Contacts of the strand formed by residues 381 - 388 (chain F) 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 381 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196F LYS* 5.5 2.9 - - + -
197F ARG* 3.4 11.9 - - - +
198F LEU* 4.0 23.6 - - + +
249F GLU 4.6 0.4 - - - -
250F LEU* 3.6 1.8 - - - -
251F GLU* 3.1 65.1 + - + +
367F ILE* 6.5 0.2 - - - -
379F MET* 3.6 6.4 - - - +
380F LYS* 1.3 101.3 - - + +
382F THR* 1.3 68.1 + - - +
383F THR* 5.4 3.6 - - + -
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Residues in contact with THR 382 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195F GLN* 2.8 28.5 - - + +
196F LYS* 3.2 8.0 - - - +
197F ARG* 2.8 41.7 + - + +
249F GLU 3.5 5.8 - - - -
250F LEU* 3.2 15.3 - - + +
344F LEU* 3.5 27.1 - - + +
367F ILE* 3.4 19.9 - - - +
379F MET* 4.0 0.7 - - - +
381F LYS* 1.3 79.9 + - - +
383F THR* 1.3 66.3 + - - +
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Residues in contact with THR 383 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F GLU* 5.3 1.4 + - - -
193F VAL* 4.5 5.7 - - - +
195F GLN 3.4 7.1 + - - -
196F LYS* 3.3 25.5 - - + -
247F ARG 3.4 1.4 - - - +
248F VAL* 3.3 5.7 - - - +
249F GLU* 2.9 73.5 + - + +
250F LEU 6.1 0.2 - - - -
381F LYS* 5.4 3.6 - - + -
382F THR* 1.3 82.0 - - - +
384F MET* 1.3 66.7 + - - +
385F LYS* 4.0 11.7 - - - +
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Residues in contact with MET 384 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193F VAL* 3.8 1.3 - - - +
194F PHE* 2.9 57.2 + - + -
195F GLN* 3.1 40.0 + - + -
227F TRP* 4.4 0.7 - - - -
246F LEU* 4.2 12.3 - - + -
247F ARG 3.4 5.2 - - - -
248F VAL* 4.8 7.0 - - + -
265F PHE* 6.3 0.2 - - + -
290F PHE* 4.5 14.1 - - + -
334F TRP* 3.3 35.9 - - + -
335F TRP* 5.4 4.5 - - + +
344F LEU* 3.7 23.1 - - + -
383F THR* 1.3 76.1 + - - +
385F LYS* 1.3 60.6 + - - +
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Residues in contact with LYS 385 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F GLU* 2.7 36.1 + - - +
191F TRP* 3.4 39.2 - - + +
192F THR 4.0 0.2 - - - -
193F VAL* 3.8 25.1 - - + +
194F PHE 4.4 0.2 - - - +
245F ALA 3.9 0.2 - - - +
246F LEU* 3.4 0.9 - - - +
247F ARG* 2.8 49.9 + - - +
249F GLU* 2.8 41.6 + - - -
383F THR* 4.4 8.7 - - - +
384F MET* 1.3 74.4 - - - +
386F ILE* 1.3 68.2 + - - +
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Residues in contact with ILE 386 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191F TRP* 3.7 2.8 - - - -
192F THR* 2.9 49.1 + - + +
194F PHE* 3.6 27.6 - - + -
233F ILE* 5.4 4.5 - - + +
236F ILE* 4.1 31.0 - - + -
237F SER* 4.7 11.9 - - - -
244F TYR* 4.2 17.3 - - + -
245F ALA 3.2 11.2 - - - +
246F LEU* 3.9 7.6 - - + -
265F PHE* 4.1 17.9 - - + -
385F LYS* 1.3 80.9 - - - +
387F ILE* 1.3 63.7 + - - +
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Residues in contact with ILE 387 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154F GLN* 3.2 20.6 - - - +
189F ASN* 3.6 22.4 - - + +
190F GLY 3.5 27.4 - - - +
191F TRP* 3.7 35.7 - - + -
192F THR* 5.0 0.4 - - - -
244F TYR* 3.4 6.9 - - - -
245F ALA 2.6 38.8 + - - +
386F ILE* 1.3 77.3 - - - +
388F PRO* 1.3 85.7 - - + +
391F ARG* 4.1 8.3 - - + -
392F LEU* 4.6 14.6 - - + -
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Residues in contact with PRO 388 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152F ASP* 3.9 8.7 - - - +
154F GLN* 3.6 24.2 - - + -
242F ILE* 5.5 4.0 - - + +
243F PRO 3.2 10.8 - - - +
244F TYR* 3.6 22.6 - - + +
387F ILE* 1.3 97.0 - - + +
389F PHE* 1.3 56.7 + - - +
390F ASN* 3.1 17.7 - - - +
391F ARG* 2.8 38.9 + - + +
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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