Contacts of the helix formed by residues 591 - 599 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104B HIS* 6.3 0.2 - - - -
105B GLY* 4.2 14.2 - - - +
440D SER* 4.7 0.4 - - - -
590D MET* 1.3 76.9 - - - +
592D ASP* 1.3 64.4 + - - +
593D HIS* 3.2 5.8 - - + +
594D GLN* 3.1 18.4 + - + +
595D LEU* 2.9 27.2 + - - +
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Residues in contact with ASP 592 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B ARG* 3.8 18.5 - - - +
440D SER* 3.8 14.1 - - - +
443D SER* 3.6 32.9 - - - +
444D GLY* 3.7 15.0 - - - +
590D MET 3.9 0.8 + - - -
591D ASP* 1.3 75.2 - - - +
593D HIS* 1.3 67.5 + - - +
595D LEU* 3.4 3.5 + - - +
596D TRP* 2.9 30.5 + - - +
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Residues in contact with HIS 593 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B ARG* 5.2 9.6 - - + -
591D ASP* 3.2 5.1 - - + +
592D ASP* 1.3 83.7 + - - +
594D GLN* 1.3 60.7 + - - +
596D TRP* 3.8 6.8 - - + +
597D GLU* 2.9 33.1 + - - +
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Residues in contact with GLN 594 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590D MET* 3.7 23.1 - - + -
591D ASP* 3.1 23.5 + - + +
593D HIS* 1.3 80.5 - - - +
595D LEU* 1.3 54.9 + - - +
597D GLU* 3.4 2.9 + - - +
598D THR* 2.2 40.5 + - - +
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Residues in contact with LEU 595 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432D VAL* 5.9 0.7 - - + -
437D ALA* 4.8 2.5 - - + +
440D SER* 4.0 9.9 - - - +
441D ALA* 3.7 32.1 - - + +
444D GLY 5.2 0.2 - - - +
504D MET* 3.5 23.1 - - + -
540D PRO* 6.2 1.3 - - + -
587D LEU* 4.8 12.3 - - + +
590D MET* 3.5 30.4 - - + -
591D ASP 2.9 11.6 + - - +
592D ASP* 3.7 9.2 - - - +
594D GLN* 1.3 75.3 - - - +
596D TRP* 1.3 58.8 + - - +
598D THR* 4.4 0.4 - - - -
599D THR* 2.9 58.9 + - + +
600D MET* 3.2 13.4 + - - -
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Residues in contact with TRP 596 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B ASN* 4.1 17.9 - - + -
295B ARG* 3.6 42.2 - - + -
296B GLU* 4.8 2.9 - - + -
444D GLY* 4.1 20.5 + - - +
445D ARG* 5.4 1.6 - - - -
446D ASN* 4.5 35.5 - - + +
592D ASP 2.9 16.4 + - - +
593D HIS* 3.8 7.0 - - - +
595D LEU* 1.3 77.7 - - - +
597D GLU* 1.3 61.2 + - - +
600D MET* 4.0 13.8 + - + -
601D ASP* 3.1 59.6 + - + +
602D PRO* 5.4 1.6 - - - +
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Residues in contact with GLU 597 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593D HIS 2.9 19.0 + - - +
594D GLN* 3.9 3.6 - - - +
596D TRP* 1.3 76.9 - - - +
598D THR* 1.3 60.9 + - - +
601D ASP* 4.7 5.3 - - - +
604D HIS* 4.5 17.7 - - - +
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Residues in contact with THR 598 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539D GLN 5.5 1.0 - - - +
541D PRO* 3.6 37.2 - - + -
590D MET* 3.6 11.8 - - + +
594D GLN* 2.2 30.1 + - - +
595D LEU 4.1 0.4 - - - -
597D GLU* 1.3 82.1 - - - +
599D THR* 1.3 66.0 + - + +
600D MET 3.8 0.4 - - - -
605D ARG* 3.6 20.9 + - - +
606D LEU 5.1 0.2 + - - -
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Residues in contact with THR 599 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430D PHE* 4.7 3.3 - - - -
504D MET* 3.3 28.3 - - - +
538D ALA* 5.1 8.8 - - - +
539D GLN 4.3 7.6 - - - +
540D PRO* 3.6 38.4 - - + -
541D PRO* 3.9 5.6 - - + -
590D MET* 5.2 0.4 - - + -
595D LEU* 2.9 20.7 + - + +
598D THR* 1.3 88.0 - - + +
600D MET* 1.3 62.5 + - - +
601D ASP 3.6 1.6 - - - -
605D ARG* 3.2 24.2 + - - +
606D LEU 5.7 0.3 - - - +
607D MET* 4.4 7.3 - - - +
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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