Contacts of the strand formed by residues 327 - 333 (chain C) in PDB entry 6RKU
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 GLN 327 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224C ASN* 4.4 1.2 - - - +
241C TYR* 4.0 32.9 - - + +
242C ILE 3.2 13.0 - - - +
243C ARG* 3.1 44.6 + - + +
321C TYR* 3.0 31.3 + - + +
322C SER* 5.0 0.5 - - - -
324C THR 3.5 10.5 + - - +
325C GLN* 3.0 2.8 - - - +
326C LEU* 1.3 79.6 - - - +
328C VAL* 1.3 61.5 + - - +
27H T 5.7 2.1 + - - -
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Residues in contact with VAL 328 (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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241C TYR* 3.9 5.7 - - - -
242C ILE* 3.0 34.6 + - + +
265C PRO* 4.3 22.9 - - + -
266C TYR 5.0 8.1 - - - +
268C VAL* 5.2 4.7 - - + -
325C GLN* 4.2 21.5 - - - +
327C GLN* 1.3 75.8 - - - +
329C SER* 1.3 75.2 + - - +
26H T 6.1 3.1 - - - -
27H T 5.5 6.5 - - - +
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Residues in contact with SER 329 (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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239C LYS* 4.4 20.0 - - - -
240C VAL 3.4 11.2 - - - -
241C TYR* 4.6 16.4 - - - +
242C ILE* 5.4 0.7 - - - +
328C VAL* 1.3 94.4 - - - +
330C PHE* 1.3 67.7 + - - +
25H C 3.7 22.3 + - - +
26H T 3.8 14.3 - - - -
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Residues in contact with PHE 330 (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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181C ASN* 3.1 39.5 - - - -
182C ILE 4.8 0.7 - - - -
183C PRO* 3.5 35.9 - - + -
184C PRO* 6.1 0.4 - - + -
217C PHE* 5.6 11.7 - + - -
239C LYS* 3.6 9.1 - - - +
240C VAL* 3.1 39.5 + - + +
242C ILE* 5.1 8.5 - - + -
266C TYR* 4.9 22.0 - + - -
267C GLN* 5.9 1.3 - - - -
329C SER* 1.3 84.5 + - - +
331C GLY* 1.3 59.7 + - - +
332C ILE* 3.3 25.8 + - + -
25H C 5.9 1.1 - - - -
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Residues in contact with GLY 331 (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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181C ASN* 3.3 26.1 + - - +
238C GLY 4.3 4.0 - - - -
239C LYS* 5.1 2.9 - - - -
330C PHE* 1.3 73.1 - - - +
332C ILE* 1.3 64.6 + - - -
333C ASN* 3.2 7.4 + - - +
24H G 5.7 1.1 - - - -
25H C 4.8 23.8 - - - -
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Residues in contact with ILE 332 (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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181C ASN 4.1 4.7 - - - +
183C PRO* 3.7 29.2 - - + -
215C PRO* 5.5 3.8 - - + -
228C GLY 5.6 0.2 - - - +
229C ILE* 4.8 12.6 - - + -
232C ALA* 3.8 29.4 - - + -
233C TYR* 6.0 4.7 - - + -
236C GLY 4.8 2.2 - - - +
237C ARG* 3.8 4.0 - - - +
238C GLY 3.3 31.4 + - - +
239C LYS 5.4 0.2 - - - -
240C VAL* 4.0 25.4 - - + +
330C PHE* 3.3 23.4 + - + -
331C GLY* 1.3 72.0 - - - +
333C ASN* 1.3 66.8 + - - +
334C MET* 4.6 16.6 - - + -
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Residues in contact with ASN 333 (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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178C MET* 6.0 1.0 - - - +
179C ALA 3.6 19.6 + - - +
180C THR* 3.4 4.4 + - - -
181C ASN* 2.8 44.4 + - + +
236C GLY 3.5 9.8 - - - +
237C ARG* 3.2 33.7 + - - +
331C GLY 3.2 7.9 + - - +
332C ILE* 1.3 78.2 - - - +
334C MET* 1.3 62.9 + - - +
335C VAL* 3.6 14.8 + - - +
344C ILE* 5.1 3.5 - - - +
24H G 5.2 11.7 + - - -
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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