Contacts of the strand formed by residues 256 - 260 (chain g) in PDB entry 5A2Q
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 ILE 256 (chain g).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249g CYS* 3.5 26.0 - - - -
250g ALA 3.3 14.6 - - - +
251g ALA* 4.5 1.6 - - - -
255g SER* 1.3 76.0 - - - +
257g LYS* 1.3 65.2 + - - +
258g ILE 4.2 0.4 - - - +
268g ASP 3.5 2.1 - - - +
269g GLU* 3.5 6.8 - - - -
270g LEU* 3.0 47.9 + - + +
286g CYS* 3.6 36.6 - - + -
289g LEU* 3.8 17.0 - - + -
298g LEU* 6.4 0.2 - - + -
300g ALA* 3.9 11.9 - - + -
302g TYR* 4.2 15.5 - - + +
310g TRP* 4.3 10.5 - - + +
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Residues in contact with LYS 257 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231g ASP 6.0 0.9 - - - -
248g LEU 3.5 2.4 - - - +
249g CYS* 4.5 0.4 - - - -
250g ALA* 2.9 43.6 + - + +
252g THR* 5.0 6.5 - - - +
255g SER* 3.9 16.8 - - - +
256g ILE* 1.3 75.2 - - - +
258g ILE* 1.3 64.5 + - - +
259g TRP* 3.5 28.8 + - + +
266g ILE* 3.3 27.1 - - + +
268g ASP 4.0 3.1 - - - -
269g GLU* 2.9 47.5 + - + -
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Residues in contact with ILE 258 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5g MET* 4.7 23.3 - - + -
247g TRP* 3.6 46.0 - - + -
248g LEU 3.9 3.4 - - - +
249g CYS* 3.5 17.7 - - - +
257g LYS* 1.3 70.3 - - - +
259g TRP* 1.3 60.5 + - - +
266g ILE* 3.8 2.4 - - - +
267g VAL* 2.9 40.8 + - + +
268g ASP* 3.6 13.0 + - + +
270g LEU* 4.9 9.2 - - + -
291g TRP* 4.0 13.7 - - + -
298g LEU* 3.7 27.8 - - + -
312g VAL* 6.0 1.1 - - + -
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Residues in contact with TRP 259 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216g ALA* 5.2 2.6 - - + +
230g LEU* 3.6 49.2 - - + +
231g ASP* 3.8 30.3 - - - -
232g GLY* 5.7 0.4 - - - -
247g TRP* 3.4 9.7 - - - +
248g LEU* 2.9 44.2 + - + +
250g ALA* 4.3 13.7 - - + +
257g LYS* 3.8 37.0 - - + +
258g ILE* 1.3 73.1 - - - +
260g ASP* 1.3 61.1 + - - +
261g LEU* 3.8 10.5 + - + -
264g LYS* 4.3 14.8 - - + -
265g ILE 4.1 3.6 - - - -
266g ILE* 3.8 41.7 - - + -
267g VAL* 4.5 0.2 - - - -
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Residues in contact with ASP 260 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245g ARG 5.2 0.2 - - - +
246g TYR* 4.0 8.3 - - - +
247g TRP* 3.4 33.5 + - - +
258g ILE 4.0 0.6 + - - -
259g TRP* 1.3 71.4 - - - +
261g LEU* 1.3 62.9 + - - +
262g GLU* 3.9 11.6 + - - +
263g GLY* 4.6 6.6 + - - +
264g LYS* 3.0 30.3 + - - -
265g ILE* 3.1 28.5 + - + +
267g VAL* 4.2 7.8 - - + +
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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