Contacts of the helix formed by residues 589 - 601 (chain C) in PDB entry 6DBT
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 LEU 589 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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585C ALA 3.0 14.2 + - - +
586C LEU* 2.9 22.1 + - + +
588C ASP* 1.3 78.9 - - + +
590C GLU* 1.3 62.5 + - - +
591C GLU* 3.3 2.2 - - - -
592C ASP* 3.3 16.4 + - + +
593C ILE* 3.0 32.2 + - + +
646C ILE* 4.4 22.4 - - + -
649C ILE* 6.0 0.7 - - + -
663C PHE* 3.7 32.5 - - + -
675C ARG* 4.9 9.4 - - - +
1019C LYS* 3.6 37.5 - - + -
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Residues in contact with GLU 590 (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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586C LEU 3.8 0.4 + - - -
587C LYS* 3.1 29.6 + - + +
588C ASP 3.1 4.1 + - - +
589C LEU* 1.3 77.5 - - - +
591C GLU* 1.3 71.0 + - + +
593C ILE* 3.0 13.5 - - - +
594C MET* 3.0 28.5 + - + +
713C VAL* 3.5 19.3 - - + +
714C GLY* 4.4 14.4 + - - +
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Residues in contact with GLU 591 (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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588C ASP 4.5 3.4 + - - +
589C LEU* 3.3 0.9 - - - -
590C GLU* 1.3 85.6 - - + +
592C ASP* 1.3 91.7 + - - +
594C MET* 3.8 4.9 - - - +
595C GLU* 2.9 35.8 + - + +
1019C LYS* 5.5 2.6 - - - +
1023C LYS* 5.1 18.6 + - - +
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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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589C LEU* 3.3 19.2 + - + +
590C GLU 3.3 0.6 - - - -
591C GLU* 1.3 104.2 + - - +
593C ILE* 1.3 60.7 + - + +
595C GLU* 3.8 8.0 - - - +
596C GLY* 2.9 25.3 + - - -
663C PHE* 5.0 28.0 - - + +
1019C LYS* 4.0 26.3 - - - +
1023C LYS* 5.2 8.1 + - - -
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Residues in contact with ILE 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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586C LEU* 5.0 13.9 - - + +
589C LEU* 3.0 22.9 + - + +
590C GLU* 3.0 20.9 - - - +
592C ASP* 1.3 77.7 - - + +
594C MET* 1.3 63.9 + - + +
596C GLY* 3.2 1.7 + - - -
597C LEU* 3.0 30.2 + - + +
611C PHE* 5.4 11.9 - - + -
649C ILE* 4.3 29.8 - - + -
662C ILE* 4.5 9.3 - - + +
663C PHE* 5.5 2.0 - - + -
713C VAL* 3.5 37.7 - - + -
718C ARG* 4.3 6.7 - - - +
720C PHE* 5.1 12.3 - - + -
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Residues in contact with MET 594 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590C GLU* 3.0 18.8 + - + +
591C GLU* 3.8 5.4 - - - +
593C ILE* 1.3 79.3 - - + +
595C GLU* 1.3 57.0 + - - +
597C LEU* 3.2 11.9 + - - +
598C ARG* 3.0 56.6 + - + +
713C VAL* 4.2 10.3 - - + -
714C GLY* 4.1 17.7 - - - -
718C ARG* 3.0 44.6 - - - +
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Residues in contact with GLU 595 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591C GLU* 2.9 27.9 + - + +
592C ASP* 3.8 10.1 - - - +
594C MET* 1.3 74.1 - - - +
596C GLY* 1.3 61.8 + - - +
598C ARG* 3.2 10.9 + - - +
599C GLU* 2.9 47.3 + - - +
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Residues in contact with GLY 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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592C ASP 2.9 15.5 + - - -
593C ILE 3.2 3.6 + - - -
595C GLU* 1.3 78.9 - - - +
597C LEU* 1.3 62.8 + - - +
599C GLU* 4.2 6.7 - - - +
600C ARG* 3.2 26.5 + - - +
662C ILE* 4.0 27.8 - - - +
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Residues in contact with LEU 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 ILE* 3.0 22.3 + - + +
594C MET* 3.5 20.2 - - - +
595C GLU 3.2 0.2 - - - -
596C GLY* 1.3 77.8 - - - +
598C ARG* 1.3 79.9 + - - +
600C ARG* 4.9 2.0 - - + -
601C ALA 3.0 19.8 + - - -
602C LEU* 3.1 20.2 + - + +
603C ASP 4.4 7.6 - - - +
607C CYS* 3.4 37.5 - - + -
611C PHE* 4.6 18.2 - - + -
651C ILE* 4.7 5.6 - - + -
662C ILE* 4.1 24.0 - - + -
718C ARG* 5.1 4.0 - - - +
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Residues in contact with ARG 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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594C MET* 3.0 39.9 + - + +
595C GLU* 3.2 13.2 + - - +
597C LEU* 1.3 122.0 + - - +
599C GLU* 1.3 60.4 + - - +
601C ALA* 2.9 22.6 + - - +
602C LEU 4.0 6.1 + - - +
604C ASP* 3.2 35.4 + - - +
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Residues in contact with GLU 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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595C GLU* 2.9 32.1 + - - +
596C GLY* 4.2 5.9 - - - +
598C ARG* 1.3 77.5 - - - +
600C ARG* 1.3 97.7 + - - +
601C ALA* 3.2 4.7 + - - +
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Residues in contact with ARG 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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596C GLY 3.2 17.8 + - - +
597C LEU* 4.2 2.9 - - - +
599C GLU* 1.3 100.1 + - - +
601C ALA* 1.3 68.9 + - - +
602C LEU* 4.1 27.3 - - + +
660C ILE* 4.9 23.8 - - + +
661C THR* 4.2 21.3 + - - +
662C ILE* 5.4 7.4 - - + +
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Residues in contact with ALA 601 (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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597C LEU 3.0 4.4 + - - -
598C ARG* 2.9 20.7 + - - +
599C GLU 4.2 3.4 - - - +
600C ARG* 1.3 79.3 - - - +
602C LEU* 1.3 66.4 + - - +
603C ASP* 4.9 1.4 - - - +
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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