Contacts of the strand formed by residues 325 - 335 (chain B) in PDB entry 5F6L
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 GLY 325 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324B LYS* 1.3 79.7 - - - +
326B ALA* 1.3 60.3 + - - -
327B TRP* 3.5 8.8 - - - -
396B ILE 3.8 0.9 - - - +
397B ASN* 3.5 8.7 - - - -
398B LEU* 2.8 33.8 + - - +
399B PRO* 4.9 1.5 - - - +
400B GLU 5.2 0.6 - - - +
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Residues in contact with ALA 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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325B GLY* 1.3 71.8 - - - -
327B TRP* 1.3 68.6 + - - +
395B TYR* 3.7 18.2 - - + +
396B ILE 3.2 4.7 - - - +
397B ASN* 3.6 13.4 + - - +
496B THR* 3.6 24.0 - - - +
497B TYR* 3.5 2.9 - - - -
498B ARG* 3.0 25.7 + - - +
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Residues in contact with TRP 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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322B VAL* 3.6 30.4 - - + +
324B LYS 2.8 24.3 + - - -
325B GLY* 3.5 15.7 - - - -
326B ALA* 1.3 81.9 - - - +
328B TYR* 1.3 61.7 + - - +
346B TRP* 4.0 2.5 - - + -
394B PHE 3.6 0.7 - - - +
395B TYR* 3.4 7.5 - - - -
396B ILE* 2.9 40.5 + - + +
497B TYR* 4.2 3.6 - - - +
498B ARG* 3.2 57.7 - - + -
499B PRO 3.3 29.8 - - - -
500B MET* 3.9 18.2 - - - -
502B ASP* 3.7 8.7 - - + -
503B MET* 3.6 32.3 - - + -
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Residues in contact with TYR 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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327B TRP* 1.3 76.1 - - - +
329B PHE* 1.3 81.1 + - - +
330B GLU* 4.0 16.3 + - + +
393B GLY* 3.2 21.3 - - - -
394B PHE 3.2 26.7 - - - -
395B TYR* 3.9 10.3 - + + -
450B TYR* 3.6 21.8 - + - +
453B GLY* 5.3 0.3 + - - -
488B PHE* 3.5 31.2 - + + -
490B TYR 4.2 5.0 + - - -
492B PRO* 3.3 37.6 - - + +
495B LEU* 4.3 8.1 - - + -
497B TYR* 3.5 29.2 - + + -
498B ARG 3.0 6.4 + - - +
500B MET* 3.0 25.5 + - - +
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Residues in contact with PHE 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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328B TYR* 1.3 79.8 - - - +
330B GLU* 1.3 70.0 + - - +
331B ILE* 3.8 17.5 - - + -
345B GLY 3.5 20.9 - - - -
346B TRP* 3.4 37.9 - + - -
393B GLY* 3.6 2.4 - - - -
394B PHE* 2.9 59.4 + + + -
470B PRO* 3.4 27.4 - - + -
471B ALA 4.3 0.4 - - - -
482B ILE* 3.8 21.1 - - + -
483B ASN 3.5 12.3 - - - +
484B PHE* 4.2 9.0 - - + -
488B PHE* 3.7 6.7 - - - -
500B MET* 4.0 7.2 - - + -
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Residues in contact with GLU 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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328B TYR* 4.0 9.6 + - + -
329B PHE* 1.3 78.3 - - - +
331B ILE* 1.3 68.7 + - - +
332B THR* 5.7 0.9 - - - +
391B VAL* 3.7 19.2 - - + +
392B LEU 3.2 13.2 - - - +
393B GLY* 4.4 2.5 - - - -
482B ILE* 3.5 2.9 - - - +
483B ASN* 2.8 48.6 + - + +
488B PHE* 3.6 20.9 - - + +
489B LYS* 2.8 27.8 + - - +
490B TYR* 2.9 33.8 + - - +
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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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329B PHE* 3.8 19.3 - - + -
330B GLU* 1.3 80.4 - - - +
332B THR* 1.3 64.9 + - - +
333B VAL* 5.4 0.2 - - + -
344B LEU* 3.9 29.2 - - + -
391B VAL* 3.6 1.3 - - - -
392B LEU* 2.7 42.1 + - + +
394B PHE* 3.8 17.7 - - + -
471B ALA 4.5 2.7 - - - +
472B ILE* 3.6 25.8 - - + -
480B VAL* 3.6 31.9 - - + -
481B SER 3.3 7.4 - - - +
482B ILE* 3.8 15.0 - - + -
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Residues in contact with THR 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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330B GLU* 5.7 0.9 - - - +
331B ILE* 1.3 73.7 - - - +
333B VAL* 1.3 70.2 + - - +
334B ASP* 3.2 21.3 + - - +
389B GLY* 4.7 6.3 - - - +
390B ASP 3.5 10.8 - - - +
391B VAL* 3.7 24.9 - - + +
480B VAL* 3.2 4.0 - - - +
481B SER* 2.9 38.4 + - - -
489B LYS* 6.0 0.3 - - - +
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Residues in contact with VAL 333 (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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332B THR* 1.3 75.1 - - - +
334B ASP* 1.3 60.0 + - - +
335B GLU 4.1 7.4 - - - +
336B MET* 3.9 32.1 - - + -
342B ALA* 5.7 0.2 - - + -
344B LEU* 5.1 2.2 - - + -
386B TYR* 4.1 15.7 - - + -
387B GLY 3.3 24.9 - - - +
388B GLN* 3.8 10.5 - - - -
389B GLY* 2.8 31.4 + - - -
390B ASP 3.0 7.7 + - - +
392B LEU* 3.7 24.5 - - + -
479B THR 4.0 4.9 - - - +
480B VAL* 4.2 11.9 - - + -
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Residues in contact with ASP 334 (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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306B THR* 4.2 1.6 - - - +
332B THR* 3.2 19.0 + - - +
333B VAL* 1.3 74.7 - - - +
335B GLU* 1.3 62.7 + - + +
388B GLN* 3.7 14.4 + - - +
479B THR* 2.9 27.8 + - + +
480B VAL 3.5 4.2 - - - -
481B SER* 2.6 39.7 + - - -
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Residues in contact with GLU 335 (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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333B VAL* 3.4 3.0 - - - +
334B ASP* 1.3 82.6 - - + +
336B MET* 1.3 64.1 + - - +
337B PRO* 3.6 22.3 - - + +
388B GLN* 3.4 14.8 - - - +
477B SER 4.9 2.3 - - - +
478B CYS* 3.3 5.2 - - - +
479B THR* 2.8 44.6 + - - +
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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