Contacts of the strand formed by residues 256 - 263 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251L GLU* 3.8 2.3 - - - -
252L ARG* 2.9 55.2 + - - +
253L GLY 3.4 12.7 + - - +
254L GLY 3.1 4.8 - - - +
255L GLY* 1.3 79.6 - - - +
257L GLN* 1.3 59.6 + - - +
308L VAL 4.6 4.7 - - - +
310L LYS* 5.0 16.4 - - + +
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Residues in contact with GLN 257 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A ILE* 4.6 2.8 - - - +
315A SER* 2.5 38.0 + - - -
249L ILE* 4.0 18.6 - - + +
250L GLU 3.4 15.2 - - - +
251L GLU* 4.4 3.6 - - - +
252L ARG* 2.5 32.7 + - - -
255L GLY 4.5 8.1 - - - +
256L ARG* 1.3 75.5 - - - +
258L ARG* 1.3 56.7 + - - +
308L VAL* 3.5 18.0 + - + +
310L LYS* 6.0 0.4 - - - +
312L ALA 4.1 8.1 - - - +
313L ASN* 5.1 0.2 - - - -
314L ALA* 3.2 29.9 + - + +
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Residues in contact with ARG 258 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487A GLU* 4.7 13.7 + - - -
489A GLN* 5.3 3.8 - - - +
248L VAL 3.9 0.3 - - - +
249L ILE* 3.4 5.2 - - - +
250L GLU* 2.9 71.4 + - + +
251L GLU 4.7 3.6 + - - -
252L ARG* 4.0 24.1 - - + +
257L GLN* 1.3 75.2 - - - +
259L ILE* 1.3 61.6 - - - +
260L VAL* 4.0 8.3 + - + +
293L ARG* 4.1 17.6 - - - +
295L GLU* 5.2 2.0 + - - -
303L ARG* 3.7 18.1 - - - +
305L VAL* 3.7 16.0 - - + +
306L ILE 3.3 14.4 - - - +
307L ASP* 3.6 13.7 + - - +
308L VAL* 4.4 4.9 - - - +
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Residues in contact with ILE 259 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247L ALA* 4.3 2.7 - - + -
248L VAL 3.3 8.3 - - - +
249L ILE* 4.2 16.6 - - + -
258L ARG* 1.3 72.9 - - - +
260L VAL* 1.3 61.1 + - - +
261L VAL* 4.3 11.4 - - + -
304L VAL 3.7 1.4 - - - +
305L VAL* 3.6 3.3 - - - +
306L ILE* 2.9 54.5 + - + +
308L VAL* 4.2 12.6 - - + -
314L ALA* 3.7 21.3 - - + +
317L ILE* 3.9 23.3 - - + -
318L LEU* 3.9 32.1 - - + +
321L LEU* 4.2 7.6 - - + -
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Residues in contact with VAL 260 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246L ARG 4.0 0.5 - - - +
247L ALA* 3.2 3.2 - - - -
248L VAL* 2.8 44.4 + - + +
250L GLU* 3.5 34.3 - - + +
258L ARG* 4.0 16.4 - - + +
259L ILE* 1.3 76.2 - - - +
261L VAL* 1.3 63.0 + - - +
262L THR* 4.1 15.7 + - + +
303L ARG* 3.3 43.1 - - + +
304L VAL 3.6 4.5 - - - +
305L VAL* 4.8 3.8 - - + -
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Residues in contact with VAL 261 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245L SER* 3.8 15.7 - - - +
246L ARG 3.5 3.4 - - - +
247L ALA* 3.9 16.4 - - + -
259L ILE* 4.3 11.4 - - + -
260L VAL* 1.3 74.8 - - - +
262L THR* 1.3 60.7 + - - +
263L GLU 3.7 18.2 - - - +
264L ILE* 4.1 14.8 - - + -
273L MET* 5.1 0.4 - - + -
302L VAL* 4.0 2.0 - - + +
303L ARG* 3.4 5.5 + - - -
304L VAL* 2.9 51.0 + - + +
306L ILE* 4.6 7.4 - - + -
327L LEU* 4.1 24.2 - - + -
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Residues in contact with THR 262 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246L ARG* 3.0 25.7 + - - +
248L VAL* 6.4 1.1 - - + -
260L VAL* 4.1 20.9 - - + +
261L VAL* 1.3 76.6 - - - +
263L GLU* 1.3 68.5 + - - +
302L VAL* 3.2 40.6 + - - +
303L ARG* 5.0 6.7 - - + +
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Residues in contact with GLU 263 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220L THR 3.8 7.6 - - - +
221L ALA* 3.4 18.9 - - + +
222L GLY* 2.8 36.6 + - - +
245L SER* 3.1 8.0 - - - -
246L ARG* 2.9 62.9 + - + -
261L VAL* 3.7 2.8 - - - +
262L THR* 1.3 87.1 + - - +
264L ILE* 1.3 63.2 + - - +
302L VAL* 4.7 2.5 - - - -
485L ARG 4.5 2.9 - - - +
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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