Contacts of the helix formed by residues 441 - 448 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412A THR 4.6 3.6 - - - -
413A ASP* 3.3 27.1 - - - -
414A ARG* 3.9 4.7 - - - +
415A VAL* 3.9 3.4 - - - -
439A GLY 3.8 0.6 + - - -
440A ALA* 1.3 75.3 - - - +
442A CYS* 1.3 63.6 + - - +
443A GLU* 3.5 6.4 + - - +
444A ASP* 2.9 43.3 + - - +
445A ILE* 3.2 16.8 + - - +
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Residues in contact with CYS 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A LYS* 4.7 0.4 - - - -
406A ILE* 4.0 5.6 - - - -
408A GLY* 4.1 13.9 - - - -
413A ASP* 3.0 34.1 + - - +
415A VAL* 3.9 9.6 - - - -
441A SER* 1.3 69.8 - - - +
443A GLU* 1.3 59.1 + - - +
445A ILE 3.5 0.5 + - - -
446A ALA* 2.9 30.5 + - - +
463A ASN* 3.3 44.0 - - - +
466A ALA* 4.0 18.2 - - - -
467A SER* 3.7 7.0 - - - +
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Residues in contact with GLU 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A ASP* 3.2 16.5 + - - +
441A SER* 3.1 4.7 - - - +
442A CYS* 1.3 77.0 - - - +
444A ASP* 1.3 67.1 + - - +
446A ALA* 3.3 5.0 + - + +
447A ARG* 3.1 65.1 + - + +
467A SER* 3.5 15.7 + - - +
311F LYS* 3.8 30.6 + - - -
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Residues in contact with ASP 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439A GLY 5.1 0.3 - - - +
440A ALA* 4.0 1.9 - - - -
441A SER* 2.9 35.0 + - - +
443A GLU* 1.3 78.5 - - - +
445A ILE* 1.3 63.0 + - - +
447A ARG* 3.3 6.9 + - - +
448A VAL* 3.3 24.8 + - - +
437B GLU* 5.5 1.0 - - - +
438B TYR* 2.9 41.5 + - + +
305F ASN* 5.5 3.1 + - - +
311F LYS* 4.6 15.9 - - - +
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Residues in contact with ILE 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415A VAL* 3.7 18.4 - - + -
431A GLU* 4.7 0.9 - - - +
435A ALA* 3.6 31.4 - - + -
440A ALA* 4.2 6.5 - - + -
441A SER 3.2 6.1 + - - +
442A CYS 3.9 1.1 - - - +
444A ASP* 1.3 76.1 - - - +
446A ALA* 1.3 67.9 + - - +
448A VAL* 3.0 25.8 + - - +
450A HIS* 4.0 6.7 - - + -
459A PHE* 3.6 26.5 - - + -
460A ARG* 4.0 11.9 - - - +
463A ASN* 3.2 43.5 - - + +
434B LEU* 4.8 9.9 - - + -
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Residues in contact with ALA 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442A CYS 2.9 18.6 + - - +
443A GLU* 3.7 8.5 - - + +
445A ILE* 1.3 77.2 - - - +
447A ARG* 1.3 59.3 + - + +
460A ARG* 2.9 39.8 + - - +
463A ASN* 4.2 0.4 - - - +
464A LEU* 3.7 43.0 - - + +
467A SER* 5.2 0.4 - - - -
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Residues in contact with ARG 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A GLU* 3.1 51.6 + - + +
444A ASP* 3.8 5.8 - - - +
445A ILE 3.1 1.2 - - - -
446A ALA* 1.3 79.6 - - + +
448A VAL* 1.3 63.1 + - - +
449A CYS 3.4 2.9 + - - -
460A ARG* 4.2 3.4 - - - +
333B ASP* 4.2 7.4 - - - +
336B ILE* 5.1 3.4 - - - +
337B ILE* 5.0 8.9 - - - +
340B GLU* 3.1 39.7 + - - -
437B GLU* 4.7 6.1 - - - +
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Residues in contact with VAL 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444A ASP* 3.3 14.7 + - + +
445A ILE* 3.0 11.1 + - + +
447A ARG* 1.3 75.9 - - - +
449A CYS* 1.3 76.5 + - - +
450A HIS* 2.9 31.8 + - + -
460A ARG* 3.2 10.4 + - - -
430B ASN 4.9 0.2 - - - +
433B ALA* 3.8 21.8 - - + +
434B LEU* 3.7 36.1 - - + +
437B GLU* 3.8 28.9 - - + +
438B TYR* 5.7 0.4 - - + -
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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