Contacts of the helix formed by residues 370 - 378 (chain B) 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 370 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B GLY* 4.1 13.5 + - - -
218B ILE 4.5 1.6 + - - -
219B ASP* 3.8 26.9 - - - -
368B GLY 4.1 0.2 + - - -
369B LYS* 1.3 76.8 - - - +
371B GLU* 1.3 64.0 + - - +
372B GLU* 3.4 9.6 + - - +
373B GLN* 2.9 33.9 + - - +
374B LEU* 3.1 20.6 + - - +
407B LEU* 3.6 2.0 - - - -
419B HIS* 3.6 11.6 - - - -
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Residues in contact with GLU 371 (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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219B ASP* 3.1 12.8 + - - +
221B GLU* 4.0 3.6 - - - +
370B SER* 1.3 71.7 - - - +
372B GLU* 1.3 68.6 + - - +
374B LEU* 3.2 5.3 + - - +
375B LYS* 2.9 43.7 + - - +
381B TYR* 2.6 34.2 + - + +
383B VAL* 4.3 11.7 - - - +
385B LYS* 5.2 1.7 + - - -
405B LYS* 2.6 29.4 + - - +
407B LEU* 3.5 24.9 - - + +
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Residues in contact with GLU 372 (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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218B ILE 4.4 1.0 - - - +
219B ASP* 3.6 8.8 - - - +
220B MET* 3.1 53.9 + - + +
221B GLU 4.8 1.4 + - - -
370B SER* 3.2 11.4 + - - +
371B GLU* 1.3 85.2 - - - +
373B GLN* 1.3 58.0 + - + +
375B LYS* 3.8 9.0 + - + +
376B GLU* 2.9 32.9 + - - +
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Residues in contact with GLN 373 (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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217B GLY* 4.6 11.4 - - - +
368B GLY 3.9 5.1 + - - +
369B LYS* 3.3 34.0 - - + +
370B SER* 2.9 38.6 + - - +
371B GLU 3.2 0.2 - - - -
372B GLU* 1.3 79.2 - - + +
374B LEU* 1.3 62.2 + - - +
376B GLU* 3.3 6.3 + - - +
377B GLU* 3.0 37.7 + - - +
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Residues in contact with LEU 374 (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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369B LYS* 3.8 24.7 - - + +
370B SER 3.1 9.4 + - - +
371B GLU* 3.8 4.7 - - - +
373B GLN* 1.3 77.6 - - - +
375B LYS* 1.3 62.7 + - - +
377B GLU* 3.1 5.6 + - - +
378B GLY 3.0 17.2 + - - -
379B ILE* 3.0 35.4 + - + -
381B TYR* 3.7 40.2 - - + -
407B LEU* 3.8 34.1 - - + -
416B LEU* 3.9 22.7 - - + -
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Residues in contact with LYS 375 (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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371B GLU* 2.9 29.9 + - + +
372B GLU* 3.8 8.0 + - + +
374B LEU* 1.3 76.1 - - - +
376B GLU* 1.3 63.4 + - - +
378B GLY* 3.1 13.4 + - - +
379B ILE 5.1 1.1 - - - +
381B TYR* 3.3 29.4 - - + +
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Residues in contact with GLU 376 (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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372B GLU 2.9 19.1 + - - +
373B GLN* 3.6 7.2 - - - +
375B LYS* 1.3 77.6 - - - +
377B GLU* 1.3 62.7 + - + +
378B GLY 3.6 0.5 + - - -
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Residues in contact with GLU 377 (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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369B LYS* 3.2 40.0 + - - +
373B GLN* 3.0 28.7 + - - +
374B LEU* 3.1 6.5 + - - +
376B GLU* 1.3 81.2 - - + +
378B GLY* 1.3 62.3 + - - +
379B ILE* 3.4 26.8 + - + +
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Residues in contact with GLY 378 (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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374B LEU 3.0 3.9 + - - -
375B LYS* 3.1 11.9 + - - -
376B GLU 3.3 1.0 + - - -
377B GLU* 1.3 79.3 - - - +
379B ILE* 1.3 64.3 + - - +
380B GLU* 3.7 1.9 + - - +
2005B SO4 3.9 4.3 + - - -
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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