Contacts of the strand formed by residues 208 - 214 (chain C) in PDB entry 5KX8
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 THR 208 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286A HIS* 5.4 7.4 - - + +
420A ASP* 3.8 33.1 + - + +
204C TYR* 3.5 2.4 - - - -
205C VAL* 2.8 43.2 + - - -
206C ASN* 3.6 0.5 - - - +
207C ASN* 1.4 76.2 + - - +
209C THR* 1.3 72.2 + - - +
210C VAL* 3.6 12.8 + - + +
249C LEU* 4.8 10.8 - - + -
263C VAL* 5.9 7.2 - - + -
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Residues in contact with THR 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A ASN* 4.7 11.2 + - - -
202C LYS* 3.6 32.8 - - + -
203C GLY 3.5 12.3 - - - +
204C TYR* 3.7 18.4 - - + -
207C ASN 3.6 4.5 + - - -
208C THR* 1.3 79.7 - - - +
210C VAL* 1.3 64.3 + - - +
263C VAL* 4.8 0.7 - - - +
264C TYR* 3.1 45.2 + - + +
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Residues in contact with VAL 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C VAL* 4.0 9.0 - - + -
202C LYS* 3.7 5.7 - - - +
203C GLY* 2.8 43.3 + - - +
205C VAL* 3.7 32.1 - - + -
208C THR* 3.8 14.6 - - + +
209C THR* 1.3 80.5 - - - +
211C ALA* 1.3 59.2 + - - +
212C VAL* 4.1 4.5 - - + -
249C LEU* 3.5 28.5 - - + -
261C VAL* 3.9 14.6 - - + -
262C TYR 3.4 9.0 - - - +
264C TYR* 3.9 9.0 - - - +
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Residues in contact with ALA 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C MET* 4.8 4.5 - - + -
200C VAL* 4.2 10.8 - - + -
201C TYR 3.4 5.8 - - - -
210C VAL* 1.3 71.3 - - - +
212C VAL* 1.3 62.0 + - - +
260C LEU 3.7 1.2 - - - +
261C VAL* 3.4 2.1 - - - -
262C TYR* 2.7 41.7 + - + +
264C TYR* 4.2 2.4 - - - +
501C 6YE 3.5 49.4 - - + +
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Residues in contact with VAL 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C LEU* 4.2 22.4 - - + -
176C VAL* 4.3 0.7 - - + -
177C THR* 3.6 26.7 - - + -
180C PHE* 3.8 25.6 - - + -
200C VAL* 3.5 2.5 - - - -
201C TYR* 2.7 45.9 + - + +
203C GLY* 5.0 0.7 - - - -
210C VAL* 4.1 19.7 - - + -
211C ALA* 1.3 77.4 - - - +
213C LYS* 1.3 59.9 + - - +
259C CYS* 4.1 17.7 - - + -
260C LEU 3.4 8.3 - - - +
261C VAL* 4.4 4.9 - - + -
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Residues in contact with LYS 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C PHE* 4.5 21.0 - - - +
198C GLY* 4.6 3.8 - - - +
199C VAL 3.4 11.2 - - - +
200C VAL* 4.2 18.8 - - + +
211C ALA 4.1 0.6 - - - -
212C VAL* 1.3 72.1 - - - +
214C LYS* 1.4 59.5 + - - +
215C LEU* 4.0 26.2 + - + +
233C GLU* 5.5 3.0 + - - -
258C LEU 3.8 1.2 - - - +
259C CYS* 3.2 5.1 - - - -
260C LEU* 2.7 48.3 + - + +
262C TYR* 4.1 24.3 + - + +
329C ASP* 2.6 39.1 + - - +
501C 6YE 4.2 9.3 - - + -
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Residues in contact with LYS 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C PHE* 3.9 27.4 - - + -
180C PHE* 4.1 22.5 - - + +
182C GLU* 4.8 7.5 + - - -
198C GLY* 4.3 0.2 - - - -
199C VAL* 3.0 30.8 + - + +
201C TYR* 3.3 39.3 + - + -
212C VAL 3.9 2.0 + - - -
213C LYS* 1.4 70.2 - - - +
215C LEU* 1.3 67.9 + - - +
216C ALA* 3.4 2.9 + - - +
257C ASP* 3.8 33.4 - - + +
258C LEU 3.5 3.4 - - - -
259C CYS* 3.6 16.4 - - - -
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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