Contacts of the strand formed by residues 403 - 409 (chain E) 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 MET 403 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221E GLU* 3.7 30.5 - - + +
222E ILE* 3.9 22.1 - - + +
225E ASN* 3.2 27.4 - - + +
385E LYS* 4.1 29.2 - - + -
386E PHE 3.1 20.4 - - - +
387E PRO* 3.9 4.7 - - + -
388E PHE* 3.8 5.3 - - - -
402E GLY* 1.3 78.3 - - - +
404E VAL* 1.3 64.2 + - - +
405E LYS* 4.1 8.0 + - + -
419E HIS 4.0 1.0 - - - +
420E ILE* 3.7 1.4 - - - -
421E LEU* 2.7 37.9 + - + +
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Residues in contact with VAL 404 (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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385E LYS* 3.4 4.5 - - - +
386E PHE 2.9 31.8 + - - +
388E PHE* 3.7 26.5 - - + -
403E MET* 1.3 74.4 - - - +
405E LYS* 1.3 62.2 + - - +
406E ILE* 4.3 6.7 - - + -
419E HIS 3.5 6.7 - - - +
420E ILE* 4.0 13.5 - - + -
428E MET* 4.0 10.5 - - - -
458E ALA* 3.9 21.5 - - + +
459E PHE* 3.9 25.8 - - + +
462E ALA* 3.4 20.3 - - + +
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Residues in contact with LYS 405 (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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219E ASP* 2.9 34.1 + - - +
221E GLU* 2.6 33.0 + - - +
222E ILE* 4.4 15.0 - - + -
371E GLU* 2.6 28.7 + - - -
383E VAL* 4.2 11.0 - - + -
384E GLY 3.5 3.4 - - - +
385E LYS* 4.2 16.2 - - + +
403E MET* 4.1 4.7 - - - -
404E VAL* 1.3 74.6 - - - +
406E ILE* 1.3 66.4 + - - +
407E LEU* 4.0 16.4 - - + -
417E GLY 4.0 0.2 - - - +
418E ALA* 3.6 3.1 - - - -
419E HIS* 2.7 51.6 + - + +
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Residues in contact with ILE 406 (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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382E LYS 3.5 0.5 - - - +
383E VAL* 3.3 7.3 - - - +
384E GLY 2.9 37.0 + - - +
404E VAL* 4.4 2.0 - - + -
405E LYS* 1.3 74.6 - - - +
407E LEU* 1.3 71.8 + - - +
408E GLY 4.1 0.2 + - - -
415E VAL* 4.4 7.0 - - + -
417E GLY 3.6 2.9 - - - +
418E ALA* 3.8 18.8 - - + -
442E CYS* 3.8 20.2 - - - -
459E PHE* 3.7 21.3 - - + -
462E ALA* 3.7 29.4 - - + +
463E ASN* 3.6 39.5 - - - +
466E ALA* 4.1 4.7 - - + +
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Residues in contact with LEU 407 (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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219E ASP* 4.8 0.7 - - - +
369E LYS 3.3 24.9 - - - +
370E SER* 3.5 3.8 - - - +
371E GLU* 3.4 29.4 - - + +
374E LEU* 3.8 19.3 - - + -
381E TYR* 3.9 13.0 - - + -
382E LYS 3.3 2.5 - - - +
383E VAL* 3.9 24.0 - - + -
405E LYS* 4.0 16.8 - - - -
406E ILE* 1.3 83.0 - - - +
408E GLY* 1.3 58.7 + - - +
415E VAL* 3.7 2.8 - - - +
416E LEU* 2.8 25.6 + - - -
417E GLY 2.9 19.4 + - - +
419E HIS* 4.2 11.9 - - + +
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Residues in contact with GLY 408 (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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381E TYR* 3.1 7.9 - - - +
382E LYS* 2.6 46.9 + - - -
406E ILE* 4.0 3.2 - - - +
407E LEU* 1.3 75.2 - - - +
409E GLN* 1.3 62.0 + - - -
413E ASP 5.0 0.2 - - - -
414E ARG 3.2 8.7 - - - -
416E LEU* 4.4 2.0 - - - -
442E CYS* 4.0 19.3 - - - -
466E ALA* 5.0 0.6 - - - +
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Residues in contact with GLN 409 (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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379E ILE* 4.1 8.9 - - - +
380E GLU 3.9 4.9 - - - +
382E LYS* 3.9 3.6 - - - -
408E GLY* 1.3 71.6 - - - -
410E LYS* 1.3 62.0 + - - +
411E SER* 3.6 15.1 + - - +
412E THR* 3.4 22.7 + - - +
413E ASP* 2.7 31.9 + - - -
414E ARG* 2.7 23.4 + - - +
416E LEU* 3.9 26.5 - - + +
2019E SO4 2.7 36.6 + - - +
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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