Contacts of the helix formed by residues 350 - 354 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349F ILE* 1.3 76.1 - - - +
351F TYR* 1.3 59.6 + - - +
352F ASN* 2.9 31.9 + - - +
353F CYS* 2.8 50.2 + - + +
354F VAL* 3.6 6.2 + - - +
437F GLU* 5.8 2.0 - - - +
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Residues in contact with TYR 351 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308F PHE* 3.7 17.8 - - - -
323F ALA 4.4 8.7 + - - -
324F GLY* 4.7 4.5 - - - -
325F PRO* 3.8 27.1 - - + +
330F LYS* 3.8 17.7 - - + -
334F GLU* 2.6 31.5 + - - -
349F ILE* 3.7 29.8 - - + +
350F ASP* 1.3 73.8 + - - +
352F ASN* 1.3 60.5 + - - +
353F CYS 3.1 0.2 - - - -
354F VAL* 3.2 30.3 + - + +
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Residues in contact with ASN 352 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350F ASP* 2.9 26.4 + - - +
351F TYR* 1.3 77.6 - - - +
353F CYS* 1.3 63.6 + - - +
354F VAL 3.4 1.9 + - - +
367F VAL* 3.9 0.3 - - - +
368F GLY* 3.1 50.1 + - - +
369F LYS* 3.5 27.1 + - - +
416F LEU 4.9 3.2 + - - -
436F LEU* 4.4 6.1 - - - +
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Residues in contact with CYS 353 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448E VAL* 5.8 0.2 - - - +
449E CYS* 4.3 9.5 + - + +
350F ASP* 2.8 34.4 + - + +
352F ASN* 1.3 86.8 - - - +
354F VAL* 1.3 58.4 + - - +
355F PRO* 3.2 13.2 - - - +
367F VAL* 3.6 13.8 - - + +
433F ALA* 4.3 11.5 - - - +
436F LEU* 4.2 33.7 - - + -
437F GLU* 4.5 16.6 - - + +
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Residues in contact with VAL 354 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449E CYS* 4.4 13.0 - - + -
325F PRO* 3.8 22.4 - - + -
327F LEU* 4.0 9.2 - - + -
329F HIS* 4.1 11.2 - - + -
330F LYS* 4.4 11.2 - - + -
349F ILE* 4.6 9.9 - - + -
350F ASP 3.7 4.9 - - - +
351F TYR* 3.2 46.2 + - + +
352F ASN 4.7 1.0 - - - +
353F CYS* 1.3 77.0 - - - +
355F PRO* 1.3 75.3 - - - +
356F SER* 3.9 2.9 + - - -
366F TRP* 4.4 1.7 - - - +
367F VAL* 4.3 6.1 - - - +
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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