Contacts of the helix formed by residues 587 - 600 (chain J) in PDB entry 6AH0
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 GLY 587 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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534J LYS 5.6 0.2 + - - -
535J GLU 3.9 0.2 - - - -
536J ASP* 2.1 51.7 - - - +
537J ILE 3.2 2.7 - - - -
586J GLY* 1.3 72.7 - - - +
588J PRO* 1.3 65.8 - - - +
589J LYS 3.1 3.4 - - - -
590J ALA* 2.9 16.7 + - - +
591J GLN* 3.5 6.4 + - - -
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Residues in contact with PRO 588 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542J HIS* 5.6 6.4 - - - -
586J GLY 3.7 2.4 - - - +
587J GLY* 1.3 72.7 - - - +
589J LYS* 1.3 61.2 + - - +
590J ALA 3.4 0.3 + - - -
591J GLN* 3.7 2.3 + - - +
592J LYS* 3.6 15.1 + - - -
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Residues in contact with LYS 589 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587J GLY 3.0 1.2 + - - -
588J PRO* 1.3 79.2 - - - +
590J ALA* 1.3 61.6 + - - +
592J LYS* 3.6 1.7 + - - -
593J LYS* 3.6 12.6 + - - -
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Residues in contact with ALA 590 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534J LYS 5.6 2.9 - - - -
535J GLU* 6.3 0.9 - - - +
536J ASP 5.6 2.1 - - - +
567J LEU* 5.4 8.7 - - - +
586J GLY* 6.0 0.9 - - - -
587J GLY 2.9 10.0 + - - +
589J LYS* 1.3 77.7 - - - +
591J GLN* 1.3 62.9 + - - +
593J LYS* 3.1 12.0 + - - -
594J PHE* 3.2 9.5 + - - -
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Residues in contact with GLN 591 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586J GLY* 5.7 3.8 - - - +
587J GLY 3.5 8.4 + - - -
588J PRO* 3.7 3.1 + - - -
589J LYS 3.4 0.4 - - - -
590J ALA* 1.3 75.3 - - - +
592J LYS* 1.3 52.3 + - - +
594J PHE* 3.1 3.1 + - - +
595J LYS* 2.6 34.5 + - - -
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Residues in contact with LYS 592 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588J PRO 3.6 12.1 + - - -
589J LYS 3.6 4.0 + - - -
590J ALA 3.2 0.8 - - - -
591J GLN* 1.3 76.6 - - - +
593J LYS* 1.3 60.0 + - - +
595J LYS* 3.6 1.7 + - - +
596J ARG* 3.1 17.8 + - - -
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Residues in contact with LYS 593 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589J LYS 3.6 8.1 + - - -
590J ALA 3.1 7.5 + - - -
592J LYS* 1.3 75.3 - - - +
594J PHE* 1.3 62.9 + - - +
596J ARG* 3.2 4.0 + - - -
597J LEU* 3.0 18.0 + - - -
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Residues in contact with PHE 594 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590J ALA 3.2 8.9 + - - -
591J GLN* 3.1 6.6 + - - +
593J LYS* 1.3 72.9 - - - +
595J LYS* 1.3 65.6 + - - +
597J LEU* 3.2 3.5 + - - +
598J MET* 3.0 19.4 + - - -
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Residues in contact with LYS 595 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591J GLN 2.6 20.1 + - - -
592J LYS* 4.0 2.2 - - - +
593J LYS 3.2 0.2 - - - -
594J PHE* 1.3 73.6 - - - +
596J ARG* 1.3 61.6 + - - +
598J MET* 3.3 1.8 + - - +
599J LEU* 3.2 20.1 + - - -
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Residues in contact with ARG 596 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592J LYS 3.1 14.9 + - - -
593J LYS* 3.2 5.1 + - - +
595J LYS* 1.3 76.1 - - - +
597J LEU* 1.3 55.6 + - - +
600J HIS* 2.9 28.6 + - - +
601J ARG 3.2 6.4 + - - -
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Residues in contact with LEU 597 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593J LYS 3.0 13.0 + - - -
594J PHE* 3.2 4.9 + - - +
596J ARG* 1.3 77.7 - - - +
598J MET* 1.3 59.4 + - - +
599J LEU 3.4 0.2 + - - -
601J ARG* 4.4 5.4 - - - +
602J ILE* 2.9 29.6 + - - -
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Residues in contact with MET 598 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594J PHE 3.0 13.6 + - - -
595J LYS* 3.3 2.4 + - - +
597J LEU* 1.3 77.3 - - - +
599J LEU* 1.3 60.9 + - - +
602J ILE* 4.0 8.3 - - - +
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Residues in contact with LEU 599 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595J LYS 3.2 12.9 + - - -
597J LEU 4.2 0.2 - - - -
598J MET* 1.3 77.1 - - - +
600J HIS* 1.3 62.1 + - - +
601J ARG 3.7 0.2 - - - -
602J ILE 3.4 13.7 - - - +
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Residues in contact with HIS 600 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596J ARG* 2.9 16.4 + - - +
599J LEU* 1.3 72.0 - - - +
601J ARG* 1.3 63.0 + - - +
602J ILE 4.5 0.9 - - - +
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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