Contacts of the helix formed by residues 441 - 448 (chain E) in PDB entry 1ZMD
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 SER 441 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344A GLY* 2.8 42.4 + - - -
412E THR 4.3 0.2 - - - -
413E ASP* 3.1 22.7 - - - -
414E ARG* 4.0 1.3 - - - +
415E VAL* 3.6 3.4 - - - -
439E GLY 3.8 1.7 + - - -
440E ALA* 1.3 75.1 - - - +
442E CYS* 1.3 63.7 + - - +
443E GLU 3.4 0.9 + - - -
444E ASP* 2.8 42.1 + - - +
445E ILE* 3.3 10.6 + - - +
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Residues in contact with CYS 442 (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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406E ILE* 3.7 28.7 - - - -
408E GLY* 3.9 15.5 - - - -
413E ASP* 2.8 34.5 + - - +
415E VAL* 3.9 6.7 - - - -
441E SER* 1.3 71.2 - - - +
443E GLU* 1.3 63.1 + - - +
445E ILE* 3.3 2.4 + - - +
446E ALA* 3.0 19.9 + - - +
463E ASN* 3.4 35.1 - - - +
466E ALA* 3.8 10.5 - - - -
467E SER* 3.7 5.6 - - - +
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Residues in contact with GLU 443 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A GLY 3.3 15.5 - - - +
345A GLY* 3.6 13.1 - - - -
346A ALA* 4.3 9.5 + - - +
413E ASP* 2.8 19.1 + - - +
441E SER* 3.7 5.2 - - - +
442E CYS* 1.3 74.9 - - - +
444E ASP* 1.3 67.3 + - - +
446E ALA* 3.2 5.3 + - + +
447E ARG* 2.9 62.9 + - + +
467E SER* 3.4 16.2 + - - +
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Residues in contact with ASP 444 (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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307A ARG* 2.9 32.3 + - - +
341A GLY 5.7 1.2 - - - +
344A GLY* 4.0 7.4 - - - +
345A GLY 4.2 7.6 - - - +
346A ALA* 5.1 0.9 - - - -
440E ALA* 3.4 5.0 - - + -
441E SER* 2.8 46.8 + - - +
443E GLU* 1.3 73.3 - - - +
445E ILE* 1.3 62.7 + - + +
447E ARG* 3.4 5.0 + - - +
448E VAL* 3.3 25.5 + - - +
434F LEU* 5.3 2.7 - - + -
437F GLU* 5.2 0.5 - - - +
438F TYR* 2.6 34.4 + - + -
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Residues in contact with ILE 445 (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 VAL* 3.9 18.4 - - + -
431E GLU* 4.0 9.4 - - - +
435E ALA* 4.0 20.0 - - + -
440E ALA* 5.0 0.7 - - + -
441E SER 3.7 6.7 - - - +
442E CYS 3.3 5.5 + - - +
443E GLU 3.2 0.6 - - - -
444E ASP* 1.3 75.6 - - + +
446E ALA* 1.3 67.6 + - - +
448E VAL* 3.1 16.5 + - - +
450E HIS* 3.4 19.2 - - + -
459E PHE* 3.7 33.0 - - + -
460E ARG* 3.9 4.2 - - - +
463E ASN* 3.2 41.5 - - + +
434F LEU* 5.0 10.1 - - + -
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Residues in contact with ALA 446 (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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442E CYS 3.0 16.8 + - - +
443E GLU* 3.6 10.5 - - + +
445E ILE* 1.3 76.1 - - - +
447E ARG* 1.3 59.9 + - + +
460E ARG* 2.8 39.1 + - - +
463E ASN* 4.2 0.6 - - - +
464E LEU* 3.7 43.6 - - + +
467E SER* 5.1 0.7 - - - -
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Residues in contact with ARG 447 (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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346A ALA* 4.6 16.8 - - - +
348A HIS* 6.2 0.2 - - - -
443E GLU* 2.9 50.9 + - + +
444E ASP* 3.9 4.9 - - - +
445E ILE 3.1 0.2 - - - -
446E ALA* 1.3 77.1 - - + +
448E VAL* 1.3 65.3 + - - +
449E CYS* 3.4 2.6 + - - +
460E ARG* 4.0 5.9 + - - +
333F ASP* 4.3 4.0 - - - +
336F ILE* 5.1 3.2 - - - +
337F ILE* 4.6 11.7 - - - +
340F GLU* 2.7 43.2 + - - -
346F ALA 5.6 2.0 + - - -
437F GLU* 5.6 3.6 - - - +
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Residues in contact with VAL 448 (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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431E GLU* 5.6 0.2 - - - +
444E ASP 3.3 16.3 + - - +
445E ILE* 3.1 10.5 + - - +
447E ARG* 1.3 76.6 - - - +
449E CYS* 1.3 62.7 + - - +
450E HIS* 2.8 34.9 + - + +
460E ARG* 3.0 12.7 + - - -
353F CYS 5.9 0.2 - - - +
430F ASN 4.7 1.3 - - - +
433F ALA* 3.8 30.5 - - + +
434F LEU* 3.8 35.0 - - + +
437F GLU* 3.8 26.5 - - + -
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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