Contacts of the helix formed by residues 441 - 448 (chain B) in PDB entry 1ZMC
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412B THR 4.3 0.2 - - - -
413B ASP* 3.0 22.0 - - - -
414B ARG* 4.0 0.9 - - - +
415B VAL* 3.6 3.3 - - - +
439B GLY 3.8 0.9 + - - -
440B ALA* 1.3 75.9 - - - +
442B CYS* 1.3 64.5 + - - +
443B GLU 3.2 2.3 + - - -
444B ASP* 2.6 52.5 + - - +
445B ILE* 3.2 11.6 + - - +
344F GLY* 3.0 39.0 + - - -
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Residues in contact with CYS 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406B ILE* 3.8 17.0 - - - -
408B GLY* 4.0 15.0 - - - -
413B ASP* 2.8 32.9 + - - +
415B VAL* 3.9 7.0 - - - -
441B SER* 1.3 72.3 - - - +
443B GLU* 1.3 62.0 + - - +
445B ILE 3.4 1.2 + - - -
446B ALA* 3.0 23.7 + - - +
463B ASN* 3.2 36.7 - - - +
466B ALA* 3.7 20.0 - - - -
467B SER* 3.7 5.2 - - - +
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Residues in contact with GLU 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B ASP* 2.9 13.6 + - - +
441B SER* 3.1 3.3 - - - +
442B CYS* 1.3 75.9 - - - +
444B ASP* 1.3 68.8 + - - +
446B ALA* 3.1 5.8 + - + +
447B ARG* 2.8 60.9 + - + +
467B SER* 3.2 21.7 + - - +
344F GLY 3.5 15.5 - - - +
345F GLY* 3.8 11.7 - - - -
346F ALA* 4.4 9.6 + - + +
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Residues in contact with ASP 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A LEU* 5.1 1.3 - - + -
437A GLU* 5.4 0.5 - - - +
438A TYR* 2.5 33.8 + - + -
440B ALA* 3.3 7.7 - - + -
441B SER* 2.6 46.3 + - - +
443B GLU* 1.3 76.9 - - - +
445B ILE* 1.3 63.2 + - + +
447B ARG* 3.4 8.4 + - - +
448B VAL* 3.3 20.0 + - - +
307F ARG* 3.0 31.5 + - - +
341F GLY 5.5 2.1 - - - +
344F GLY* 3.8 9.3 - - - +
345F GLY 4.1 6.8 - - - +
346F ALA* 5.1 0.7 - - - -
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Residues in contact with ILE 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A LEU* 4.4 12.8 - - + -
415B VAL* 3.8 15.9 - - + -
431B GLU* 4.2 7.2 - - - +
435B ALA* 3.7 31.4 - - + -
440B ALA* 4.9 0.9 - - + -
441B SER 3.2 5.4 + - - +
442B CYS 3.8 0.7 - - - +
443B GLU 3.2 0.2 - - - -
444B ASP* 1.3 77.4 - - + +
446B ALA* 1.3 61.9 + - - +
448B VAL* 3.2 23.1 + - - +
450B HIS* 3.5 13.2 - - + -
459B PHE* 3.7 29.4 - - + -
460B ARG* 3.9 4.0 - - - +
463B ASN* 3.4 44.4 - - + +
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Residues in contact with ALA 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442B CYS 3.0 17.5 + - - +
443B GLU* 3.1 8.5 + - + +
445B ILE* 1.3 76.2 - - - +
447B ARG* 1.3 60.8 + - + +
448B VAL 3.3 0.2 - - - -
460B ARG* 2.8 37.5 + - - -
463B ASN* 4.3 0.2 - - - +
464B LEU* 3.8 42.9 - - + +
467B SER* 5.4 0.7 - - - -
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Residues in contact with ARG 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A ASP* 4.0 5.4 - - - +
336A ILE* 5.5 2.0 - - - +
337A ILE* 4.6 10.5 - - - +
340A GLU* 2.8 44.2 + - - -
346A ALA 5.4 2.6 + - - -
437A GLU* 5.6 3.5 - - - +
443B GLU* 2.8 48.6 + - + +
444B ASP* 3.4 4.7 + - - +
445B ILE 3.2 0.2 - - - -
446B ALA* 1.3 79.9 - - + +
448B VAL* 1.3 63.9 + - - +
449B CYS* 3.5 2.3 + - - +
460B ARG* 3.9 7.1 + - - +
346F ALA* 4.7 15.6 - - - +
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Residues in contact with VAL 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A CYS 6.0 0.2 - - - +
430A ASN 4.8 0.9 - - - +
433A ALA* 4.1 27.1 - - + +
434A LEU* 3.6 37.0 - - + +
437A GLU* 4.0 26.5 - - + -
444B ASP 3.3 16.4 - - - +
445B ILE* 3.2 9.8 + - - +
447B ARG* 1.3 77.8 - - - +
449B CYS* 1.3 57.6 + - - +
450B HIS* 2.7 38.6 + - + +
460B ARG* 3.0 11.5 + - - -
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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