Contacts of the strand formed by residues 325 - 332 (chain B) in PDB entry 5D3V
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 325 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253B LEU* 4.4 11.0 - - + -
256B HIS* 3.1 14.6 + - + +
257B ILE* 3.6 18.1 - - + -
258B GLU* 2.8 33.6 + - - +
275B GLN* 4.8 5.9 + - - -
290B ALA* 3.9 26.0 - - + +
292B PHE* 3.8 22.6 - + - -
301B CYS* 3.8 15.0 - - + -
302B LYS 3.3 4.9 - - - +
303B ARG* 3.9 45.6 + - + -
304B LYS* 4.1 2.0 - - - +
323B SER 3.7 0.4 - - - -
324B LEU* 1.3 106.8 - - + +
326B ILE* 1.3 65.9 + - - +
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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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258B GLU* 3.7 14.1 - - + +
259B GLY* 5.8 1.3 - - - -
301B CYS* 3.2 4.6 - - - -
302B LYS* 2.7 67.7 + - + +
304B LYS* 3.8 32.8 - - + +
325B TYR* 1.3 78.5 - - - +
327B PHE* 1.3 76.2 + - - +
328B ARG* 3.6 13.2 - - - +
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Residues in contact with PHE 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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257B ILE* 3.6 13.7 - - + +
258B GLU 2.8 21.5 + - - +
259B GLY* 3.3 22.2 - - - +
260B TRP* 3.8 26.2 - + - +
261B GLU* 3.7 46.9 - - + -
299B VAL* 4.3 11.0 - - + -
301B CYS* 4.0 4.0 - - - -
326B ILE* 1.3 76.0 - - - +
328B ARG* 1.3 72.1 + - - +
329B GLY* 3.7 36.1 - - - -
330B ARG* 3.7 26.0 - - + -
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Residues in contact with ARG 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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261B GLU* 5.7 0.2 - - - +
287B GLN* 5.2 3.8 - - - +
289B ARG* 3.5 33.7 - - - +
300B TYR* 3.0 33.2 + - + +
301B CYS 3.8 0.4 - - - -
302B LYS* 3.4 57.9 - - - +
326B ILE* 3.3 14.9 + - - +
327B PHE* 1.3 91.9 - - - +
329B GLY* 1.3 60.1 + - - +
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Residues in contact with GLY 329 (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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299B VAL* 3.4 7.1 - - - +
300B TYR* 2.9 50.9 + - - +
327B PHE* 3.7 13.2 - - - -
328B ARG* 1.3 80.6 - - - +
330B ARG* 1.3 62.9 + - - +
366B LYS* 6.0 3.1 - - - -
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Residues in contact with ARG 330 (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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260B TRP* 3.7 9.7 - - - -
261B GLU* 2.9 30.5 + - - -
262B GLY* 4.1 2.7 - - - -
263B SER* 2.8 52.3 + - - +
268B ILE* 3.4 20.0 - - - +
297B LEU* 3.8 19.1 - - + +
298B LEU 3.2 10.8 - - - +
299B VAL* 4.0 11.7 - - + -
300B TYR* 4.1 2.0 + - - -
327B PHE* 3.7 14.8 - - + -
329B GLY* 1.3 75.2 - - - +
331B ILE* 1.3 68.9 + - - +
363B ASN* 4.1 8.5 + - - -
366B LYS* 4.9 10.1 + - - +
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Residues in contact with ILE 331 (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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297B LEU* 3.5 5.6 - - - +
298B LEU* 2.8 43.4 + - + +
300B TYR* 4.5 9.4 - - + +
330B ARG* 1.3 81.6 - - - +
332B ASN* 1.3 76.1 + - - +
333B THR* 3.3 0.3 + - - -
335B VAL* 4.4 2.2 - - + +
336B MET* 3.8 26.2 - - + -
361B ILE* 3.6 29.6 - - + -
363B ASN* 3.9 38.4 - - + +
370B PHE* 3.9 20.9 - - + -
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Residues in contact with ASN 332 (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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296B ASN* 3.5 16.3 - - - +
297B LEU* 4.2 6.1 - - + +
331B ILE* 1.3 74.9 - - - +
333B THR* 1.3 64.3 + - - +
334B GLU* 2.9 31.3 + - - +
335B VAL* 3.0 33.2 + - + +
336B MET 3.5 5.0 + - - -
394B ARG* 5.7 0.7 - - - -
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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