Contacts of the strand formed by residues 54 - 58 (chain A) in PDB entry 4AEJ
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 GLY 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A LYS 3.4 2.6 + - - -
53A SER* 1.3 74.3 - - - +
55A GLU* 1.3 61.3 + - - -
56A TYR* 3.1 14.6 - - - -
72A PHE* 3.6 20.2 - - - -
73A CYS 2.8 31.2 + - - -
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Residues in contact with GLU 55 (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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54A GLY* 1.3 71.3 - - - -
56A TYR* 1.3 76.2 + - - +
57A TRP* 5.4 4.9 + - + +
70A LYS* 3.1 46.2 + - + +
71A VAL 3.3 9.6 - - - +
72A PHE* 4.5 2.3 - - - +
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Residues in contact with TYR 56 (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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31A ASP 4.1 6.5 - - - -
32A GLY* 3.5 14.4 - - - +
44A LEU* 3.6 25.4 - - + -
51A LEU* 3.5 36.2 - - + +
52A LYS 2.6 31.2 + - - -
54A GLY* 3.1 32.1 - - - -
55A GLU* 1.3 77.1 - - - +
57A TRP* 1.3 69.1 + - - +
58A VAL* 4.1 1.1 - - + -
70A LYS* 3.5 4.7 - - - +
71A VAL* 2.8 36.2 + - - +
73A CYS* 3.6 29.8 - - + -
75A MSE 4.8 2.2 - - + -
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Residues in contact with TRP 57 (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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32A GLY* 2.7 17.5 + - - -
33A SER* 3.6 16.4 - - - +
34A ARG* 3.4 78.1 - - + +
37A PRO* 3.4 9.7 - - + +
38A ALA 3.3 18.5 + - - -
55A GLU* 5.4 4.7 + - + +
56A TYR* 1.3 79.1 - - - +
58A VAL* 1.3 63.9 + - - +
68A ALA* 3.5 29.6 - - + -
69A ILE 3.2 13.7 - - - -
70A LYS* 3.9 29.5 - - + +
121A ASN* 3.3 31.4 - - - -
123A GLU* 4.5 1.8 - - - -
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Residues in contact with VAL 58 (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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37A PRO* 4.0 2.0 - - - -
38A ALA* 3.0 14.1 - - + +
39A ARG 3.8 7.4 - - - +
40A ASN* 3.7 25.1 - - - +
41A CYS* 4.0 5.4 - - - +
44A LEU* 5.7 0.9 - - + -
56A TYR* 4.1 1.8 - - + -
57A TRP* 1.3 79.3 - - - +
59A ASP* 1.3 61.7 + - - +
60A PRO* 4.2 7.6 - - + -
68A ALA* 3.4 1.7 - - - +
69A ILE* 2.8 55.4 + - + +
71A VAL* 3.8 30.7 - - + -
73A CYS* 4.5 3.8 - - - -
80A THR* 4.2 10.1 - - + -
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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