Contacts of the strand formed by residues 316 - 320 (chain B) 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 THR 316 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B LEU* 4.0 17.0 - - + -
286B ARG* 4.6 3.0 + - - -
314B VAL* 4.6 1.6 - - - -
315B GLU* 1.3 101.8 + - - +
317B LEU* 1.3 63.3 + - - +
318B LEU* 3.8 20.9 + - + +
387B ASN* 3.6 19.4 + - - +
389B GLU* 4.1 14.6 - - + -
410B ALA* 3.0 27.4 - - - +
411B VAL* 3.0 18.7 + - - +
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Residues in contact with LEU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B THR* 3.1 38.1 - - + +
306B MET* 4.9 4.3 - - + -
309B LEU* 4.2 14.1 - - + -
314B VAL* 4.6 8.3 - - + -
316B THR* 1.3 71.4 - - - +
318B LEU* 1.3 66.7 + - - +
319B CYS 5.3 0.2 - - - +
377B LEU* 3.7 40.6 - - + -
381B TYR* 5.1 5.6 - - + -
386B ALA* 4.4 6.2 - - + +
387B ASN 2.9 16.3 + - - +
388B LEU* 3.6 19.4 - - + +
389B GLU 2.9 28.1 + - - +
408B ILE* 5.0 2.7 - - + -
409B GLY 3.5 5.2 - - - +
410B ALA* 4.0 4.5 - - + -
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Residues in contact with LEU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B LEU* 3.3 42.4 - - + -
284B ILE* 4.1 17.0 - - + -
287B PHE* 3.9 34.1 - - + -
316B THR* 3.9 17.5 - - + +
317B LEU* 1.3 80.3 - - - +
319B CYS* 1.3 59.5 + - - +
389B GLU 3.7 2.9 - - - +
391B VAL* 5.1 3.1 - - + -
401B PHE* 3.2 32.3 - - + -
408B ILE* 3.4 3.9 - - - +
409B GLY 2.6 41.0 + - - +
410B ALA* 4.9 0.7 - - - -
411B VAL* 5.4 2.5 - - + +
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Residues in contact with CYS 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B LEU* 3.8 0.8 + - + -
318B LEU* 1.3 75.9 - - - +
320B PHE* 1.3 69.9 + - - +
323B LEU* 3.8 28.3 - - - -
374B SER* 4.5 6.3 - - - -
377B LEU* 4.5 12.8 - - + -
388B LEU* 4.2 11.2 - - + -
389B GLU 3.0 8.5 + - - -
390B PHE* 3.2 34.5 - - + -
391B VAL* 2.8 30.8 + - - +
407B GLY 3.7 1.8 - - - -
408B ILE* 4.5 9.0 - - + +
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Residues in contact with PHE 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B CYS* 1.3 77.6 - - - +
321B ALA* 1.3 70.4 + - - +
322B ASP* 3.5 46.4 - - + -
323B LEU* 2.8 32.4 + - + +
374B SER* 5.1 0.3 - - - -
391B VAL* 3.4 17.9 - - + -
392B SER* 4.2 2.0 - - - -
393B ASP* 3.4 50.5 - - + -
401B PHE* 5.0 0.4 - - + -
402B VAL* 3.4 32.3 - - + -
406B GLY 6.0 0.2 - - - -
407B GLY* 3.0 27.4 + - - +
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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