Contacts of the strand formed by residues 321 - 326 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313E GLU* 3.6 35.2 + - + +
314E MET 3.0 21.3 - - - +
315E GLU* 3.7 18.3 - - + +
319E GLY 3.6 2.8 + - - +
320E ASP* 1.3 76.2 - - - +
322E VAL* 1.3 72.6 + - - +
348E THR* 5.0 0.2 + - - -
440E TRP* 4.5 0.2 - - - -
449E LYS* 4.3 28.3 - - - +
451E SER* 5.0 3.8 + - - -
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Residues in contact with VAL 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313E GLU* 3.6 2.8 - - - +
314E MET* 3.1 48.5 + - + +
321E LYS* 1.3 83.8 - - - +
323E LYS* 1.3 67.1 + - - +
348E THR* 3.3 26.7 - - - +
349E ALA* 3.6 18.8 - - + +
440E TRP* 3.7 38.8 - - + +
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Residues in contact with LYS 323 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245E GLU* 3.5 33.7 + - - +
311E LEU* 4.1 18.6 - - + -
312E ILE 3.4 10.1 - - - +
313E GLU* 4.2 8.5 - - + +
314E MET* 5.6 0.2 - - - -
322E VAL* 1.3 80.2 - - - +
324E ALA* 1.3 61.1 + - - +
325E HIS* 4.3 4.0 - - + -
346E ARG* 5.6 7.8 - - - +
347E GLY* 4.5 7.4 - - - -
348E THR* 3.0 25.4 + - - +
349E ALA* 2.8 27.0 + - - -
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Residues in contact with ALA 324 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310E LEU 4.2 0.2 - - - +
311E LEU* 3.7 2.0 - - - +
312E ILE* 2.8 43.5 + - + +
314E MET* 5.1 0.2 - - + -
323E LYS* 1.3 75.3 - - - +
325E HIS* 1.3 59.2 + - - +
326E TYR* 4.1 11.2 - - + -
345E TYR* 3.7 23.1 - - + -
346E ARG 4.2 0.7 - - - -
349E ALA* 3.9 12.1 - - + -
437E TRP* 4.0 19.7 - - + -
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Residues in contact with HIS 325 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245E GLU* 5.5 6.2 + - + +
249E TRP* 4.2 20.3 - + - -
309E GLU* 2.9 29.4 + - - +
310E LEU 3.5 7.3 + - - -
311E LEU* 4.5 13.6 - - + +
323E LYS* 5.8 4.9 - - + -
324E ALA* 1.3 73.6 - - - +
326E TYR* 1.3 95.8 + - - +
327E GLY* 3.8 3.2 + - - -
345E TYR* 3.0 5.5 - - - -
346E ARG* 2.7 82.0 + - + +
455E ARG* 5.2 3.1 - - - -
457E PHE* 5.8 1.0 - - - -
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Residues in contact with TYR 326 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309E GLU* 3.4 3.5 - - - +
310E LEU* 2.8 42.6 + - + +
312E ILE* 4.4 8.5 - - + -
324E ALA* 4.1 16.6 - - + -
325E HIS* 1.3 79.2 - - - +
327E GLY* 1.3 66.7 + - - +
328E GLY 3.2 11.4 + - - +
342E VAL* 3.7 22.2 - - + -
343E ASN 3.5 15.9 - - - +
344E LYS 3.4 4.3 - - - -
345E TYR* 3.3 37.9 - + + -
350E GLY 4.6 1.0 + - - -
351E ASN* 3.0 33.6 + - - -
352E ALA 4.1 0.5 + - - -
353E LEU* 3.5 30.0 + - + +
354E MET* 3.7 14.1 - - + -
437E TRP* 4.6 2.0 - + - -
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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