Contacts of the strand formed by residues 256 - 263 (chain c) in PDB entry 6QX2
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 ARG 256 (chain c).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251c GLU* 3.8 2.5 - - - -
252c ARG* 2.9 64.3 + - + +
253c GLY 2.7 31.8 + - - +
254c GLY* 3.1 19.8 + - - +
255c GLY* 1.3 79.8 - - - +
257c GLN* 1.3 61.4 + - - +
308c VAL 4.4 3.6 - - - +
310c LYS* 4.8 20.2 - - + +
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Residues in contact with GLN 257 (chain c).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249c ILE* 4.0 19.6 - - + +
250c GLU 3.4 16.4 - - - +
251c GLU* 4.9 3.6 - - - +
252c ARG* 2.8 30.0 + - - -
255c GLY 4.1 6.0 + - - +
256c ARG* 1.3 75.0 - - - +
258c ARG* 1.3 59.7 + - - +
308c VAL* 3.5 16.4 + - + +
312c ALA 4.2 7.7 - - - +
313c ASN* 5.2 0.2 - - - -
314c ALA* 3.2 30.5 + - + +
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Residues in contact with ARG 258 (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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248c VAL 3.9 0.2 - - - +
249c ILE* 3.4 5.5 - - - -
250c GLU* 2.9 70.7 + - + +
251c GLU 4.5 4.2 + - - -
252c ARG* 3.9 24.3 - - - +
257c GLN* 1.3 76.3 - - - +
259c ILE* 1.3 63.3 + - - +
260c VAL* 4.0 6.8 + - + +
293c ARG* 4.1 17.2 - - - +
295c GLU* 5.1 2.6 + - - -
303c ARG* 3.7 19.3 - - - +
305c VAL* 3.6 15.3 - - + +
306c ILE 3.3 14.6 - - - +
307c ASP* 3.6 13.2 + - - +
308c VAL* 4.4 4.0 - - - +
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Residues in contact with ILE 259 (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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247c ALA* 4.3 9.6 - - + -
248c VAL 3.3 8.7 - - - +
249c ILE* 4.3 13.0 - - + -
258c ARG* 1.3 73.9 - - - +
260c VAL* 1.3 62.1 + - - +
261c VAL* 4.2 4.3 - - + -
304c VAL 3.7 1.7 - - - +
305c VAL* 3.6 3.5 - - - +
306c ILE* 2.9 53.6 + - + +
308c VAL* 4.2 13.7 - - + -
314c ALA* 3.7 23.8 - - + +
317c ILE* 3.9 22.9 - - + -
318c LEU* 3.9 33.2 - - + +
321c LEU* 4.2 7.2 - - + -
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Residues in contact with VAL 260 (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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246c ARG 4.1 0.5 - - - +
247c ALA* 3.2 3.0 - - - -
248c VAL* 2.8 44.9 + - + +
250c GLU* 3.1 35.4 - - + +
258c ARG* 4.0 15.3 - - + +
259c ILE* 1.3 76.7 - - - +
261c VAL* 1.3 62.8 + - - +
262c THR* 4.1 16.0 + - + +
303c ARG* 3.3 42.2 - - + +
304c VAL 3.5 4.7 - - - +
305c VAL* 4.8 4.0 - - + -
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Residues in contact with VAL 261 (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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245c SER* 3.9 15.7 - - - +
246c ARG 3.5 4.5 - - - +
247c ALA* 3.9 16.4 - - + -
259c ILE* 4.3 11.0 - - + -
260c VAL* 1.3 74.3 - - - +
262c THR* 1.3 61.8 + - - +
263c GLU 3.7 18.2 - - - +
264c ILE* 4.1 15.0 - - + -
273c MET* 5.1 0.2 - - + -
302c VAL* 4.0 2.1 - - + +
303c ARG* 3.4 5.2 + - - -
304c VAL* 2.9 51.5 + - + +
306c ILE* 4.6 8.5 - - + -
327c LEU* 4.1 24.0 - - + -
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Residues in contact with THR 262 (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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246c ARG* 3.0 26.4 + - - +
248c VAL* 6.3 1.6 - - + -
260c VAL* 4.1 20.4 - - + +
261c VAL* 1.3 76.4 - - - +
263c GLU* 1.3 70.1 + - - +
302c VAL* 3.2 41.8 + - - +
303c ARG* 5.1 4.9 - - + +
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Residues in contact with GLU 263 (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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220c THR 3.8 6.5 - - - +
221c ALA* 3.4 18.7 - - + +
222c GLY* 2.8 36.9 + - - +
245c SER* 3.1 9.1 - - - -
246c ARG* 2.9 63.4 + - + -
261c VAL* 3.7 2.4 - - - +
262c THR* 1.3 87.6 + - - +
264c ILE* 1.3 63.4 + - - +
302c VAL* 4.8 2.2 - - - -
485c ARG 4.6 2.1 - - - +
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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