Contacts of the strand formed by residues 378 - 383 (chain B) in PDB entry 5FS9
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 378 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B ARG* 4.2 2.0 - - - +
301B LYS* 5.5 2.6 - - - +
302B SER* 4.8 5.1 - - - -
374B VAL* 3.2 7.6 - - - -
375B SER* 2.9 37.9 + - - +
376B SER* 4.2 9.4 - - - +
377B GLY* 1.3 80.8 - - - +
379B LEU* 1.3 66.8 + - - +
380B LEU* 6.1 0.2 - - + -
390B GLU* 4.2 24.3 + - + +
391B THR* 3.9 20.3 - - - +
392B ASP* 2.9 36.7 + - - +
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Residues in contact with LEU 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B VAL* 4.1 31.6 - - + +
280B ARG* 3.9 39.9 - - + +
372B VAL* 4.6 6.7 - - + -
373B GLY 3.4 2.9 - - - +
374B VAL* 4.2 8.7 - - + -
378B LYS* 1.3 73.9 - - - +
380B LEU* 1.3 59.5 + - - +
381B ILE* 4.0 1.3 - - + -
389B VAL 3.6 0.5 - - - +
390B GLU* 3.2 6.1 - - - +
391B THR* 2.8 44.5 + - + +
392B ASP 3.8 3.8 - - - +
393B HIS* 3.8 30.7 - - - +
394B ILE* 3.8 22.9 - - + -
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Residues in contact with LEU 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B SER 4.5 0.2 - - - -
372B VAL* 3.4 2.9 - - - -
373B GLY* 2.7 40.3 + - - +
375B SER* 3.9 30.7 - - - +
378B LYS* 6.1 0.2 - - + -
379B LEU* 1.3 73.4 - - - +
381B ILE* 1.3 61.2 + - - +
382B LYS* 3.9 30.9 + - + +
388B LYS* 4.2 22.4 - - + -
389B VAL 3.5 19.5 - - - +
390B GLU* 4.1 16.8 - - + -
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Residues in contact with ILE 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B THR* 4.1 24.0 - - + -
306B ILE* 4.8 4.5 - - + -
333B LEU* 4.4 9.4 - - + -
369B VAL* 3.9 24.0 - - + -
371B SER 3.6 4.3 - - - +
372B VAL* 4.1 8.3 - - + -
380B LEU* 1.3 74.6 - - - +
382B LYS* 1.3 63.2 + - - +
383B LEU* 3.9 24.0 + - + +
388B LYS* 3.3 4.9 - - - +
389B VAL* 2.8 46.8 + - + +
391B THR* 4.2 15.3 - - + -
394B ILE* 3.8 30.1 - - + -
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Residues in contact with LYS 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B VAL* 3.7 3.6 - - - +
370B GLN* 2.8 27.2 + - + +
371B SER* 2.8 34.3 + - - +
380B LEU* 4.1 28.0 - - + +
381B ILE* 1.3 74.6 - - - +
383B LEU* 1.3 64.3 + - - +
387B ARG 3.8 4.0 - - - -
388B LYS* 4.0 36.4 - - + +
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Residues in contact with LEU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B LEU* 4.5 6.3 - - + -
364B MET* 4.7 10.3 - - + -
367B ALA* 3.6 27.1 - - + -
368B ILE 3.3 17.3 - - - +
369B VAL* 3.9 12.6 - - + -
370B GLN* 4.1 7.4 - - - +
381B ILE* 3.9 25.4 - - + +
382B LYS* 1.3 78.2 - - - +
384B LYS* 1.3 66.5 + - - +
385B ASP* 3.6 12.6 - - - +
386B GLY* 3.0 15.8 + - - -
387B ARG* 2.9 47.0 + - + +
389B VAL* 4.7 6.5 - - + -
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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