Contacts of the helix formed by residues 583 - 588 (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 ASP 583 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353B ASP* 4.0 9.7 - - - +
522B CYS* 3.4 32.5 - - + +
524B THR* 4.8 3.5 - - - +
530B ILE* 4.7 0.4 - - - -
456D TYR* 6.0 2.4 - - - -
457D VAL 5.2 4.2 - - - +
458D GLY* 5.7 2.6 - - - -
581D PRO* 4.1 8.1 - - - +
582D GLN* 1.3 75.6 + - - +
584D GLY* 1.3 65.0 + - - +
585D ASP 3.3 2.7 - - - -
586D VAL* 3.0 5.2 + - - -
587D ILE* 2.9 51.8 + - + +
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Residues in contact with GLY 584 (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* 4.9 2.5 - - - -
580D LYS* 4.6 2.0 - - - +
581D PRO* 3.0 27.3 + - - -
582D GLN 3.3 1.2 + - - -
583D ASP* 1.3 78.4 + - - +
585D ASP* 1.3 57.7 + - - +
587D ILE* 4.2 8.5 - - - -
588D ALA* 2.9 26.0 + - - +
592D THR* 3.3 25.2 - - - +
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Residues in contact with ASP 585 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B ARG* 3.6 31.1 + - - +
530B ILE* 5.2 7.8 - - + +
580D LYS* 2.4 32.1 + - - +
582D GLN 5.2 0.4 + - - -
583D ASP 3.3 0.8 - - - -
584D GLY* 1.3 75.7 - - - +
586D VAL* 1.3 61.9 + - + +
589D PRO* 3.4 24.2 - - - +
592D THR* 2.6 35.6 + - - +
599D ASN* 5.5 3.7 + - - +
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Residues in contact with VAL 586 (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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522B CYS* 3.9 25.8 - - + -
524B THR* 3.4 35.0 + - + +
525B ALA* 3.7 21.3 - - + +
528B ARG* 4.3 21.3 - - + +
530B ILE* 4.2 18.8 - - + -
583D ASP 3.0 8.1 + - - +
585D ASP* 1.3 79.8 - - - +
587D ILE* 1.3 60.7 + - - +
588D ALA 3.4 0.4 - - - -
589D PRO* 3.6 11.3 - - - +
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Residues in contact with ILE 587 (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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524B THR* 3.8 22.7 - - + -
457D VAL 4.1 19.3 - - - +
563D TYR* 5.0 3.3 - - - -
566D ARG* 4.0 36.9 - - + +
567D GLN* 2.9 22.3 + - - -
569D PHE* 4.8 7.0 - - + -
570D VAL* 4.0 23.1 - - + -
581D PRO* 5.2 0.7 - - + -
583D ASP* 2.9 47.4 + - - +
584D GLY* 4.1 4.5 - - - +
586D VAL* 1.3 74.9 - - - +
588D ALA* 1.3 60.6 + - - +
589D PRO* 3.7 3.1 - - - +
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Residues in contact with ALA 588 (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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566D ARG 4.6 0.9 - - - +
567D GLN* 3.5 19.5 - - - +
570D VAL* 3.7 30.5 - - + -
584D GLY 2.9 14.3 + - - +
587D ILE* 1.3 82.3 - - - +
589D PRO* 1.3 64.5 - - - +
590D LEU 3.0 7.8 + - - -
591D ILE* 3.0 20.7 + - + -
592D THR* 3.3 9.9 + - - +
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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