Contacts of the helix formed by residues 350 - 354 (chain G) 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 ASP 350 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349G ILE* 1.3 76.0 - - - +
351G TYR* 1.3 59.1 + - - +
352G ASN* 3.0 30.0 + - - +
353G CYS* 2.9 50.2 + - + +
354G VAL* 3.8 5.7 + - - +
437G GLU* 6.0 1.3 - - - +
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Residues in contact with TYR 351 (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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308G PHE* 3.6 8.7 - - - -
322G VAL* 5.5 0.2 - - - +
323G ALA 4.3 12.2 + - - -
324G GLY* 4.8 4.7 - - - -
325G PRO* 3.9 28.2 - - + +
330G LYS* 3.9 15.3 - - + -
334G GLU* 2.5 29.7 + - - -
349G ILE* 3.6 37.3 - - + +
350G ASP* 1.3 72.8 + - - +
352G ASN* 1.3 58.9 + - - +
353G CYS 3.1 1.1 + - - -
354G VAL* 3.4 31.3 + - + +
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Residues in contact with ASN 352 (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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350G ASP* 2.9 22.7 + - - +
351G TYR* 1.3 77.9 - - - +
353G CYS* 1.3 59.7 + - - +
354G VAL 3.4 1.0 - - - +
367G VAL* 3.8 0.5 - - - +
368G GLY* 3.1 37.9 + - - +
369G LYS* 3.4 42.2 + - - +
373G GLN* 5.6 0.3 + - - -
416G LEU 4.8 3.2 + - - -
436G LEU* 4.0 9.5 - - - +
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Residues in contact with CYS 353 (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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350G ASP* 2.9 33.9 + - + +
352G ASN* 1.3 83.4 - - - +
354G VAL* 1.3 58.1 + - - +
355G PRO* 3.1 13.0 - - - +
367G VAL* 3.5 13.5 - - + +
433G ALA* 4.4 9.7 - - - +
436G LEU* 4.1 34.8 - - + -
437G GLU* 4.5 17.3 - - + +
448H VAL* 6.0 0.2 - - - +
449H CYS* 4.2 10.8 + - + +
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Residues in contact with VAL 354 (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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325G PRO* 4.0 20.8 - - + +
327G LEU* 4.2 5.2 - - + -
329G HIS* 3.9 18.2 - - + +
330G LYS* 4.4 9.2 - - + -
349G ILE* 4.5 10.5 - - + -
350G ASP 3.9 4.9 - - - +
351G TYR* 3.4 42.6 + - + +
352G ASN 3.4 0.9 - - - +
353G CYS* 1.3 77.0 - - - +
355G PRO* 1.3 76.5 - - - +
356G SER* 4.6 3.3 + - - -
366G TRP 4.6 1.0 - - - +
367G VAL* 4.2 5.3 - - - +
368G GLY 5.6 0.2 + - - -
449H CYS* 4.1 14.6 - - + -
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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