Contacts of the helix formed by residues 301 - 311 (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 GLY 301 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300C PHE* 1.3 82.9 - - - +
302C VAL* 1.3 62.4 + - - -
303C VAL* 3.6 2.9 - - - -
304C ASP* 4.0 7.4 - - - -
305C THR* 2.3 38.6 + - - -
405C PHE 4.4 3.1 + - - -
406C GLY* 6.1 1.8 - - - -
408C ILE* 3.0 15.0 + - - +
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Residues in contact with VAL 302 (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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301C GLY* 1.3 69.6 - - - -
303C VAL* 1.3 71.0 - - + +
304C ASP 3.0 1.1 - - - -
305C THR* 3.3 1.0 + - - -
306C MET* 2.8 40.0 + - + +
325C MET* 3.7 41.3 - - + -
341C TYR* 5.2 6.5 - - + -
373C LEU* 3.9 15.0 - - + -
408C ILE* 3.6 21.9 - - + +
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Residues in contact with VAL 303 (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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301C GLY* 5.1 1.3 - - - -
302C VAL* 1.3 85.0 - - + +
304C ASP* 1.3 70.0 + - - +
306C MET* 4.3 3.0 - - - +
307C ASN* 3.2 40.6 + - - +
341C TYR* 5.5 9.6 - - + -
420C MET* 4.4 8.3 - - + +
421C LEU 5.0 4.7 - - - +
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Residues in contact with ASP 304 (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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299C CYS* 4.3 10.9 - - + -
300C PHE 3.8 20.7 - - - +
301C GLY* 3.9 3.8 + - - +
302C VAL 3.0 0.6 - - - -
303C VAL* 1.3 90.2 - - - +
305C THR* 1.3 60.7 + - - +
306C MET 3.3 0.2 - - - -
307C ASN* 3.3 7.2 + - - +
308C ALA* 2.8 30.2 + - - +
418C LEU* 3.3 36.9 - - + +
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Residues in contact with THR 305 (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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299C CYS* 3.2 19.2 + - - +
300C PHE 3.3 7.3 + - - -
301C GLY 2.3 28.2 + - - -
302C VAL 4.1 0.9 - - - -
304C ASP* 1.3 75.4 - - - +
306C MET* 1.3 59.7 + - + +
308C ALA* 3.3 5.3 + - - +
309C LEU* 2.9 28.9 + - - +
314C VAL* 4.5 0.8 - - + +
317C LEU* 3.1 35.9 - - + -
408C ILE* 3.4 13.1 + - + -
409C GLY* 3.7 17.7 - - - +
410C ALA* 3.8 4.9 - - + -
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Residues in contact with MET 306 (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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302C VAL* 2.8 22.9 + - - +
303C VAL 4.3 2.5 - - - +
305C THR* 1.3 81.6 - - + +
307C ASN* 1.3 53.6 + - - +
309C LEU* 3.3 16.2 + - + +
310C GLN* 2.6 38.4 + - - +
317C LEU* 4.7 3.8 - - + -
341C TYR* 3.6 41.7 - - + +
373C LEU* 3.9 24.7 - - + -
376C TRP* 4.2 10.8 - - - -
377C LEU* 3.5 35.7 - - + -
408C ILE* 4.6 8.7 - - + -
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Residues in contact with ASN 307 (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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303C VAL* 3.2 27.7 + - - +
304C ASP* 3.6 8.4 + - - +
306C MET* 1.3 81.9 - - - +
308C ALA* 1.3 53.5 + - - +
310C GLN* 3.4 10.5 - - - +
311C GLU* 2.6 40.8 + - + +
418C LEU* 5.9 4.4 - - + +
419C SER 3.3 13.7 + - - +
420C MET* 2.5 52.5 + - - +
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Residues in contact with ALA 308 (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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299C CYS* 4.0 20.0 - - - -
304C ASP 2.8 21.0 + - - +
305C THR* 3.7 3.1 - - - +
307C ASN* 1.3 72.5 - - - +
309C LEU* 1.3 54.4 + - - +
311C GLU* 2.4 26.9 - - - +
313C ALA 3.7 7.4 + - - +
314C VAL* 3.4 22.8 - - + +
412C MET* 4.1 12.1 - - + -
416C LEU* 4.7 11.1 - - + +
418C LEU* 5.2 6.0 - - + +
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Residues in contact with LEU 309 (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 2.9 16.9 + - - +
306C MET* 3.5 27.4 - - + +
308C ALA* 1.3 74.7 - - - +
310C GLN* 1.3 69.3 + - - +
311C GLU 2.9 7.3 - - - +
312C GLY 3.9 5.5 - - - +
313C ALA* 4.9 0.7 - - - -
314C VAL* 3.4 30.6 - - + +
317C LEU* 4.2 13.5 - - + -
376C TRP* 4.7 8.5 - - + -
377C LEU* 3.7 17.3 - - + -
381C TYR* 5.2 5.4 - - - +
384C TYR* 3.2 55.0 - - + +
386C ALA* 4.7 6.3 - - + -
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Residues in contact with GLN 310 (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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306C MET 2.6 22.8 + - - +
307C ASN* 3.4 13.7 - - - +
309C LEU* 1.3 77.8 - - - +
311C GLU* 1.3 62.3 + - + +
312C GLY 4.5 1.0 - - - +
339C ILE* 5.7 7.7 - - - +
376C TRP* 5.5 4.8 - - - -
384C TYR* 3.8 28.3 + - - -
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Residues in contact with GLU 311 (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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307C ASN* 2.6 22.3 + - + +
308C ALA* 2.4 26.4 - - - +
309C LEU 2.9 3.1 - - - +
310C GLN* 1.3 76.4 - - + +
312C GLY* 1.3 77.0 + - - +
313C ALA 3.6 0.2 - - - -
414C TYR* 5.7 0.4 + - - +
416C LEU* 4.3 18.8 - - + -
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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