Contacts of the strand formed by residues 321 - 326 (chain B) in PDB entry 1FZB
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 321 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B GLU* 3.6 33.9 + - + +
314B MET 3.1 21.5 - - - +
315B GLU* 3.5 19.3 + - + +
319B GLY 3.7 3.5 + - - +
320B ASP* 1.3 75.5 - - - +
322B VAL* 1.3 71.8 + - - +
348B THR* 5.0 0.2 + - - -
440B TRP* 4.5 0.4 - - - -
449B LYS* 4.2 28.5 - - - +
451B SER* 5.1 4.4 + - - -
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Residues in contact with VAL 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B GLU* 3.6 3.1 - - - +
314B MET* 3.1 48.9 + - + +
321B LYS* 1.3 84.7 - - - +
323B LYS* 1.3 65.1 + - - +
348B THR* 3.3 27.1 - - - +
349B ALA* 3.6 18.8 - - + +
440B TRP* 3.6 39.9 - - + +
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Residues in contact with LYS 323 (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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245B GLU* 3.5 34.4 + - - +
311B LEU* 4.1 18.2 - - + -
312B ILE 3.4 10.1 - - - +
313B GLU* 4.2 7.9 - - + -
314B MET* 5.6 0.2 - - - -
322B VAL* 1.3 80.2 - - - +
324B ALA* 1.3 59.3 + - - +
325B HIS* 5.7 4.3 - - + +
346B ARG* 5.7 7.8 - - - +
347B GLY* 3.6 7.6 - - - -
348B THR* 3.0 25.4 + - - +
349B ALA* 2.8 27.7 + - - -
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Residues in contact with ALA 324 (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 LEU 4.1 0.3 - - - +
311B LEU* 3.7 2.4 - - - +
312B ILE* 2.7 49.1 + - + +
323B LYS* 1.3 74.3 - - - +
325B HIS* 1.3 58.7 + - - +
326B TYR* 4.1 11.2 - - + -
345B TYR* 3.8 21.5 - - + -
346B ARG 4.3 0.4 - - - -
349B ALA* 3.9 13.7 - - + -
437B TRP* 4.0 20.6 - - + -
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Residues in contact with HIS 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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245B GLU* 5.4 6.7 + - + +
249B TRP* 4.3 17.0 - + - -
309B GLU* 3.0 31.6 + - - +
310B LEU 3.5 6.2 + - - -
311B LEU* 4.5 17.1 - - + +
323B LYS* 5.7 4.9 - - + -
324B ALA* 1.3 72.3 - - - +
326B TYR* 1.3 93.6 + - - +
327B GLY* 3.8 2.6 + - - -
344B LYS 3.4 0.3 - - - +
345B TYR* 3.0 7.2 - - - -
346B ARG* 2.8 84.2 + - + +
455B ARG* 5.3 2.5 - - - -
457B PHE* 5.9 1.4 - - - -
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Residues in contact with TYR 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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309B GLU* 3.3 2.8 - - - +
310B LEU* 2.8 47.9 + - + +
312B ILE* 4.4 2.5 - - + -
324B ALA* 4.1 17.3 - - + -
325B HIS* 1.3 80.3 - - - +
327B GLY* 1.3 64.9 + - - +
328B GLY 3.1 11.5 + - - +
342B VAL* 3.7 20.6 - - + -
343B ASN 3.4 15.7 - - - +
344B LYS 3.4 3.8 - - - -
345B TYR* 3.4 35.7 - + + -
350B GLY 4.6 0.9 + - - -
351B ASN* 2.6 34.0 + - - -
352B ALA 4.1 0.5 + - - -
353B LEU* 3.4 30.4 + - + +
354B MET* 3.7 15.7 - - + -
437B TRP* 4.7 1.3 - + - -
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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