Contacts of the helix formed by residues 412 - 422 (chain G) in PDB entry 1ZUM
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 THR 412 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311G GLN* 4.2 2.5 - - - +
410G PHE* 3.3 11.9 - - - -
411G LYS* 1.3 96.2 - - + +
413G ILE* 1.3 65.0 + - - +
414G GLU* 3.4 17.4 + - - +
415G GLU* 3.1 26.0 + - - +
416G VAL 3.1 18.4 + - - -
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Residues in contact with ILE 413 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278G MET* 3.8 18.6 - - + -
311G GLN* 4.5 3.4 - - - +
410G PHE* 4.4 0.6 - - - -
412G THR* 1.3 74.3 - - - +
414G GLU* 1.3 83.4 + - - +
416G VAL* 3.3 19.7 - - + +
417G VAL* 3.3 11.5 + - - +
438G LYS* 4.0 31.6 - - + -
441G TYR* 3.7 24.2 - - + -
442G LEU* 3.6 41.3 - - + -
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Residues in contact with GLU 414 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412G THR* 3.4 19.9 - - - +
413G ILE* 1.3 91.7 - - - +
415G GLU* 1.3 62.5 + - - +
417G VAL* 3.4 11.7 + - - +
418G GLY* 3.6 7.6 + - - -
441G TYR* 3.6 24.9 - - + +
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Residues in contact with GLU 415 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410G PHE* 3.8 6.4 - - - +
411G LYS* 2.8 35.1 + - - +
412G THR* 3.1 21.3 + - - +
414G GLU* 1.3 77.3 - - - +
416G VAL* 1.3 62.2 + - - +
418G GLY* 3.2 5.4 + - - -
419G ARG* 2.8 63.0 + - + +
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Residues in contact with VAL 416 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276G ILE* 4.1 28.3 - - + -
278G MET* 4.9 0.2 - - - -
309G PHE* 3.7 42.4 - - + -
410G PHE* 3.6 29.6 - - + -
412G THR 3.1 8.7 + - - +
413G ILE* 3.3 19.7 - - + +
415G GLU* 1.3 80.8 - - - +
417G VAL* 1.3 57.2 + - - +
419G ARG* 4.5 4.9 - - - +
420G ALA* 2.8 30.4 + - - +
442G LEU* 4.5 7.4 - - + -
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Residues in contact with VAL 417 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413G ILE 3.3 16.6 + - - +
414G GLU* 3.6 7.6 - - - +
415G GLU 3.2 0.8 - - - -
416G VAL* 1.3 76.9 - - - +
418G GLY* 1.3 59.7 + - - +
420G ALA* 3.9 3.0 - - - +
421G ASN* 3.0 48.6 + - - +
441G TYR* 3.7 20.6 - - + +
442G LEU* 3.5 24.2 - - + -
445G ALA* 3.9 20.4 - - + +
446G LEU* 4.9 5.6 - - + +
72H LEU* 5.6 4.0 - - + -
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Residues in contact with GLY 418 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414G GLU 3.6 4.9 + - - -
415G GLU 3.2 6.7 + - - -
417G VAL* 1.3 83.6 - - - +
419G ARG* 1.3 56.3 + - - +
421G ASN* 3.4 4.3 + - - +
422G ASN* 2.9 30.5 + - - +
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Residues in contact with ARG 419 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307G ARG* 3.1 16.4 + - - -
309G PHE* 3.9 19.2 - - + -
389G VAL 4.8 3.0 + - - -
390G GLN* 5.0 5.9 + - - -
391G ASP* 2.8 48.0 + - - +
408G LEU* 3.8 17.0 - - - +
409G LYS 2.9 27.9 + - - -
410G PHE* 3.7 7.1 - - - +
415G GLU* 2.8 58.8 + - + +
416G VAL* 3.9 4.5 - - - +
418G GLY* 1.3 75.3 - - - +
420G ALA* 1.3 63.5 + - - +
422G ASN* 3.2 17.8 + - - +
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Residues in contact with ALA 420 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274G PRO* 3.8 25.5 - - + +
276G ILE* 4.1 7.4 - - + -
307G ARG* 3.0 29.0 + - - +
309G PHE* 4.3 5.5 - - + -
416G VAL 2.8 21.9 + - - +
417G VAL 3.9 0.2 - - - +
419G ARG* 1.3 73.9 - - - +
421G ASN* 1.3 62.1 + - - +
422G ASN 3.5 0.2 + - - -
423G SER* 4.1 2.6 - - - -
446G LEU* 3.7 26.9 - - + -
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Residues in contact with ASN 421 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417G VAL* 3.0 32.5 + - - +
418G GLY* 4.0 4.7 - - - +
420G ALA* 1.3 75.6 - - - +
422G ASN* 1.3 54.7 + - - +
423G SER* 2.7 23.6 + - - +
445G ALA 2.9 24.0 + - - -
446G LEU* 3.5 10.6 - - - +
447G GLN* 2.8 59.1 + - - +
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Residues in contact with ASN 422 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307G ARG* 4.4 4.0 + - - -
391G ASP* 5.8 4.0 - - - +
418G GLY 2.9 19.3 + - - +
419G ARG* 3.2 16.1 + - - +
421G ASN* 1.3 72.8 - - - +
423G SER* 1.3 60.7 + - - +
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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