Contacts of the helix formed by residues 441 - 448 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412C THR 4.3 4.7 - - - -
413C ASP* 3.1 30.1 - - - -
414C ARG* 4.0 1.6 - - - +
415C VAL* 3.6 2.7 - - - -
439C GLY 3.8 1.2 + - - -
440C ALA* 1.3 76.0 - - - +
442C CYS* 1.3 65.8 + - - +
443C GLU* 3.4 5.9 + - - +
444C ASP* 2.8 44.1 + - - +
445C ILE* 3.3 15.8 + - - +
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Residues in contact with CYS 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406C ILE* 3.8 27.4 - - - -
408C GLY* 3.9 19.7 - - - -
413C ASP* 2.8 34.5 + - - +
415C VAL* 3.9 6.3 - - - -
441C SER* 1.3 71.8 - - - +
443C GLU* 1.3 64.3 + - - +
445C ILE 3.3 2.1 + - - -
446C ALA* 2.9 22.2 + - - +
463C ASN* 3.4 34.3 - - - +
466C ALA* 3.9 8.1 - - - -
467C SER* 3.8 6.3 - - - +
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Residues in contact with GLU 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413C ASP* 2.8 18.5 + - - +
441C SER* 3.1 4.7 - - - +
442C CYS* 1.3 75.3 - - - +
444C ASP* 1.3 67.1 + - - +
446C ALA* 3.1 6.0 + - + +
447C ARG* 2.7 63.4 + - + +
467C SER* 3.4 16.8 + - - +
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Residues in contact with ASP 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440C ALA* 3.4 4.2 - - + -
441C SER* 2.8 47.2 + - - +
443C GLU* 1.3 74.8 - - - +
445C ILE* 1.3 64.1 + - + +
447C ARG* 3.3 12.5 + - - +
448C VAL* 3.3 18.8 + - - +
434D LEU* 5.3 2.7 - - + -
437D GLU* 5.3 3.6 - - + +
438D TYR* 2.6 42.0 + - + -
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Residues in contact with ILE 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415C VAL* 3.7 20.9 - - + -
431C GLU* 4.0 8.3 - - - +
435C ALA* 3.8 25.8 - - + -
440C ALA* 5.0 0.9 - - + -
441C SER 3.3 6.2 + - - +
442C CYS 3.7 1.1 - - - +
443C GLU 3.2 0.4 - - - -
444C ASP* 1.3 76.6 - - + +
446C ALA* 1.3 64.3 + - - +
448C VAL* 3.1 16.5 + - - -
450C HIS* 3.5 18.4 - - + -
459C PHE* 3.6 29.4 - - + -
460C ARG* 3.9 3.9 - - - +
463C ASN* 3.4 45.8 - - + +
434D LEU* 4.8 10.1 - - + -
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Residues in contact with ALA 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442C CYS 2.9 14.0 + - - +
443C GLU* 3.1 14.6 + - + +
445C ILE* 1.3 77.9 - - - +
447C ARG* 1.3 60.2 + - + +
460C ARG* 2.9 40.2 + - - +
463C ASN* 4.2 0.4 - - - +
464C LEU* 3.8 41.6 - - + +
467C SER* 5.2 0.7 - - - -
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Residues in contact with ARG 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443C GLU* 2.7 51.3 + - + +
444C ASP* 3.8 5.4 - - - +
445C ILE 3.1 0.4 - - - -
446C ALA* 1.3 77.5 - - + +
448C VAL* 1.3 65.0 + - - +
449C CYS 3.5 2.3 + - - -
460C ARG* 4.2 5.6 + - - +
333D ASP* 4.6 2.6 - - - +
336D ILE* 5.3 2.6 - - - +
337D ILE* 4.6 11.7 - - - +
340D GLU* 2.9 42.6 + - - -
346D ALA 5.5 2.6 + - - -
437D GLU* 5.8 4.0 - - - +
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Residues in contact with VAL 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444C ASP 3.3 15.9 + - - +
445C ILE* 3.1 9.9 + - - +
447C ARG* 1.3 77.0 - - - +
449C CYS* 1.3 62.9 + - - +
450C HIS* 2.8 36.6 + - + +
460C ARG* 3.1 12.7 + - - -
353D CYS 5.8 0.2 - - - +
430D ASN 4.8 1.3 - - - +
433D ALA* 3.9 28.9 - - + +
434D LEU* 3.9 35.2 - - + +
437D GLU* 4.0 24.9 - - + -
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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