Contacts of the strand formed by residues 324 - 328 (chain B) in PDB entry 1YQZ
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 ASN 324 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418A ALA* 4.6 2.0 - - - +
419A TYR 5.2 2.0 - - - +
186B LEU* 3.5 41.2 - - + +
187B MET* 6.1 0.3 - - - +
294B LEU* 3.7 21.5 - - + -
322B GLY 3.0 22.1 + - - +
323B ASN* 1.3 80.5 + - - +
325B ILE* 1.3 72.0 + - - +
333B PHE 4.9 1.7 - - - +
334B ALA* 3.2 3.3 - - - +
335B SER* 2.9 60.2 + - - +
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Residues in contact with ILE 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A ALA* 3.6 20.6 - - + +
419A TYR 3.5 33.0 + - - +
420A ALA* 3.6 15.3 - - + +
423A TYR* 3.7 21.3 - - + -
158B TYR* 5.5 3.1 - - - +
162B GLU* 5.4 0.3 - - - +
324B ASN* 1.3 81.5 + - - +
326B VAL* 1.3 68.0 + - - +
332B THR* 3.6 17.9 - - + -
333B PHE 3.3 11.7 - - - +
334B ALA* 3.8 11.0 - - + -
393B ASP* 3.6 31.9 - - + -
440B FAD 5.0 3.1 + - - +
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Residues in contact with VAL 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A ALA* 4.6 4.7 - - - -
423A TYR* 3.9 5.1 + - - -
158B TYR* 3.7 30.1 - - + +
161B LEU* 5.3 8.7 - - + -
162B GLU* 3.7 20.2 - - + +
184B ASN* 3.9 23.1 - - - +
325B ILE* 1.3 76.8 - - - +
327B LYS* 1.3 73.8 + - - +
328B PHE* 5.6 1.6 - - + -
332B THR* 3.6 2.3 - - - +
333B PHE* 2.9 56.2 + - + +
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Residues in contact with LYS 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A TYR* 3.1 29.8 - - - +
420A ALA* 5.2 0.8 - - - +
422A PRO* 3.9 18.2 - - + -
423A TYR* 3.1 27.9 + - + +
47B TYR* 4.9 11.1 + - - +
161B LEU* 5.6 0.2 - - - +
162B GLU* 4.4 11.9 + - - +
165B GLU* 2.7 36.7 + - - +
326B VAL* 1.3 87.6 - - - +
328B PHE* 1.3 63.1 + - - +
329B PHE* 2.7 30.4 + - - +
331B TYR 3.4 4.9 - - - +
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Residues in contact with PHE 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B LEU* 3.4 55.0 - - + -
164B LEU* 4.0 8.1 - - + -
165B GLU* 3.5 5.4 - - + -
195B ILE* 3.5 46.4 - - + -
198B GLU* 4.0 8.5 - - + +
199B LEU* 3.8 19.7 - - + -
326B VAL* 4.2 2.6 + - + -
327B LYS* 1.3 74.5 - - - +
329B PHE* 1.3 104.7 + + - +
331B TYR* 2.9 25.9 + - - +
333B PHE* 3.8 17.5 - + + -
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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