Contacts of the helix formed by residues 591 - 599 (chain D) in PDB entry 4QG0
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 ILE 591 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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485D PRO* 3.8 23.1 - - + -
486D LYS* 4.1 4.9 - - + +
487D VAL* 3.7 23.3 - - + -
567D GLN* 3.7 25.6 - - - +
570D VAL* 3.6 23.6 - - + +
571D GLN* 3.6 21.1 - - - +
574D ALA* 5.0 2.2 - - + -
588D ALA* 3.0 11.1 + - + +
590D LEU* 1.3 81.8 - - - +
592D THR* 1.3 67.3 + - - +
593D PRO 3.3 2.2 - - - -
594D GLN* 3.1 50.2 + - - +
595D LYS* 5.2 0.2 - - - +
598D TRP* 5.3 0.6 - - + -
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Residues in contact with THR 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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570D VAL* 3.9 17.9 - - + -
580D LYS* 5.0 3.1 - - - -
584D GLY* 3.3 35.0 - - - +
585D ASP* 2.6 27.5 + - - +
588D ALA 3.3 6.8 + - - +
589D PRO* 4.5 1.7 + - - +
591D ILE* 1.3 74.7 - - - +
593D PRO* 1.4 72.0 - - - +
595D LYS* 3.4 11.9 + - - +
598D TRP* 4.0 21.8 - - + -
599D ASN* 3.3 18.4 + - - -
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Residues in contact with PRO 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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589D PRO 3.3 22.0 - - - +
590D LEU* 4.1 4.7 - - - +
591D ILE 3.4 5.4 - - - +
592D THR* 1.4 99.3 - - - +
594D GLN* 1.3 61.6 + - - +
595D LYS 3.0 7.2 + - - +
596D LYS* 4.5 1.4 + - - -
599D ASN* 4.2 11.3 + - - +
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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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571D GLN* 2.9 42.0 + - - +
574D ALA* 4.2 9.3 - - + +
575D ASP* 5.0 0.2 - - - +
590D LEU 5.4 1.9 + - - +
591D ILE* 3.1 33.0 + - - +
593D PRO* 1.3 77.9 - - - +
595D LYS* 1.3 68.9 + - + +
596D LYS* 3.5 11.4 + - - +
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Residues in contact with LYS 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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574D ALA* 2.4 42.2 + - + +
575D ASP 4.9 1.0 + - - -
577D ASN* 3.5 32.6 + - - +
592D THR 3.4 1.7 + - - +
593D PRO 3.0 4.4 + - - -
594D GLN* 1.3 83.1 - - + +
596D LYS* 1.3 60.8 + - - +
597D GLU* 3.8 17.1 + - - +
598D TRP* 3.1 59.1 + - + +
599D ASN* 2.9 24.3 + - - -
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Residues in contact with LYS 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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593D PRO 5.0 2.0 - - - -
594D GLN 3.5 10.6 + - - +
595D LYS* 1.3 67.3 - - - +
597D GLU* 1.3 85.2 + - + +
598D TRP 3.1 2.5 - - - -
599D ASN* 2.9 33.9 + - - +
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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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577D ASN* 4.2 17.5 - - - +
595D LYS* 3.8 19.4 - - + +
596D LYS* 1.3 104.9 + - + +
598D TRP* 1.3 69.2 + - + +
599D ASN 3.3 1.5 + - - -
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Residues in contact with TRP 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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570D VAL* 3.9 28.0 - - + -
573D CYS* 4.0 9.2 - - + -
574D ALA* 3.6 36.6 - - + -
577D ASN* 5.5 0.8 + - - -
578D PHE 3.3 26.8 + - - -
579D THR* 4.6 0.4 - - - +
580D LYS* 3.5 57.5 + - + +
581D PRO* 4.3 4.5 - - + -
591D ILE* 5.3 0.7 - - + -
592D THR* 4.0 24.0 - - + +
595D LYS* 3.1 37.4 + - + +
597D GLU* 1.3 84.4 - - + +
599D ASN* 1.3 69.8 + - - +
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Residues in contact with ASN 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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580D LYS* 5.9 0.9 + - - -
585D ASP* 5.5 3.0 + - - +
592D THR* 3.3 21.0 + - - -
593D PRO* 4.2 9.3 + - - +
595D LYS 2.9 23.5 + - - +
596D LYS* 2.9 21.1 + - - +
597D GLU 3.3 1.5 - - - -
598D TRP* 1.3 88.5 + - - +
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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