHE 4.7 0.9 - - - +
210K ASP 5.5 1.0 - - - +
211K LYS* 5.3 1.4 - - - -
212K PRO* 3.6 21.5 - - + +
41L PRO* 6.6 0.4 - - + -
44L LEU* 3.6 27.1 - - + -
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Residues in contact with ASN 202 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200K ASP* 3.0 13.2 + - - +
201K PRO* 1.3 74.6 - - - +
203K PHE* 1.3 53.9 + - - +
204K ALA 2.5 17.1 + - - -
205K SER* 2.6 31.9 + - - -
206K LEU* 3.2 4.9 + - - +
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Residues in contact with PHE 203 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85K ALA 6.1 1.3 - - - -
86K LYS* 5.0 19.7 - - + -
195K ASN* 4.1 8.7 - - - -
196K PRO* 3.1 41.5 - - + +
197K LEU* 4.0 11.4 - - + +
200K ASP* 3.3 21.7 + - + +
202K ASN* 1.3 76.5 - - - +
204K ALA* 1.3 59.5 + - - +
206K LEU* 3.4 39.3 - - + -
207K ALA* 3.5 20.7 + - + +
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Residues in contact with ALA 204 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197K LEU* 4.5 12.3 - - - +
200K ASP 3.1 11.3 + - - +
201K PRO 2.9 18.2 - - - +
202K ASN 2.5 6.5 + - - -
203K PHE* 1.3 73.4 - - - +
205K SER* 1.3 51.6 - - - +
207K ALA* 3.2 6.8 + - - +
208K GLY 2.9 8.5 + - - -
209K PHE* 2.8 41.8 + - + +
211K LYS 4.0 0.9 - - - +
212K PRO* 3.7 26.2 - - + -
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Residues in contact with SER 205 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201K PRO 3.9 4.4 + - - -
202K ASN* 2.6 36.9 + - - -
204K ALA* 1.3 70.2 - - - +
206K LEU* 1.3 52.7 + - - -
207K ALA 2.7 7.5 + - - -
208K GLY* 2.6 23.8 + - - +
209K PHE 3.8 12.6 - - - +
210K ASP* 5.8 2.2 - - - -
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Residues in contact with LEU 206 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202K ASN 3.2 2.4 + - - +
203K PHE* 3.4 45.7 - - + -
205K SER* 1.3 80.0 + - - +
207K ALA* 1.3 55.8 + - - +
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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