Contacts of the helix formed by residues 591 - 600 (chain C) in PDB entry 4Z2C
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 591 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A GLY* 4.2 16.0 - - - +
440C SER* 4.6 2.0 - - - -
590C MET* 1.3 77.9 - - - +
592C ASP* 1.3 67.6 + - - +
593C HIS* 4.2 8.3 - - + +
594C GLN* 3.3 26.1 + - + +
595C LEU* 3.2 22.3 + - - +
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Residues in contact with ASP 592 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ASN* 5.5 5.2 - - - +
108A GLY 5.8 0.5 - - - +
295A ARG* 5.1 11.0 - - + +
439C GLY 4.8 0.2 - - - +
440C SER* 4.1 21.6 + - - -
443C SER* 3.2 33.4 - - - +
444C GLY* 4.5 7.1 - - - +
591C ASP* 1.3 76.1 - - - +
593C HIS* 1.3 59.1 + - - +
595C LEU* 3.2 4.3 + - - +
596C TRP* 2.9 30.8 + - - +
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Residues in contact with HIS 593 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A ARG* 6.1 3.1 - - + -
591C ASP* 4.2 5.1 - - + +
592C ASP* 1.3 79.1 - - - +
594C GLN* 1.3 60.5 + - + +
596C TRP* 3.9 5.7 - - - +
597C GLU* 2.9 35.7 + - + +
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Residues in contact with GLN 594 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589C GLU 4.8 1.2 - - - +
590C MET* 3.2 30.5 - - + +
591C ASP* 3.3 22.7 + - + +
592C ASP 3.3 0.6 - - - -
593C HIS* 1.3 76.1 - - + +
595C LEU* 1.3 60.0 + - - +
597C GLU* 5.0 1.1 - - - -
598C THR* 2.3 46.5 + - + +
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Residues in contact with LEU 595 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437C ALA* 4.6 2.2 - - + +
440C SER* 3.6 15.9 - - - +
441C ALA* 3.5 38.4 - - + +
444C GLY 5.5 0.2 - - - +
504C MET* 3.6 16.6 - - + -
587C LEU* 4.2 24.0 - - + +
590C MET* 3.7 20.5 - - + -
591C ASP 3.2 17.5 + - - +
592C ASP* 3.5 4.5 - - - +
594C GLN* 1.3 77.2 - - - +
596C TRP* 1.3 57.6 + - - +
598C THR* 3.9 0.4 - - - -
599C THR* 2.4 55.8 + - - +
600C MET* 3.4 12.8 + - - -
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Residues in contact with TRP 596 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444C GLY* 3.6 23.3 - - - +
445C ARG* 3.9 10.5 - - - -
446C ASN* 4.0 20.2 - - + -
450C GLN* 3.4 17.5 - - - -
592C ASP 2.9 17.7 + - - +
593C HIS* 3.9 5.6 - - - +
595C LEU* 1.3 77.3 - - - +
597C GLU* 1.3 80.1 + - + +
598C THR 3.0 2.1 + - - -
600C MET* 3.0 42.6 + - + -
601C ASP* 2.9 65.8 + - + -
602C PRO* 4.1 7.4 - - + -
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Residues in contact with GLU 597 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593C HIS* 2.9 22.9 + - + +
594C GLN* 4.4 1.6 - - - +
596C TRP* 1.3 84.7 - - + +
598C THR* 1.3 62.8 + - + +
601C ASP* 4.4 7.1 - - - +
604C HIS* 4.0 22.6 + - - +
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Residues in contact with THR 598 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539C GLN 5.4 1.7 - - - +
541C PRO* 3.7 30.7 - - + +
590C MET* 4.1 7.3 - - - -
594C GLN* 2.3 40.7 + - + +
595C LEU* 3.5 2.9 + - - -
597C GLU* 1.3 84.8 - - + +
599C THR* 1.3 70.1 + - - +
600C MET 4.0 0.2 - - - -
604C HIS 3.9 4.8 - - - +
605C ARG* 3.9 17.5 - - - -
606C LEU 4.9 0.9 + - - -
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Residues in contact with THR 599 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430C PHE* 4.9 4.5 - - - -
504C MET* 3.2 17.3 - - + +
538C ALA* 5.2 6.9 - - - +
539C GLN 5.0 1.8 - - - -
540C PRO* 3.6 41.1 - - + -
541C PRO* 3.6 4.0 - - + -
587C LEU* 5.7 0.2 - - + -
590C MET* 5.6 2.9 - - + -
595C LEU* 2.4 41.2 + - + +
598C THR* 1.3 90.3 - - - +
600C MET* 1.3 61.0 + - - +
605C ARG* 3.3 24.6 - - - +
606C LEU 5.7 0.8 - - - +
607C MET* 5.0 4.0 - - - +
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Residues in contact with MET 600 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430C PHE* 4.1 23.3 - - + -
441C ALA* 4.3 4.9 - - + +
444C GLY 4.0 13.5 - - - +
445C ARG* 3.6 28.3 - - + -
450C GLN* 3.6 12.4 + - - +
452C ILE* 4.2 13.2 - - + -
504C MET* 3.7 11.9 - - + +
595C LEU* 3.6 32.1 - - - +
596C TRP* 3.0 25.7 + - + +
599C THR* 1.3 91.2 - - - +
601C ASP* 1.3 61.9 + - - +
602C PRO* 3.2 5.2 - - - +
605C ARG* 2.9 25.3 + - - +
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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