Contacts of the strand formed by residues 249 - 255 (chain A) in PDB entry 1WZ2
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 TYR 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A VAL* 3.5 11.5 - - + -
244A ASN* 2.7 53.1 + - + +
247A ALA* 3.7 11.2 - - + +
248A THR* 1.3 93.8 + - - +
250A VAL* 1.3 73.9 + - - +
264A ILE* 4.9 0.2 - - + -
265A VAL* 3.2 15.5 - - - +
266A SER* 3.3 37.2 - - - -
267A LYS 3.9 4.7 - - - +
285A GLU* 3.4 1.7 - - - +
286A PHE* 2.8 38.5 + - + +
288A GLY* 4.3 10.5 - - - -
291A LEU* 4.6 12.3 - - + -
313A VAL* 4.3 0.9 + - - +
315A PRO* 5.4 3.1 - - + +
319A THR 4.0 5.4 - - - -
320A GLY* 4.0 17.0 + - - -
321A VAL* 4.1 11.7 - - + -
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Residues in contact with VAL 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A TYR* 1.3 85.5 - - - +
251A LYS* 1.3 66.7 + - - +
252A ALA* 5.5 4.0 - - + -
263A TRP 3.4 1.0 - - - +
264A ILE* 2.9 26.0 - - - +
265A VAL* 2.8 26.6 + - + +
266A SER 4.3 2.7 - - - +
267A LYS* 3.9 27.6 - - + -
270A ALA* 4.3 13.5 - - + -
282A VAL* 4.4 9.9 - - + -
284A GLU 3.0 6.5 - - - +
285A GLU* 3.4 33.9 - - + +
286A PHE* 3.9 8.0 - - - -
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Residues in contact with LYS 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ILE* 3.8 31.9 - - + -
250A VAL* 1.3 74.8 - - - +
252A ALA* 1.3 66.5 + - - +
262A THR* 4.0 16.2 - - + -
263A TRP 3.2 3.8 - - - -
264A ILE* 3.9 10.1 - - + -
282A VAL* 4.1 2.1 - - - +
283A ILE* 3.0 38.1 + - + +
284A GLU* 2.5 43.1 + - + +
286A PHE* 4.1 7.9 - - + -
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Residues in contact with ALA 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A VAL* 5.4 4.9 - - + -
251A LYS* 1.3 79.3 - - - +
253A LYS* 1.3 64.6 + - - +
254A VAL* 4.2 2.6 - - + +
262A THR* 3.2 7.0 - - - -
263A TRP 2.7 33.8 + - - +
280A ILE* 4.0 14.1 - - + -
281A GLU 3.0 22.7 - - - +
282A VAL* 3.4 12.8 - - + -
283A ILE* 4.0 8.1 - - - -
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Residues in contact with LYS 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A ALA* 1.3 76.8 - - - +
254A VAL* 1.3 61.5 + - - +
255A ARG* 4.1 22.7 - - - +
260A GLU* 2.9 29.4 - - - +
261A GLU 3.2 8.3 - - - +
262A THR* 4.2 11.4 - - + +
279A GLU 3.5 0.4 - - - +
280A ILE* 3.3 5.7 - - - +
281A GLU* 3.1 30.4 + - + +
283A ILE* 3.2 34.2 - - + +
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Residues in contact with VAL 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A ALA* 4.2 3.8 - - + +
253A LYS* 1.3 80.0 - - - +
255A ARG* 1.3 63.0 + - - +
256A ARG 4.1 0.3 + - - -
259A LYS 4.1 1.0 - - - +
260A GLU* 3.9 1.4 - - - -
261A GLU* 2.9 29.2 + - - +
263A TRP* 3.8 55.3 - - + +
273A LEU* 6.3 0.2 - - + -
278A ARG* 3.8 34.8 - - + -
279A GLU 3.3 2.7 - - - -
280A ILE* 4.1 21.5 - - + -
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Residues in contact with ARG 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A LYS* 4.1 19.4 - - - +
254A VAL* 1.3 77.8 - - - +
256A ARG* 1.3 64.7 + - - +
258A ASP 5.3 2.5 - - - +
259A LYS 3.7 6.7 - - - +
260A GLU* 3.5 32.6 + - + +
278A ARG* 3.2 10.7 - - - -
279A GLU* 2.9 72.6 + - + +
281A GLU* 3.9 26.2 + - - +
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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