Contacts of the strand formed by residues 203 - 207 (chain E) in PDB entry 1KYZ
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 SER 203 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E LEU* 3.6 8.0 - - - +
202E LYS* 1.3 83.1 - - - +
204E LEU* 1.3 64.1 + - - +
225E ILE* 4.0 2.2 - - - +
226E LYS* 3.8 17.1 + - - +
228E ILE* 4.9 4.9 - - - +
258E LYS 4.4 2.1 + - - -
259E ALA* 3.5 18.0 - - - +
260E ASP* 3.7 27.1 + - - +
261E ALA* 3.6 17.3 + - - +
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Residues in contact with LEU 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198E PHE* 4.0 15.7 - - + -
201E LEU* 4.1 10.1 - - + -
203E SER* 1.3 77.9 + - - +
205E VAL* 1.3 63.1 + - - +
215E ILE* 3.8 13.5 - - + +
218E ILE* 3.7 41.3 - - + -
225E ILE* 3.7 14.5 - - + +
226E LYS 3.4 6.0 + - - -
227E GLY* 3.6 2.3 - - - -
228E ILE* 2.8 28.5 + - - +
259E ALA* 4.3 2.9 - - - -
261E ALA* 3.4 37.2 - - + +
262E VAL 4.0 1.3 - - - +
263E PHE* 3.9 19.3 - - + +
294E ILE* 4.8 1.1 - - + -
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Residues in contact with VAL 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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204E LEU* 1.3 75.8 - - - +
206E ASP* 1.3 63.8 + - - +
207E VAL* 3.5 5.9 + - + -
228E ILE* 3.3 21.5 - - + -
230E PHE* 3.7 26.9 - - + -
256E ILE* 4.2 3.6 - - + -
257E PRO* 4.1 24.0 - - + +
259E ALA* 3.8 15.0 - - + +
261E ALA 3.2 14.7 + - - +
262E VAL* 3.4 20.4 - - + +
263E PHE 2.9 21.3 + - - +
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Residues in contact with ASP 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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204E LEU 4.1 0.6 + - - -
205E VAL* 1.3 69.9 - - - +
207E VAL* 1.3 59.4 + - - +
209E GLY* 3.3 25.5 + - - -
214E VAL* 3.5 24.3 - - - +
215E ILE* 4.2 21.6 + - + +
228E ILE 2.8 14.7 + - - +
229E ASN* 4.4 1.9 + - - +
230E PHE 3.0 27.9 + - - +
263E PHE* 3.2 41.6 - - + +
264E MET 3.4 10.7 - - - +
1697E SAH 4.5 2.3 + - - -
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Residues in contact with VAL 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205E VAL* 4.3 4.9 - - + +
206E ASP* 1.3 67.6 - - - +
208E GLY* 1.3 66.1 + - - +
230E PHE* 3.9 12.3 - - + -
252E MET* 3.8 39.5 - - + -
256E ILE* 4.1 27.8 - - + -
262E VAL* 3.5 25.1 - - + -
263E PHE 2.9 13.0 + - - +
264E MET* 3.5 26.0 - - + +
267E ILE* 3.5 18.3 - - + +
283E CYS* 4.5 2.7 - - - -
1697E SAH 5.1 0.2 - - + -
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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