Contacts of the strand formed by residues 316 - 320 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283C LEU* 4.0 17.2 - - + +
286C ARG* 4.6 3.0 + - - -
314C VAL* 4.6 2.0 - - - -
315C GLU* 1.3 101.7 + - - +
317C LEU* 1.3 62.8 + - - +
318C LEU* 3.8 20.8 + - + +
387C ASN* 3.5 20.3 + - - +
389C GLU* 4.1 14.8 - - + -
410C ALA* 3.0 8.4 - - - +
411C VAL* 3.0 37.6 + - - +
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Residues in contact with LEU 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305C THR* 3.1 37.7 - - + +
306C MET* 4.7 4.3 - - + -
309C LEU* 4.2 14.4 - - + -
314C VAL* 4.6 8.1 - - + -
316C THR* 1.3 73.5 - - - +
318C LEU* 1.3 64.7 + - - +
319C CYS 3.9 0.2 - - - -
377C LEU* 3.6 42.0 - - + -
381C TYR* 5.1 5.2 - - + -
386C ALA* 4.4 5.8 - - + +
387C ASN 2.9 15.3 + - - +
388C LEU* 3.6 18.5 - - + +
389C GLU* 2.9 28.6 + - - +
408C ILE* 5.0 3.4 - - + -
409C GLY 3.5 4.3 - - - +
410C ALA* 4.0 5.2 - - + -
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Residues in contact with LEU 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283C LEU* 3.3 43.5 - - + +
284C ILE* 4.1 17.0 - - + -
287C PHE* 3.9 32.8 - - + -
316C THR* 3.8 18.4 - - + +
317C LEU* 1.3 79.3 - - - +
319C CYS* 1.3 59.8 + - - +
389C GLU 3.7 2.7 - - - +
391C VAL* 5.1 2.7 - - + -
401C PHE* 3.2 33.5 - - + -
408C ILE* 3.4 3.9 - - - +
409C GLY 2.6 40.8 + - - +
410C ALA* 4.9 0.4 - - - -
411C VAL* 5.5 2.2 - - + +
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Residues in contact with CYS 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317C LEU* 3.8 1.0 + - + -
318C LEU* 1.3 76.4 - - - +
320C PHE* 1.3 70.3 + - - +
323C LEU* 3.8 28.5 - - - -
374C SER* 4.5 6.7 - - - -
377C LEU* 4.5 13.0 - - + -
388C LEU* 4.2 11.9 - - + -
389C GLU 3.0 7.7 + - - -
390C PHE* 3.2 35.6 - - + -
391C VAL* 2.8 30.8 + - - +
401C PHE* 4.5 0.2 - - - -
407C GLY 3.7 1.3 - - - -
408C ILE* 4.5 8.1 - - + +
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Residues in contact with PHE 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C CYS* 1.3 78.0 - - - +
321C ALA* 1.3 71.5 + - - +
322C ASP* 3.5 48.9 - - + -
323C LEU* 2.8 30.9 + - + +
324C ASP 5.3 0.2 - - - -
374C SER* 5.1 0.2 - - - -
390C PHE* 4.8 0.2 - - - -
391C VAL* 3.4 17.5 - - + -
392C SER* 4.3 1.8 - - - -
393C ASP* 3.4 50.3 - - + -
401C PHE* 5.0 1.1 - - + -
402C VAL* 3.4 29.4 - - + -
407C GLY* 3.0 27.9 + - - +
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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