Contacts of the helix formed by residues 441 - 448 (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 SER 441 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412G THR 4.7 2.5 - - - -
413G ASP* 3.1 26.0 - - - -
414G ARG* 3.9 7.4 - - - +
415G VAL* 3.8 2.9 - - - -
439G GLY 3.9 0.4 + - - -
440G ALA* 1.3 76.0 - - - +
442G CYS* 1.3 64.1 + - - +
443G GLU* 3.3 8.1 + - - +
444G ASP* 2.9 47.4 + - - +
445G ILE* 3.2 13.2 + - - +
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Residues in contact with CYS 442 (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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382G LYS* 4.6 0.4 - - - -
406G ILE* 3.9 17.3 - - - -
408G GLY* 4.0 15.5 - - - -
413G ASP* 2.8 35.4 + - - +
415G VAL* 3.6 8.4 - - - +
441G SER* 1.3 70.5 - - - +
443G GLU* 1.3 57.1 + - - +
445G ILE 3.7 0.2 + - - -
446G ALA* 3.0 23.9 + - - +
463G ASN* 3.3 40.7 - - - +
466G ALA* 3.8 19.5 - - - -
467G SER* 3.7 5.2 - - - +
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Residues in contact with GLU 443 (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 ASP* 3.3 12.5 + - - +
441G SER* 2.9 5.7 + - - +
442G CYS* 1.3 79.1 - - - +
444G ASP* 1.3 67.9 + - - +
446G ALA* 3.3 4.7 + - + +
447G ARG* 3.1 56.8 + - + +
467G SER* 3.2 20.5 + - - +
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Residues in contact with ASP 444 (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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439G GLY 4.9 0.7 - - - +
440G ALA* 3.8 2.3 - - - -
441G SER* 2.9 38.2 + - - +
443G GLU* 1.3 78.0 - - - +
445G ILE* 1.3 64.6 + - - +
447G ARG* 3.0 16.2 + - - +
448G VAL* 3.2 17.1 + - - +
434H LEU* 5.6 0.2 - - - -
437H GLU* 5.8 0.5 - - - +
438H TYR* 2.8 41.5 + - + +
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Residues in contact with ILE 445 (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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415G VAL* 3.7 18.2 - - + -
431G GLU* 4.9 1.3 - - - +
435G ALA* 3.6 32.1 - - + -
440G ALA* 4.2 6.1 - - + -
441G SER 3.2 5.6 + - - +
442G CYS 3.8 1.3 - - - +
444G ASP* 1.3 76.9 - - - +
446G ALA* 1.3 62.9 + - - +
447G ARG 3.1 1.0 + - - -
448G VAL* 3.1 23.4 + - - +
450G HIS* 3.8 12.9 - - + -
459G PHE* 3.7 28.0 - - + +
460G ARG* 4.0 5.5 - - - +
463G ASN* 3.1 52.0 - - + +
434H LEU* 4.8 7.6 - - + -
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Residues in contact with ALA 446 (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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442G CYS 3.0 19.2 + - - +
443G GLU* 3.7 9.9 - - + +
444G ASP 3.2 0.4 - - - -
445G ILE* 1.3 77.2 - - - +
447G ARG* 1.3 59.1 + - + +
460G ARG* 3.2 34.1 + - - +
464G LEU* 3.8 42.8 - - + +
467G SER* 5.1 0.7 - - - -
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Residues in contact with ARG 447 (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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443G GLU* 3.1 44.6 + - + +
444G ASP* 3.0 7.7 + - - +
446G ALA* 1.3 78.8 - - + +
448G VAL* 1.3 65.0 + - - +
449G CYS* 3.4 3.1 + - - +
460G ARG* 4.4 2.9 - - - +
333H ASP* 4.2 7.3 - - - +
336H ILE* 5.1 3.6 - - - +
337H ILE* 4.6 11.3 - - - +
340H GLU* 3.0 42.3 + - - -
437H GLU* 4.6 7.0 - - + +
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Residues in contact with VAL 448 (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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444G ASP* 3.2 15.7 + - + +
445G ILE* 3.1 10.4 + - - +
447G ARG* 1.3 76.2 - - - +
449G CYS* 1.3 68.3 + - - +
450G HIS* 2.8 35.7 + - + +
460G ARG* 3.2 12.5 + - - -
430H ASN 4.8 0.7 - - - +
433H ALA* 4.0 7.9 - - + +
434H LEU* 3.5 51.1 - - + +
437H GLU* 4.0 26.9 - - + +
438H TYR* 5.6 0.7 - - + -
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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