Contacts of the strand formed by residues 314 - 320 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305K THR 4.6 1.3 - - - +
308K ALA* 3.5 17.7 - - + -
309K LEU* 3.5 49.9 - - + +
313K ALA* 1.3 75.0 - - - +
315K GLU* 1.3 62.5 + - - +
316K THR 4.4 2.0 - - - +
317K LEU* 4.4 8.7 - - + -
384K TYR 4.5 2.0 + - - -
386K ALA* 3.5 24.9 + - + -
410K ALA* 3.8 30.5 - - + -
412K MET* 4.3 11.0 - - + +
413K ARG* 3.4 12.1 + - - -
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Residues in contact with GLU 315 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286K ARG* 2.7 33.1 + - - -
314K VAL* 1.3 75.3 - - - +
316K THR* 1.3 63.2 + - - +
387K ASN* 2.6 45.4 + - - +
411K VAL* 3.2 23.9 + - - +
412K MET* 4.1 2.3 - - - +
413K ARG* 3.4 44.7 - - + +
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Residues in contact with THR 316 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283K LEU* 3.8 26.5 - - + -
286K ARG* 3.6 10.9 + - - -
314K VAL* 4.4 1.1 - - - -
315K GLU* 1.3 101.0 + - - +
317K LEU* 1.3 68.7 + - - +
318K LEU* 4.5 3.8 - - + +
387K ASN* 3.5 12.9 + - + +
389K GLU* 4.2 13.5 - - + -
410K ALA* 3.2 5.3 - - - +
411K VAL* 3.0 39.4 + - - +
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Residues in contact with LEU 317 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305K THR* 3.5 24.2 - - + -
306K MET* 5.3 0.7 - - + -
309K LEU* 3.9 31.0 - - + -
314K VAL* 4.4 4.7 - - + +
315K GLU 4.3 0.2 - - - -
316K THR* 1.3 73.2 - - - +
318K LEU* 1.3 71.2 + - - +
377K LEU* 4.1 20.9 - - + -
381K TYR* 4.9 5.6 - - + -
386K ALA* 4.3 9.4 - - + -
387K ASN 2.8 17.5 + - - +
388K LEU* 3.8 23.8 - - + -
389K GLU* 3.2 24.0 + - - +
408K ILE* 5.1 3.6 - - + -
409K GLY 3.4 17.3 - - - +
410K ALA* 3.8 7.6 - - + -
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Residues in contact with LEU 318 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283K LEU* 3.3 33.7 - - + +
284K ILE* 3.9 28.7 - - + -
287K PHE* 3.9 30.5 - - + -
316K THR* 4.5 9.6 - - + +
317K LEU* 1.3 86.7 - - - +
319K CYS* 1.3 62.1 + - - +
389K GLU* 3.8 4.0 - - + +
391K VAL* 5.0 5.2 - - + -
401K PHE* 3.1 30.6 - - + -
408K ILE* 3.5 6.8 - - - +
409K GLY 2.6 36.9 + - - +
410K ALA* 5.1 0.2 - - - -
411K VAL* 5.6 2.5 - - + -
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Residues in contact with CYS 319 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318K LEU* 1.3 75.6 - - - +
320K PHE* 1.3 65.7 + - - +
321K ALA 3.3 0.2 + - - -
323K LEU* 3.4 33.2 - - - -
374K SER* 4.5 6.1 - - - -
377K LEU* 4.4 17.5 - - + -
388K LEU* 4.4 12.1 - - + -
389K GLU 3.2 7.3 + - - -
390K PHE* 3.2 32.0 - - + -
391K VAL* 2.7 35.0 + - - +
401K PHE* 4.2 1.0 - - - -
407K GLY 4.0 2.5 - - - -
408K ILE* 4.9 1.1 - - + -
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Residues in contact with PHE 320 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319K CYS* 1.3 75.6 - - - +
321K ALA* 1.3 69.6 + - + +
322K ASP* 3.5 45.8 - - + -
323K LEU* 2.9 28.8 + - + +
324K ASP 5.2 0.7 - - - -
391K VAL* 3.1 19.6 - - + +
392K SER* 4.0 3.8 - - - -
393K ASP* 3.3 50.0 - - + -
401K PHE* 4.4 0.6 - - + -
402K VAL* 3.6 35.2 - - + -
407K GLY* 3.3 22.2 + - - +
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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