Contacts of the strand formed by residues 253 - 260 (chain D) in PDB entry 3ASK
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 253 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D TRP* 3.6 57.4 - - + +
215D GLN* 5.0 4.0 - - - +
247D ARG 3.9 2.9 - - - -
248D GLU* 4.1 18.6 - - + +
252D ALA* 1.3 73.5 - - - +
254D GLU* 1.3 61.8 + - - +
255D LEU 3.8 2.1 + - - -
270D ARG* 4.3 7.8 + - - -
274D VAL* 3.4 31.4 - - + +
275D ASP* 3.1 38.2 + - - -
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Residues in contact with GLU 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D TRP* 3.5 5.3 - - - -
245D ARG 3.7 1.0 - - - +
246D LYS* 3.3 8.1 - - - -
247D ARG* 2.8 79.1 + - + +
249D THR* 4.5 4.2 - - - +
252D ALA* 4.2 15.5 - - + +
253D ARG* 1.3 73.4 - - - +
255D LEU* 1.3 59.7 + - - +
256D TYR* 3.1 31.2 + - + +
270D ARG* 3.6 26.2 + - - +
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Residues in contact with LEU 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D TRP* 3.9 14.6 - - + -
217D LEU* 3.8 32.1 - - + -
225D LEU* 4.6 4.9 - - + -
243D ILE* 4.0 30.1 - - + -
245D ARG 3.9 0.2 - - - -
246D LYS* 4.1 8.7 - - + -
253D ARG 3.8 2.6 + - - -
254D GLU* 1.3 73.0 - - - +
256D TYR* 1.3 65.6 + - - +
270D ARG* 3.5 11.5 - - - +
271D ILE* 2.8 53.3 + - + +
274D VAL* 4.0 19.5 - - + -
277D VAL* 4.0 17.7 - - + -
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Residues in contact with TYR 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243D ILE* 3.7 4.7 - - - +
244D SER* 2.8 34.3 + - - +
245D ARG* 2.9 66.2 + - + +
247D ARG* 4.9 4.7 - - + -
254D GLU* 3.1 42.3 + - + -
255D LEU* 1.3 76.2 - - - +
257D ALA* 1.3 62.6 + - - +
268D ASP* 4.0 15.9 - - - +
269D CYS 3.1 6.1 - - - +
270D ARG* 3.5 45.8 + - + -
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Residues in contact with ALA 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D LEU* 4.3 2.2 - - + -
241D ALA* 3.9 15.9 - - + -
242D GLU 3.2 17.0 - - - +
243D ILE* 3.7 14.8 - - + -
244D SER* 3.6 4.2 + - - -
256D TYR* 1.3 77.7 - - - +
258D ASN* 1.3 64.9 + - - +
259D VAL 3.5 4.6 + - - -
268D ASP 4.2 0.7 - - - -
269D CYS* 2.8 34.1 + - - +
271D ILE* 4.2 15.0 - - + +
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Residues in contact with ASN 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D ALA* 3.2 18.8 - - - -
242D GLU* 2.8 39.8 + - + +
244D SER* 4.1 15.9 - - - -
257D ALA* 1.3 69.6 - - - +
259D VAL* 1.3 63.8 + - - +
260D VAL* 3.5 6.2 + - + +
265D SER* 5.3 3.6 - - - -
266D LEU 3.9 5.8 - - - -
267D ASN* 3.4 28.1 + - - +
268D ASP* 3.1 19.8 + - - +
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Residues in contact with VAL 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D LEU* 4.6 1.6 - - + -
227D TYR* 3.6 32.5 - - + -
239D TYR* 3.5 32.5 - - + -
240D ASP 3.8 3.6 - - - +
241D ALA* 3.8 8.5 - - + -
257D ALA 3.5 3.2 + - - +
258D ASN* 1.3 72.0 - - - +
260D VAL* 1.3 63.9 + - - +
261D LEU* 3.6 18.5 + - + -
265D SER* 3.6 1.2 - - - -
266D LEU* 2.8 38.0 + - + +
269D CYS* 3.7 22.2 - - + -
271D ILE* 4.2 9.4 - - + -
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Residues in contact with VAL 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D ARG* 5.8 5.8 - - - +
149D GLY* 4.5 6.1 - - - +
222D VAL* 6.6 0.4 - - + -
239D TYR* 3.8 12.5 - - - +
240D ASP* 2.8 37.1 + - + +
241D ALA* 4.7 1.3 - - - -
242D GLU 5.4 0.9 - - - +
258D ASN* 4.0 8.3 - - + +
259D VAL* 1.3 72.3 - - - +
261D LEU* 1.3 78.0 + - - +
263D ASP 5.5 3.1 - - - +
264D ASP 4.8 1.8 - - - +
265D SER* 4.0 19.3 - - - +
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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