Contacts of the strand formed by residues 414 - 418 (chain F) in PDB entry 4CDC
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 TYR 414 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214E ARG* 3.4 51.4 - - - +
222E VAL* 3.5 23.0 - - - +
223E SER 4.4 2.9 + - - -
225E VAL* 3.7 16.9 - - + +
359E TYR* 4.1 0.2 - - - -
386F VAL* 3.9 11.7 - - + -
400F ILE* 4.2 9.6 - - + -
401F VAL 3.3 20.6 - - - -
402F LYS* 3.4 28.7 - - + +
409F TRP* 3.8 4.2 - - - -
410F GLY 3.8 1.4 - - - -
411F GLU* 2.8 40.8 + - + +
412F ASN* 3.4 13.9 - - + -
413F GLY* 1.3 82.1 - - - +
415F PHE* 1.3 65.0 + - - +
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Residues in contact with PHE 415 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350E PHE* 3.6 26.5 - + - -
356E PHE* 3.7 24.9 - + - -
359E TYR* 3.4 27.4 - - + -
364E TYR* 5.0 0.2 - - + -
383F VAL* 4.4 6.7 - - + -
400F ILE* 3.8 2.8 - - - +
401F VAL* 2.9 69.2 + - + +
403F ASN* 4.3 13.5 - - + -
409F TRP* 3.7 22.2 - + + -
411F GLU* 4.4 2.5 - - - -
414F TYR* 1.3 75.2 - - - +
416F ARG* 1.3 77.0 + - - +
417F ILE* 3.9 26.2 - - + -
426F ILE* 5.0 0.9 - - + -
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Residues in contact with ARG 416 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359E TYR* 3.4 6.8 + - - -
362E GLY* 3.5 31.2 + - - +
363E ILE* 4.0 21.1 - - + +
364E TYR* 2.9 26.0 + - - +
391F ASP* 4.7 7.9 + - - -
398F TYR* 3.6 39.9 + - + -
399F TRP 3.2 11.9 - - - +
400F ILE* 4.6 11.0 - - + -
411F GLU* 3.0 35.9 + - - +
415F PHE* 1.3 81.8 - - - +
417F ILE* 1.3 62.3 + - - +
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Residues in contact with ILE 417 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350E PHE* 4.5 9.6 - - + -
363E ILE* 3.9 5.8 - - - -
364E TYR* 3.6 35.0 - - + +
398F TYR* 3.2 1.2 - - - -
399F TRP* 2.8 53.5 + - + -
401F VAL* 3.9 15.9 - - + -
415F PHE* 3.9 16.6 - - + -
416F ARG* 1.3 77.7 - - - +
418F ARG* 1.3 71.9 + - - +
423F GLU* 3.9 27.8 - - + +
424F CYS* 4.8 0.4 - - + -
426F ILE* 4.5 15.7 - - + -
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Residues in contact with ARG 418 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363E ILE* 3.6 15.1 + - + +
364E TYR 3.1 17.9 + - - +
365E HIS* 3.5 47.5 + - + +
396F MET* 3.2 50.6 - - + +
397F ASP 3.6 6.1 - - - -
399F TRP* 3.8 8.0 - - - -
417F ILE* 1.3 77.3 - - - +
419F ARG* 1.3 58.2 + - - +
421F THR* 4.3 14.6 - - - +
423F GLU* 3.6 29.4 + - + +
426F ILE* 4.4 1.0 - - - +
427F GLU* 4.4 2.3 - - - +
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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