Contacts of the strand formed by residues 322 - 329 (chain B) in PDB entry 3L5J
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 322 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B SER* 4.6 4.7 - - - -
318B HIS* 4.2 17.7 + - + +
319B THR 3.4 14.0 + - - +
320B GLN 3.4 4.5 - - - +
321B GLY* 1.3 92.5 + - - +
323B ARG* 1.3 62.6 + - - +
368B ASN* 4.3 30.3 - - + +
369B LEU 3.4 11.2 - - - -
370B THR* 4.3 20.2 - - + +
371B ASN* 4.5 3.3 - - - +
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Residues in contact with ARG 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ILE* 3.8 33.0 - - + +
317B SER* 5.8 4.9 - - - +
318B HIS* 5.6 3.8 - - - +
322B TYR* 1.3 77.9 - - - +
324B THR* 1.3 63.5 + - - +
325B VAL* 3.5 6.1 + - + +
368B ASN* 4.5 2.7 - - - -
369B LEU* 2.9 38.6 + - + +
370B THR 2.7 24.7 + - - +
371B ASN* 3.6 22.6 - - - +
372B ASP 3.0 26.7 + - - -
374B TYR* 4.4 0.6 - - - -
394B ILE* 3.5 19.2 - - - +
395B PRO 3.1 27.1 + - - -
397B CYS* 3.9 14.7 - - - +
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Residues in contact with THR 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B LYS 4.3 0.9 - - - +
314B ILE* 3.4 24.1 - - - +
318B HIS* 5.1 13.2 - - - +
323B ARG* 1.3 69.9 - - - +
325B VAL* 1.3 62.5 + - - +
326B GLN* 4.1 2.3 + - + +
366B THR* 3.6 27.8 - - + -
367B VAL 3.8 0.9 - - - +
368B ASN* 3.0 22.2 + - - +
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Residues in contact with VAL 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B TYR* 4.5 4.0 - - + -
314B ILE* 3.5 33.0 - - + +
323B ARG* 3.5 11.1 + - + +
324B THR* 1.3 73.2 - - - +
326B GLN* 1.3 64.4 + - - +
327B LEU* 4.1 28.5 - - + -
365B LEU 3.8 0.3 - - - +
366B THR* 3.3 3.8 - - - +
367B VAL* 2.8 46.7 + - + +
369B LEU* 3.8 31.2 - - + -
394B ILE* 4.5 14.4 - - + -
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Residues in contact with GLN 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B TYR* 3.4 1.6 - - - -
313B LYS* 3.0 45.4 + - + +
324B THR* 4.1 1.5 + - + -
325B VAL* 1.3 75.3 - - - +
327B LEU* 1.3 68.8 + - - +
328B VAL* 3.7 17.6 + - + +
364B LYS* 4.4 13.4 - - + +
365B LEU 3.7 3.6 - - - +
366B THR* 3.5 22.6 + - + +
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Residues in contact with LEU 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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310B PHE* 4.4 15.9 - - + -
311B TRP 3.7 4.9 - - - +
312B TYR* 3.8 20.0 - - + -
325B VAL* 4.1 14.6 - - + -
326B GLN* 1.3 71.4 - - - +
328B VAL* 1.3 61.9 + - - +
329B TRP* 4.1 13.5 - - + -
346B VAL* 3.8 30.5 - - + -
348B LEU* 3.9 20.4 - - + -
364B LYS* 3.2 4.7 - - - +
365B LEU* 2.7 54.8 + - + +
367B VAL* 4.8 2.5 - - + -
376B ALA* 4.6 1.6 - - + -
392B LEU* 4.7 2.2 - - + -
394B ILE* 4.5 15.7 - - + -
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Residues in contact with VAL 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B PHE* 3.6 4.3 - - - -
311B TRP* 2.8 50.7 + - + +
312B TYR* 4.1 4.3 - - - +
313B LYS* 5.5 4.7 - - + +
326B GLN* 3.9 26.9 - - + +
327B LEU* 1.3 79.3 - - - +
329B TRP* 1.3 67.3 + - - +
363B THR 3.6 6.7 - - - +
364B LYS* 4.7 4.9 - - + -
448B TRP* 3.4 35.2 - - + +
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Residues in contact with TRP 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B PRO* 4.8 0.4 - - + -
309B SER 3.0 19.5 - - - +
310B PHE* 3.8 14.4 - + + -
327B LEU* 3.8 20.2 - - + -
328B VAL* 1.3 83.0 - - - +
330B LYS* 1.3 66.4 + - - +
344B TYR* 3.6 36.1 - + + -
346B VAL* 4.0 20.2 - - + -
360B VAL* 4.0 14.8 - - + -
362B ALA 3.0 28.7 + - - -
363B THR* 3.0 38.4 + - + +
364B LYS 3.5 23.1 - - - -
365B LEU* 3.7 15.3 - - + -
378B LEU* 3.5 23.6 - - + -
448B TRP* 3.9 5.2 - - - -
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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
------------------------------------------------------------
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