Contacts of the strand formed by residues 54 - 57 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D GLN* 3.3 42.8 - - + +
23D TYR* 3.7 27.8 - + + -
26D LEU* 3.5 31.6 - - + -
52D PRO 4.2 7.6 - - - -
53D SER* 1.3 78.9 - - - +
55D ARG* 1.3 60.5 + - - +
56D PHE* 3.6 31.4 - + + -
220D LEU* 5.0 0.9 - - + -
228D ILE* 4.2 8.1 - - + -
249D PHE 4.5 0.2 - - - -
250D ILE* 3.2 8.8 - - - +
251D LEU* 2.8 40.9 + - + +
253D MET* 3.4 24.9 - - + -
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Residues in contact with ARG 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C PHE 3.8 10.7 + - - -
50C ALA 2.8 30.3 + - - -
51C PRO* 4.6 6.8 + - - +
52C PRO* 4.7 7.1 - - - +
19D GLU* 3.9 8.1 - - - +
22D GLN* 2.9 30.7 + - - +
53D SER* 4.4 13.8 + - - +
54D PHE* 1.3 79.7 - - - +
56D PHE* 1.3 63.0 + - - +
248D GLU* 2.6 41.7 + - - +
249D PHE 3.5 4.3 - - - -
250D ILE* 3.8 22.5 - - + +
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Residues in contact with PHE 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D GLU* 3.4 37.0 - - + +
20D GLU* 4.9 1.8 - - - -
22D GLN* 3.6 16.2 - - + -
23D TYR* 5.4 2.9 - - + -
54D PHE* 3.6 30.1 - + + -
55D ARG* 1.3 75.3 - - - +
57D SER* 1.3 63.8 + - - +
58D LEU* 4.0 1.8 - - + +
64D PRO* 3.8 29.6 - - + -
66D LEU* 5.4 4.5 - - + -
228D ILE* 3.7 38.4 - - + -
248D GLU* 3.5 5.4 - - - +
249D PHE* 2.8 61.1 + + + +
251D LEU* 5.3 0.2 - - + -
277D PHE* 4.2 9.4 - + - -
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Residues in contact with SER 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D GLU* 2.9 24.6 + - - +
56D PHE* 1.3 74.8 - - - +
58D LEU* 1.3 66.0 + - - +
59D ALA* 3.3 22.7 + - - +
62D THR* 3.8 20.8 + - - +
64D PRO* 4.8 1.6 - - - +
247D HIS 3.7 6.8 + - - -
248D GLU* 4.7 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