Contacts of the strand formed by residues 314 - 320 (chain H) in PDB entry 3E20
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 VAL 314 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305H THR* 4.6 1.8 - - + +
308H ALA* 3.5 18.6 - - + -
309H LEU* 3.5 49.9 - - + +
313H ALA* 1.3 76.1 - - - +
315H GLU* 1.3 62.5 + - - +
316H THR 4.4 1.8 - - - +
317H LEU* 4.4 9.4 - - + -
384H TYR 4.5 1.6 + - - -
386H ALA* 3.6 22.3 + - + -
410H ALA* 3.7 29.4 - - + -
412H MET* 4.2 9.9 - - + +
413H ARG* 3.3 13.4 + - - -
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Residues in contact with GLU 315 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286H ARG* 2.8 31.1 + - - -
314H VAL* 1.3 74.0 - - - +
316H THR* 1.3 64.3 + - - +
317H LEU 4.3 0.2 - - - -
387H ASN* 2.6 47.6 + - - +
411H VAL* 3.2 24.7 + - - +
412H MET* 4.0 4.5 - - - +
413H ARG* 3.1 40.3 - - + +
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Residues in contact with THR 316 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283H LEU* 3.8 26.7 - - + -
286H ARG* 3.6 11.1 + - - +
314H VAL* 4.5 0.9 - - - -
315H GLU* 1.3 100.8 + - - +
317H LEU* 1.3 68.4 + - - +
318H LEU* 4.0 3.7 + - + +
387H ASN* 3.4 12.5 + - + +
389H GLU* 4.2 14.6 - - + -
410H ALA* 3.3 5.4 - - - -
411H VAL* 3.0 38.8 + - - +
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Residues in contact with LEU 317 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305H THR* 3.6 23.8 - - + -
306H MET* 5.2 0.9 - - + -
309H LEU* 3.9 31.4 - - + -
314H VAL* 4.4 5.4 - - + -
316H THR* 1.3 74.0 - - - +
318H LEU* 1.3 70.0 + - - +
319H CYS 4.2 0.2 - - - -
377H LEU* 4.2 20.2 - - + -
381H TYR* 4.9 6.1 - - + -
386H ALA* 4.3 9.6 - - + +
387H ASN 2.8 18.0 + - - +
388H LEU* 3.7 22.7 - - + -
389H GLU* 3.1 26.4 + - - +
408H ILE* 5.1 3.8 - - + -
409H GLY 3.3 18.2 - - - +
410H ALA* 3.9 6.5 - - + -
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Residues in contact with LEU 318 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283H LEU* 3.3 37.9 - - + +
284H ILE* 3.9 25.6 - - + -
287H PHE* 3.8 30.1 - - + -
316H THR* 4.4 7.9 - - + +
317H LEU* 1.3 84.8 - - - +
319H CYS* 1.3 61.6 + - - +
389H GLU* 3.8 3.8 - - + +
391H VAL* 5.0 5.6 - - + -
401H PHE* 3.1 33.5 - - + -
408H ILE* 3.5 6.8 - - - +
409H GLY 2.7 36.2 + - - +
410H ALA* 5.1 0.4 - - - -
411H VAL* 5.6 1.8 - - + -
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Residues in contact with CYS 319 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317H LEU* 5.5 0.2 - - + -
318H LEU* 1.3 75.8 - - - +
320H PHE* 1.3 69.6 + - - +
323H LEU* 3.5 29.4 - - - -
374H SER* 4.5 6.7 - - - -
377H LEU* 4.4 17.5 - - + -
388H LEU* 4.4 12.6 - - + -
389H GLU 3.2 8.1 + - - +
390H PHE* 3.2 32.4 - - + -
391H VAL* 2.7 34.2 + - - +
401H PHE* 4.2 0.8 - - - -
407H GLY 4.0 2.9 - - - -
408H ILE* 5.2 0.7 - - + -
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Residues in contact with PHE 320 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319H CYS* 1.3 72.6 - - - +
321H ALA* 1.3 71.6 + - + +
322H ASP* 3.5 46.0 - - + -
323H LEU* 2.8 27.8 + - + +
324H ASP 5.2 0.2 - - - -
391H VAL* 3.1 19.8 - - + +
392H SER* 3.9 3.6 - - - -
393H ASP* 3.3 49.6 - - + -
401H PHE* 4.4 0.4 - - + -
402H VAL* 3.6 33.9 - - + -
407H GLY* 3.3 22.8 + - - +
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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