Contacts of the strand formed by residues 324 - 328 (chain B) in PDB entry 2Y05
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 LYS 324 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B THR* 2.7 30.2 + - - -
46B VAL 2.9 16.0 + - - -
47B ASP* 3.6 11.1 + - - -
116B SER 5.5 0.2 - - - +
119B LEU 3.2 21.3 - - - +
120B GLY* 4.0 14.8 - - - -
121B THR* 5.5 1.1 - - - +
125B PRO* 4.0 5.4 - - + -
153B ALA* 3.5 31.5 - - + +
299B LYS 3.7 9.1 + - - +
300B GLU* 3.6 8.7 - - + +
301B TYR 2.8 25.8 + - - +
323B GLY* 1.3 69.4 - - - -
325B THR* 1.3 85.0 + - - +
326B ILE* 3.5 22.4 + - + +
701B NAP 4.9 2.0 + - - -
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Residues in contact with THR 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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46B VAL* 3.7 34.5 + - + -
301B TYR* 3.5 11.2 - - + -
303B ILE* 4.0 21.5 - - + -
312B ALA* 3.7 18.8 - - + +
316B MET* 3.4 13.7 - - + +
321B ASN* 3.2 28.8 + - - +
323B GLY 3.5 0.2 + - - -
324B LYS* 1.3 101.3 + - - +
326B ILE* 1.3 64.1 + - - +
327B VAL 4.4 0.2 - - - -
701B NAP 4.9 1.2 + - - -
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Residues in contact with ILE 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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43B PHE* 3.7 31.9 - - + -
44B LEU 3.7 3.6 - - - +
45B THR* 4.8 0.4 - - - -
116B SER* 4.0 13.7 - - - +
119B LEU* 3.9 32.1 - - + -
300B GLU* 3.7 17.0 - - + +
301B TYR 3.0 8.9 + - - +
302B ILE* 3.4 15.8 - - + -
303B ILE* 2.8 27.8 + - - +
324B LYS* 3.8 26.7 - - + +
325B THR* 1.3 84.8 - - - +
327B VAL* 1.3 68.5 + - - +
328B LYS 4.3 0.7 - - - +
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Residues in contact with VAL 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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43B PHE* 3.4 3.8 - - - -
44B LEU* 2.8 52.1 + - + +
46B VAL* 4.6 6.5 - - + -
303B ILE* 3.4 9.0 - - + +
305B GLY 3.4 32.1 - - - +
306B PHE* 4.1 8.7 - - - -
309B MET* 4.0 23.3 - - + -
312B ALA* 3.5 31.2 - - + -
326B ILE* 1.3 75.5 - - - +
328B LYS* 1.3 65.6 + - - +
329B ALA 3.5 1.3 + - - +
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Residues in contact with LYS 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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42B LEU 4.0 5.6 - - - +
43B PHE* 3.9 28.5 - - + -
302B ILE* 4.0 13.9 - - + -
303B ILE 2.9 13.0 + - - +
304B GLU* 3.4 21.3 - - - +
305B GLY* 2.8 30.5 + - - -
326B ILE* 3.8 2.2 + - - +
327B VAL* 1.3 71.3 - - - +
329B ALA* 1.3 69.1 + - - +
165C LYS* 5.7 0.6 + - - +
286C ASP* 3.4 38.4 + - - +
289C LYS* 6.0 3.0 - - - +
290C TRP* 3.1 38.3 - - - +
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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