Contacts of the strand formed by residues 275 - 280 (chain A) in PDB entry 1WNZ
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 VAL 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A ALA* 4.0 6.1 - - + -
250A ALA 3.6 6.1 - - - +
251A PHE* 3.8 25.8 - - + -
266A ARG* 5.7 5.2 - - + -
273A THR 3.9 6.3 - - - +
274A PRO* 1.3 77.6 - - - +
276A LEU* 1.3 65.4 + - - +
277A LYS 3.6 21.8 - - - +
278A THR* 3.9 18.2 - - + -
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Residues in contact with LEU 276 (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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218A GLY 5.7 0.2 - - - +
219A LEU* 3.8 31.0 - - + -
220A GLU 5.8 0.7 - - - +
250A ALA* 2.8 15.0 + - + +
251A PHE 4.5 1.3 - - - -
252A GLN* 3.2 46.7 - - + +
257A ALA* 3.9 17.5 - - + -
274A PRO* 5.5 3.8 - - + +
275A VAL* 1.3 78.7 - - - +
277A LYS* 1.3 69.2 + - + +
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Residues in contact with LYS 277 (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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217A LEU* 3.0 33.1 + - + +
218A GLY* 3.0 21.9 + - - -
219A LEU* 3.7 12.6 - - + +
249A ALA* 3.2 4.9 - - - +
250A ALA* 2.9 27.5 + - + +
275A VAL* 3.6 2.5 - - - +
276A LEU* 1.3 88.9 + - - +
278A THR* 1.3 68.7 + - - +
279A PHE* 3.8 23.6 - - + -
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Residues in contact with THR 278 (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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247A THR* 4.1 14.6 - - + +
248A TYR 3.2 10.8 - - - -
249A ALA* 4.0 8.1 - - + +
262A GLU* 5.8 1.3 - - + -
275A VAL* 3.9 16.6 - - + -
277A LYS* 1.3 80.8 - - - +
279A PHE* 1.3 70.8 + - - +
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Residues in contact with PHE 279 (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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217A LEU* 5.0 15.9 - - + -
219A LEU* 5.2 3.8 - - + -
247A THR* 4.4 5.0 - - - +
248A TYR* 2.8 59.8 + - + -
249A ALA* 4.5 0.2 - - - -
250A ALA* 4.2 15.0 - - + -
259A ILE* 4.0 24.2 - - + -
277A LYS* 3.8 30.5 - - + -
278A THR* 1.3 83.0 - - - +
280A PRO* 1.3 73.7 - - + +
283A ALA* 4.3 9.9 - - + -
284A LEU* 3.9 28.5 - - + -
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Residues in contact with PRO 280 (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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244A PRO 4.2 11.0 - - - +
245A GLU 5.0 3.6 - - - +
246A TYR 3.4 9.9 - - - +
247A THR* 4.5 2.9 - - - +
279A PHE* 1.3 92.5 - - + +
281A GLY* 1.3 68.2 + - - +
282A LYS* 4.2 5.8 - - + +
283A ALA* 3.0 31.4 + - + +
284A LEU* 3.9 3.6 + - - +
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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