Contacts of the helix formed by residues 520 - 525 (chain A) in PDB entry 4PE5
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 ASN 520 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518A THR* 3.5 5.7 - - + +
519A ILE* 1.3 74.8 - - - +
521A ASN* 1.3 63.9 + - - +
522A GLU* 3.0 23.8 + - - +
523A ARG* 3.2 31.6 - - - +
524A ALA* 3.3 23.0 + - - +
529A PHE* 4.2 1.4 - - - -
688A SER* 5.1 8.2 + - - -
691A ILE* 3.7 29.5 - - - +
754A PHE* 4.3 20.4 - - + -
781D LEU* 3.5 12.1 - - - +
784D PHE* 6.0 0.7 - - - -
785D GLY* 6.2 2.0 - - - -
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Residues in contact with ASN 521 (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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520A ASN* 1.3 76.9 - - - +
522A GLU* 1.3 75.8 + - - +
524A ALA* 3.4 7.5 + - - +
525A GLN* 3.3 37.1 + - - +
778D LEU* 3.1 29.2 - - - +
781D LEU* 3.6 15.1 + - - +
782D GLN* 3.4 34.9 - - - +
785D GLY* 5.7 2.2 - - - +
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Residues in contact with GLU 522 (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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498A TRP* 3.3 26.6 - - + -
520A ASN* 3.0 23.3 + - - +
521A ASN* 1.3 91.3 + - - +
523A ARG* 1.3 60.5 + - - +
524A ALA 3.6 0.2 + - - -
525A GLN* 3.8 11.1 + - - +
526A TYR* 3.7 10.7 - - - -
691A ILE* 3.6 25.5 - - + +
694A ARG* 4.1 15.3 - - - +
695A ARG* 4.3 15.7 - - + +
785D GLY* 5.5 8.4 - - - -
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Residues in contact with ARG 523 (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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484A PHE* 3.7 0.8 - - - +
485A GLY 2.6 37.3 + - - +
486A THR* 3.9 2.4 - - - +
498A TRP* 3.6 16.4 - - + -
502A MET* 3.5 26.8 - - - +
517A LEU* 3.3 19.8 - - - +
518A THR 3.8 7.8 + - - -
520A ASN* 3.2 24.0 + - - +
521A ASN 3.3 0.4 - - - -
522A GLU* 1.3 73.6 - - - +
524A ALA* 1.3 59.4 + - - +
525A GLN 3.2 1.3 + - - -
526A TYR 3.6 1.7 + - - -
527A ILE* 3.2 31.2 + - - +
529A PHE* 4.1 11.2 - - + -
687A SER 3.7 6.7 - - - -
688A SER* 2.6 36.7 + - - +
691A ILE* 3.6 8.3 - - + +
942A GLY* 2.9 29.7 + - - -
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Residues in contact with ALA 524 (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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520A ASN 3.3 19.0 + - - +
521A ASN 3.4 0.6 + - - +
522A GLU 3.4 0.4 - - - -
523A ARG* 1.3 75.0 - - - +
525A GLN* 1.3 58.9 + - - +
526A TYR 3.1 5.8 - - - -
527A ILE 3.1 18.7 - - - +
528A GLU* 5.2 0.7 - - - -
529A PHE* 4.5 12.6 - - + +
777D ASP* 6.4 0.2 - - + -
778D LEU* 3.6 24.7 - - + +
781D LEU* 3.6 16.2 - - + -
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Residues in contact with GLN 525 (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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521A ASN* 3.3 38.6 + - - +
522A GLU* 4.0 12.2 - - - +
523A ARG 3.2 1.2 - - - -
524A ALA* 1.3 77.6 - - - +
526A TYR* 1.3 74.6 + - + +
778D LEU* 3.7 26.9 - - + +
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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