Contacts of the helix formed by residues 414 - 425 (chain E) in PDB entry 3CB4
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410E LEU* 4.0 10.1 - - + -
411E PRO* 3.6 36.1 - - + +
412E GLN 2.8 4.8 + - - -
413E ALA* 1.3 96.8 - - + +
415E LEU* 1.3 54.4 + - - +
416E GLY 3.1 3.4 - - - -
417E ASN* 2.8 35.3 + - + +
418E VAL* 3.1 11.2 + - + +
461E THR 3.8 17.9 - - - -
462E SER* 3.9 36.6 + - - -
463E ARG* 2.8 37.5 + - - +
465E TYR* 4.9 6.1 - + + -
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Residues in contact with LEU 415 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410E LEU* 3.7 20.0 - - + +
411E PRO 4.1 0.2 + - - -
412E GLN* 3.4 21.7 + - + +
414E TYR* 1.3 76.6 - - - +
416E GLY* 1.3 62.7 + - - +
418E VAL* 4.3 1.1 - - - -
419E ILE* 3.0 42.2 + - + +
432E MET* 3.7 33.9 - - + -
434E TYR* 4.2 13.0 - - + +
439E VAL* 3.7 22.0 - - + -
441E LEU* 4.6 8.1 - - + -
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Residues in contact with GLY 416 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413E ALA 5.5 0.2 - - - -
414E TYR 3.0 1.2 + - - +
415E LEU* 1.3 87.0 - - - +
417E ASN* 1.3 63.9 + - - +
419E ILE* 3.4 15.4 - - - +
420E THR* 3.3 21.3 - - - +
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Residues in contact with ASN 417 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413E ALA 5.2 3.0 - - - +
414E TYR* 2.8 22.5 + - - +
416E GLY* 1.3 74.4 - - - -
418E VAL* 1.3 59.7 + - + +
420E THR* 3.3 20.3 - - - +
421E LEU* 4.0 3.8 + - - +
461E THR* 3.2 44.0 + - - +
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Residues in contact with VAL 418 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408E MET* 3.9 10.5 - - + -
410E LEU* 3.6 21.8 - - + -
414E TYR* 3.1 13.9 + - + +
415E LEU* 3.2 6.7 + - - +
417E ASN* 1.3 79.8 - - + +
419E ILE* 1.3 62.2 + - - +
420E THR 3.1 1.1 - - - -
421E LEU* 2.9 10.0 + - - +
422E CYS* 2.8 25.7 + - - +
441E LEU* 3.8 19.5 - - + -
458E LEU* 3.8 26.9 - - + -
461E THR* 4.3 14.1 - - + -
462E SER* 4.5 13.5 - - - -
466E ALA* 4.6 0.7 - - + -
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Residues in contact with ILE 419 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415E LEU* 3.0 40.8 + - + +
416E GLY* 3.4 23.3 - - - +
418E VAL* 1.3 75.6 - - - +
420E THR* 1.3 60.6 + - - +
421E LEU 3.2 0.2 - - - -
422E CYS* 3.6 7.9 - - - -
423E VAL* 3.0 36.7 + - + +
429E GLN* 4.1 5.4 - - - +
432E MET* 5.7 2.5 - - + -
441E LEU* 3.7 28.5 - - + -
443E TYR* 3.1 26.7 - - + +
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Residues in contact with THR 420 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416E GLY 3.3 15.9 + - - +
417E ASN* 3.3 22.7 - - - +
418E VAL 3.1 1.0 - - - -
419E ILE* 1.3 82.6 - - - +
421E LEU* 1.3 65.2 + - + +
423E VAL* 3.5 13.8 - - - +
424E GLU* 3.4 16.5 - - - +
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Residues in contact with LEU 421 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417E ASN 4.1 6.5 - - - +
418E VAL* 2.9 10.2 + - + +
420E THR* 1.3 82.4 - - + +
422E CYS* 1.3 65.5 + - - +
423E VAL 3.3 0.2 - - - -
424E GLU* 2.9 17.7 + - - +
425E LYS* 3.0 21.1 + - + +
454E PHE* 3.6 31.2 - - + -
457E ARG* 3.4 67.1 - - + +
458E LEU* 3.5 12.3 - - + +
461E THR* 3.8 11.4 - - + +
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Residues in contact with CYS 422 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408E MET* 3.8 25.8 - - - -
418E VAL* 2.8 21.9 + - - +
419E ILE* 3.4 4.5 + - - +
421E LEU* 1.3 74.2 - - - +
423E VAL* 1.3 60.5 + - - +
425E LYS* 3.2 11.4 + - - +
427E GLY* 2.9 24.7 + - - -
443E TYR* 3.6 41.5 - - + -
445E ILE* 3.7 21.8 - - - +
454E PHE* 4.5 7.0 - - - -
458E LEU* 5.4 0.7 - - - -
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Residues in contact with VAL 423 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419E ILE* 3.0 27.3 + - + +
420E THR* 3.5 15.7 - - - +
422E CYS* 1.3 72.5 - - - +
424E GLU* 1.3 63.9 + - - +
426E ARG* 2.9 21.5 + - - -
427E GLY 3.9 16.6 - - - +
443E TYR* 4.0 15.0 - - + +
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Residues in contact with GLU 424 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420E THR 3.4 13.9 - - - +
421E LEU* 2.9 12.9 + - - +
423E VAL* 1.3 82.6 - - + +
425E LYS* 1.3 66.9 + - - +
426E ARG* 3.2 6.3 + - - +
449E GLU* 5.7 0.2 - - - +
457E ARG* 2.9 34.7 + - - -
503E ASN* 5.5 4.7 + - - -
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Residues in contact with LYS 425 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421E LEU* 3.0 26.9 + - + +
422E CYS 3.8 7.4 - - - +
423E VAL 3.1 0.4 - - - -
424E GLU* 1.3 87.7 + - - +
426E ARG* 1.3 67.8 + - - +
427E GLY 3.3 2.1 + - - -
445E ILE* 3.5 20.2 - - + +
446E PRO* 3.8 1.6 - - - +
449E GLU* 3.4 55.9 - - + +
452E LEU* 4.4 9.4 - - - -
453E ASP 4.2 5.9 + - - -
454E PHE* 3.9 14.2 - - + +
457E ARG* 3.5 36.0 - - - +
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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