Contacts of the strand formed by residues 378 - 383 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A ARG* 4.4 0.9 - - - +
301A LYS* 5.1 9.5 - - - +
302A SER* 4.5 6.5 - - - -
374A VAL* 3.2 5.0 - - - -
375A SER 2.9 37.2 + - - +
376A SER* 3.7 15.7 - - - +
377A GLY* 1.3 79.7 - - - +
379A LEU* 1.3 68.9 + - - +
380A LEU* 3.7 7.6 - - + +
390A GLU* 4.6 25.9 + - + +
391A THR* 3.8 16.9 - - - +
392A ASP* 2.8 38.3 + - - +
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Residues in contact with LEU 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A VAL* 4.3 16.4 - - + +
280A ARG* 3.8 40.4 - - + +
372A VAL* 4.6 2.7 - - + -
373A GLY 3.4 4.0 - - - +
374A VAL* 4.1 20.9 - - + -
377A GLY 4.1 0.2 + - - -
378A LYS* 1.3 71.7 - - - +
380A LEU* 1.3 61.0 + - - +
381A ILE* 4.0 0.9 - - + -
389A VAL 3.7 0.7 - - - +
390A GLU* 3.3 6.2 - - - -
391A THR* 2.8 44.6 + - + +
392A ASP 3.9 1.8 - - - +
393A HIS* 3.8 23.8 - - - +
394A ILE* 3.7 34.5 - - + -
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Residues in contact with LEU 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A SER 3.8 1.0 - - - +
372A VAL* 3.2 4.6 - - - -
373A GLY* 2.7 40.5 + - - +
374A VAL 5.2 0.4 - - - -
375A SER* 3.5 30.3 - - - +
378A LYS* 3.7 18.2 - - + +
379A LEU* 1.3 80.6 - - - +
381A ILE* 1.3 63.2 + - - +
382A LYS* 3.9 1.1 + - - +
389A VAL 3.5 3.8 - - - +
390A GLU* 4.0 25.4 - - + -
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Residues in contact with ILE 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A THR* 3.9 26.0 - - + -
306A ILE* 4.8 4.9 - - + -
333A LEU* 4.5 8.7 - - + -
369A VAL* 4.1 19.5 - - + -
371A SER 3.7 6.5 - - - +
372A VAL* 4.1 7.6 - - + -
379A LEU 5.1 0.4 - - - -
380A LEU* 1.3 73.4 - - - +
382A LYS* 1.3 62.1 + - - +
383A LEU* 4.1 22.6 + - + +
388A LYS* 3.4 5.4 - - - +
389A VAL* 2.7 50.5 + - + +
391A THR* 4.0 15.9 - - + -
394A ILE* 3.8 31.2 - - + -
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Residues in contact with LYS 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A VAL* 3.7 2.4 - - - +
370A GLN* 2.7 50.0 + - + +
371A SER* 2.9 26.7 + - - +
380A LEU 3.9 1.9 + - - +
381A ILE* 1.3 74.1 - - - +
383A LEU* 1.3 77.2 + - - +
384A LYS 4.9 2.2 - - - -
386A GLY* 4.0 16.3 + - - +
387A ARG 3.8 6.7 - - - +
388A LYS* 4.0 30.5 - - + +
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Residues in contact with LEU 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A LEU* 4.6 7.2 - - + -
364A MET* 4.2 13.9 - - + -
367A ALA* 3.6 29.2 - - + -
368A ILE 3.2 20.9 - - - +
369A VAL* 4.1 9.9 - - + -
370A GLN* 3.7 1.8 - - - -
381A ILE* 4.1 17.0 - - + +
382A LYS* 1.3 93.7 - - - +
384A LYS* 1.3 66.6 + - - +
385A ASP* 3.3 13.2 - - - +
386A GLY* 3.0 10.7 + - - -
387A ARG* 3.0 48.2 + - + +
388A LYS* 5.4 0.4 - - - -
389A VAL* 5.4 2.5 - - + -
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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
------------------------------------------------------------
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