Contacts of the helix formed by residues 517 - 524 (chain A) in PDB entry 3AR2
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 ALA 517 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492A LYS* 2.7 34.7 + - + +
516A GLY* 1.3 69.3 - - - -
518A PRO* 1.3 72.8 - - - +
519A GLU* 3.1 4.4 + - + +
520A GLY* 3.3 6.4 + - - +
521A VAL* 3.1 18.5 + - - +
678A ARG* 3.5 32.5 - - - +
1002A ACP 3.4 10.7 + - - +
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Residues in contact with PRO 518 (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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516A GLY 3.4 4.3 - - - +
517A ALA* 1.3 82.1 - - + +
519A GLU* 1.3 75.0 + - - +
522A ILE* 2.8 31.6 + - + +
546A LEU* 5.3 2.2 - - + -
549A ILE* 3.5 33.4 - - + -
561A CYS* 3.3 44.2 - - + +
562A LEU 3.8 3.8 - - - +
563A ALA* 3.7 17.9 - - + +
596A VAL* 5.2 0.7 - - + -
628A ASN* 6.0 0.9 - - + -
678A ARG* 4.3 4.7 - - - +
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Residues in contact with GLU 519 (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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517A ALA* 3.1 1.8 + - + -
518A PRO* 1.3 87.0 - - - +
520A GLY* 1.3 64.4 + - - +
522A ILE* 3.1 3.1 + - - +
523A ASP* 3.0 31.9 + - - +
546A LEU* 5.2 11.9 - - + +
549A ILE* 5.7 0.7 - - - +
628A ASN* 3.6 20.5 + - - +
629A LYS 5.4 0.2 + - - -
678A ARG* 2.6 47.5 + - - +
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Residues in contact with GLY 520 (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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491A ARG 5.0 6.7 - - - -
492A LYS* 6.3 0.2 - - - -
517A ALA* 3.3 9.3 + - - +
519A GLU* 1.3 78.4 - - - +
521A VAL* 1.3 61.0 + - - +
523A ASP* 3.6 6.3 + - - +
524A ARG* 3.1 44.1 + - - +
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Residues in contact with VAL 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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493A SER* 4.2 15.7 - - - -
514A VAL* 4.2 11.2 - - + -
516A GLY* 3.7 31.0 - - - +
517A ALA 3.1 15.4 + - - +
520A GLY* 1.3 72.4 - - - +
522A ILE* 1.3 68.6 + - + +
524A ARG* 3.0 19.1 + - - +
525A CYS* 3.2 17.2 + - - -
563A ALA* 3.7 23.1 - - + -
564A LEU 4.9 0.2 - - - -
565A ALA* 3.9 27.6 - - + +
591A LEU* 4.0 5.1 - - + +
593A PHE* 5.6 1.1 - - + -
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Residues in contact with ILE 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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518A PRO* 2.8 41.4 + - + +
519A GLU 3.8 2.0 - - - +
521A VAL* 1.3 71.4 - - + +
523A ASP* 1.3 63.3 + - - +
525A CYS* 3.3 24.4 + - - +
537A MET* 4.3 9.7 - - + +
542A LYS* 3.5 38.4 + - + +
545A ILE* 3.9 23.3 - - + -
546A LEU* 4.6 16.4 - - + -
549A ILE* 4.6 1.3 - - + -
563A ALA* 3.4 26.7 - - + -
593A PHE* 3.9 18.4 - - + -
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Residues in contact with ASP 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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519A GLU* 3.0 24.3 + - - +
520A GLY* 4.0 6.8 - - - +
521A VAL 3.2 0.2 - - - -
522A ILE* 1.3 78.2 - - - +
524A ARG* 1.3 60.7 + - + +
525A CYS 3.2 8.2 + - - +
526A ASN* 5.4 1.6 - - - +
542A LYS* 2.8 30.5 + - - +
546A LEU* 5.8 0.9 - - - +
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Residues in contact with ARG 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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491A ARG* 3.9 13.7 + - - +
493A SER* 2.7 36.6 + - - -
514A VAL* 4.7 2.2 - - - +
520A GLY* 3.1 41.7 + - - +
521A VAL* 3.0 12.0 + - - +
523A ASP* 1.3 79.7 - - + +
525A CYS* 1.3 56.1 + - - +
526A ASN* 5.4 1.6 - - - -
585A MET* 3.7 42.4 + - - -
588A GLU* 2.9 40.1 + - - +
589A THR* 4.4 11.0 - - + +
590A ASP 3.4 7.1 + - - +
591A LEU* 2.8 35.0 + - + +
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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