Contacts of the strand formed by residues 408 - 412 (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 ILE 408 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300K PHE* 3.3 4.1 + - - -
301K GLY* 3.0 32.2 - - - -
302K VAL* 3.5 38.4 - - + +
305K THR* 3.2 15.3 + - + +
306K MET* 4.6 10.1 - - + -
317K LEU* 5.1 1.6 - - + -
318K LEU 3.5 11.4 - - - +
319K CYS* 4.9 0.9 - - - -
323K LEU* 3.8 24.7 - - + -
373K LEU* 4.5 15.0 - - + -
377K LEU* 4.1 22.9 - - + -
401K PHE* 3.7 5.5 - - - -
405K PHE 3.4 2.8 + - - +
406K GLY* 3.4 9.4 - - - +
407K GLY* 1.3 82.6 - - - +
409K GLY* 1.3 61.1 + - - +
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Residues in contact with GLY 409 (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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287K PHE* 4.6 2.0 - - - -
299K CYS 2.9 1.6 - - - -
300K PHE 2.9 18.2 - - - -
305K THR* 3.4 9.0 - - - -
317K LEU* 3.4 3.6 - - - +
318K LEU* 2.6 43.4 + - - +
401K PHE* 3.4 9.6 - - - -
408K ILE* 1.3 75.7 - - - +
410K ALA* 1.3 57.9 + - - +
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Residues in contact with ALA 410 (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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287K PHE* 4.1 6.3 - - - -
298K TYR* 3.2 19.4 - - - +
299K CYS* 2.5 24.8 + - - +
305K THR* 4.2 4.3 - - + -
314K VAL* 3.8 29.6 - - + -
316K THR 3.2 14.4 - - - +
317K LEU* 3.8 11.9 - - + -
318K LEU* 4.3 2.0 - - - +
409K GLY* 1.3 76.8 - - - +
411K VAL* 1.3 64.6 + - - +
412K MET 3.6 1.1 + - - +
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Residues in contact with VAL 411 (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* 6.1 0.7 - - + -
286K ARG* 3.8 32.3 - - - +
287K PHE* 3.5 42.6 - - + +
290K GLU* 4.6 11.0 - - + -
297K LYS 4.0 8.5 - - - +
315K GLU* 3.2 25.8 + - + +
316K THR* 3.0 25.6 + - - +
318K LEU* 5.6 2.9 - - + -
410K ALA* 1.3 73.5 - - - +
412K MET* 1.3 64.0 + - - +
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Residues in contact with MET 412 (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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296K GLY 4.3 4.9 - - - +
297K LYS* 3.3 29.4 - - - +
298K TYR 3.6 21.1 - - - +
299K CYS* 3.2 19.1 - - - -
308K ALA* 3.1 36.1 - - + -
313K ALA 4.5 11.0 - - - +
314K VAL* 4.3 6.3 - - + +
315K GLU* 4.1 8.3 - - - +
410K ALA 3.6 1.8 + - - +
411K VAL* 1.3 79.0 - - - +
413K ARG* 1.3 59.8 + - - +
414K TYR 3.3 24.5 - - - +
416K LEU* 4.2 18.6 - - + +
418K LEU* 4.0 20.6 - - + -
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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