Contacts of the helix formed by residues 517 - 523 (chain B) in PDB entry 3A8X
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 517 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515B ASN 3.6 5.3 + - - -
516B VAL* 1.3 69.6 - - - +
518B TRP* 1.3 59.7 - - - +
519B ASP* 3.0 11.1 + - - +
520B MET* 3.0 45.0 + - - +
521B MET* 3.2 16.1 + - - +
526B VAL* 4.9 4.3 - - - +
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Residues in contact with TRP 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B ALA* 3.5 33.0 - - + -
354B SER* 4.3 12.1 - - - -
355B LEU* 4.0 29.5 - - + +
504B PHE* 4.6 7.2 - + - -
507B ILE* 4.5 5.8 - - + -
508B GLN* 3.5 56.8 + - + +
513B PHE* 3.6 47.7 + + + -
516B VAL* 3.4 27.8 + - + -
517B ASP* 1.3 71.6 - - - +
519B ASP* 1.3 59.7 + - - +
521B MET* 3.6 7.9 - - - +
522B GLU* 2.9 30.5 + - - +
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Residues in contact with ASP 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B ASP* 3.0 7.5 + - - +
518B TRP* 1.3 79.3 + - - +
520B MET* 1.3 61.1 + - - +
521B MET 3.1 1.3 - - - -
522B GLU* 3.5 12.1 + - - +
523B GLN* 3.2 42.4 + - - +
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Residues in contact with MET 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517B ASP* 3.0 29.8 + - - +
519B ASP* 1.3 76.3 - - - +
521B MET* 1.3 56.8 + - - +
523B GLN 3.9 0.9 - - - -
524B LYS 3.6 0.7 + - - -
525B GLN* 2.8 76.5 + - + +
526B VAL* 3.2 11.3 + - + -
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Residues in contact with MET 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B PHE* 3.3 15.4 - - - -
348B PHE* 4.0 26.7 - - + +
351B ALA* 3.9 18.8 - - + -
352B GLU* 3.8 32.2 - - + +
355B LEU* 3.7 17.5 - - + -
382B HIS* 5.5 0.2 - - - -
516B VAL* 3.6 27.6 - - + -
517B ASP 3.2 11.8 + - - +
518B TRP* 3.6 12.3 - - - +
519B ASP 3.1 0.4 - - - -
520B MET* 1.3 74.3 - - - +
522B GLU* 1.3 57.9 + - - +
523B GLN 3.0 4.3 - - - -
524B LYS* 3.0 18.2 + - - -
526B VAL* 3.5 22.2 - - + +
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Residues in contact with GLU 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B HIS* 4.9 15.0 + - + +
304B PRO* 3.5 25.5 - - + +
305B PHE* 4.2 3.1 - - + -
355B LEU* 3.8 32.9 - - + +
359B TYR* 5.7 2.9 - - - -
518B TRP 2.9 18.9 + - - +
519B ASP* 3.9 13.6 - - - +
521B MET* 1.3 76.5 - - - +
523B GLN* 1.3 60.8 + - + +
524B LYS 3.3 0.7 - - - -
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Residues in contact with GLN 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519B ASP* 3.2 25.3 + - - +
520B MET 3.9 0.4 + - - +
521B MET 3.0 1.4 - - - -
522B GLU* 1.3 80.5 - - + +
524B LYS* 1.3 71.1 + - - +
525B GLN* 3.2 37.3 + - - +
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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