Contacts of the strand formed by residues 54 - 57 (chain K) in PDB entry 2AAZ
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 PHE 54 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22K GLN* 3.4 40.4 - - + +
23K TYR* 3.7 27.4 - + + -
26K LEU* 3.4 33.2 - - + -
52K PRO 4.1 8.1 - - - -
53K SER* 1.3 79.5 - - - +
55K ARG* 1.3 62.0 + - - +
56K PHE* 3.6 30.3 - + + -
220K LEU* 5.0 0.7 - - + -
228K ILE* 4.3 8.1 - - + -
249K PHE 3.8 0.4 - - - +
250K ILE* 3.3 9.0 - - - +
251K LEU* 2.9 40.3 + - + +
253K MET* 3.4 26.7 - - + -
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Residues in contact with ARG 55 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K GLU* 3.9 8.0 - - - +
22K GLN* 2.9 29.4 + - - +
53K SER* 4.4 14.1 + - - +
54K PHE* 1.3 78.7 - - - +
56K PHE* 1.3 62.9 + - - +
248K GLU* 2.6 43.0 + - - +
249K PHE 3.5 4.5 - - - -
250K ILE* 3.8 22.4 - - + +
49L PHE 3.9 10.3 + - - -
50L ALA 2.7 29.9 + - - -
51L PRO* 4.6 7.0 - - - +
52L PRO* 4.8 7.7 - - - +
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Residues in contact with PHE 56 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K GLU* 3.4 37.2 - - + +
20K GLU* 4.9 1.8 - - - -
22K GLN* 3.6 17.0 - - + -
23K TYR* 5.4 4.3 - - + -
54K PHE* 3.6 30.1 - + + -
55K ARG* 1.3 74.4 - - - +
57K SER* 1.3 63.5 + - - +
58K LEU* 3.6 0.7 + - + +
64K PRO* 3.8 29.6 - - + -
66K LEU* 5.5 2.9 - - + -
228K ILE* 3.7 36.8 - - + -
248K GLU* 3.5 5.4 - - - +
249K PHE* 2.9 61.5 + + + +
251K LEU* 5.3 0.4 - - + -
277K PHE* 4.3 9.0 - + - -
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Residues in contact with SER 57 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K GLU* 2.9 25.2 + - - +
56K PHE* 1.3 73.6 - - - +
58K LEU* 1.3 66.3 + - - +
59K ALA* 3.3 22.1 + - - +
62K THR* 3.8 21.3 + - - +
64K PRO* 4.7 1.6 - - - +
247K HIS* 3.7 7.2 + - - -
248K GLU* 4.7 2.9 - - - +
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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