Contacts of the helix formed by residues 572 - 577 (chain A) in PDB entry 1Q8Z
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 SER 572 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566A GLN* 2.7 24.4 + - - -
571A ARG* 1.3 74.3 - - - +
573A PRO* 1.3 66.9 - - - +
574A GLU* 3.1 29.7 + - - -
575A VAL* 3.4 13.7 + - - +
576A LEU* 3.1 29.2 + - - +
585A ALA* 4.2 2.8 - - - +
588A TRP* 3.6 24.8 - - - -
694A ARG* 4.3 0.4 - - - -
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Residues in contact with PRO 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572A SER* 1.3 83.3 - - - +
574A GLU* 1.3 78.6 + - - +
576A LEU* 3.6 12.0 - - + +
577A LEU* 2.9 30.9 + - + +
588A TRP* 3.7 26.9 - - + -
622A ILE* 4.0 14.6 - - + -
629A LEU* 5.4 4.7 - - + -
633A LEU* 4.2 15.3 - - + -
689A LEU* 4.0 30.7 - - + +
694A ARG* 4.2 3.6 - - - +
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Residues in contact with GLU 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572A SER* 3.1 13.6 + - - -
573A PRO* 1.3 86.7 - - - +
575A VAL* 1.3 58.0 + - - +
577A LEU 3.3 0.3 + - - -
578A GLY 2.9 9.2 + - - -
579A ALA* 2.8 32.8 + - + +
580A PRO 3.2 22.2 - - - +
581A TRP* 4.1 12.4 - - + +
582A GLY 5.4 0.3 + - - -
585A ALA* 4.2 6.2 + - - -
633A LEU* 4.0 12.1 - - + +
691A PRO* 3.5 34.2 - - + +
694A ARG* 2.8 44.3 + - - -
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Residues in contact with VAL 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563A ASN 3.7 19.5 - - - +
564A SER* 5.4 0.7 - - - -
565A ILE* 3.7 37.0 - - + +
566A GLN* 3.8 5.2 - - - +
571A ARG* 3.6 24.6 - - + -
572A SER* 3.4 21.4 + - - +
573A PRO 3.2 0.4 - - - -
574A GLU* 1.3 76.7 - - - +
576A LEU* 1.3 62.8 + - - +
578A GLY* 3.5 8.9 + - - +
579A ALA 5.0 0.2 - - - -
581A TRP* 3.9 23.8 - - + +
585A ALA* 5.2 0.2 - - + -
639A TYR* 5.6 0.7 - - - -
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Residues in contact with LEU 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568A ARG* 4.2 7.9 - - - +
571A ARG* 3.9 20.4 - - + +
572A SER 3.1 19.9 + - - +
573A PRO* 3.2 8.2 + - + +
575A VAL* 1.3 77.9 - - - +
577A LEU* 1.3 68.4 + - + +
578A GLY 3.8 0.3 + - - -
615A ASP* 4.0 24.8 - - - +
618A HIS* 3.4 39.3 - - + +
619A ILE* 4.1 15.3 - - + -
622A ILE* 3.8 25.6 - - + -
639A TYR* 4.6 4.9 - - - +
643A PHE* 3.6 21.7 - - - -
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Residues in contact with LEU 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573A PRO* 2.9 21.4 + - + +
574A GLU 4.2 1.3 - - - +
576A LEU* 1.3 82.4 - - + +
578A GLY* 1.3 55.5 + - - +
579A ALA* 3.1 6.5 - - + +
619A ILE* 3.5 34.1 - - + -
629A LEU* 3.7 28.7 - - + -
633A LEU* 3.9 30.5 - - + +
634A LEU* 4.3 8.5 - - + -
637A GLY* 3.1 10.4 - - - -
638A LYS 2.8 23.4 + - - -
639A TYR* 3.2 14.6 + - - -
640A THR* 4.5 13.2 - - - +
643A PHE* 4.4 4.0 - - + -
644A PHE* 5.0 2.5 - - + -
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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