Contacts of the strand formed by residues 71 - 75 (chain A) in PDB entry 5JQE
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 ILE 71 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 4.4 6.5 - - + -
20A VAL 3.1 3.8 + - - -
21A ILE* 3.5 19.0 - - + -
22A TRP 3.0 24.6 + - - -
69A PRO* 3.5 8.5 - - - +
70A ASP* 1.3 84.2 - - + +
72A ILE* 1.3 63.9 + - - +
73A PHE* 3.7 23.6 - - + -
276A ALA* 3.9 13.5 - - + -
277A GLY 3.4 11.9 - - - +
278A ILE* 4.9 1.3 - - + -
288A ALA* 4.0 27.1 - - + -
291A PHE* 3.7 33.2 - - + -
292A LEU* 4.0 13.2 - - + -
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Residues in contact with ILE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TRP* 3.7 22.7 - - + -
55A LEU* 3.6 31.4 - - + -
59A PHE* 4.5 23.6 - - + -
69A PRO* 4.6 6.7 - - + -
70A ASP 5.4 0.2 - - - +
71A ILE* 1.3 76.0 - - - +
73A PHE* 1.3 66.3 + - - +
74A TRP* 4.7 2.2 - - + -
79A PHE* 3.3 22.5 - - + -
82A TYR* 4.8 9.0 - - + +
88A LEU* 3.7 24.2 - - + -
276A ALA* 3.3 0.5 - - - -
277A GLY* 2.9 42.7 + - - +
279A ASN* 5.3 3.4 - - + +
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Residues in contact with PHE 73 (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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21A ILE* 3.5 35.7 - - + -
22A TRP 2.8 14.0 + - - +
23A ILE* 3.7 34.7 - - + +
24A ASN 4.5 0.7 + - - -
32A LEU* 4.0 16.2 - - + -
71A ILE* 3.7 14.8 - - + -
72A ILE* 1.3 76.8 - - - +
74A TRP* 1.3 77.1 + - - +
120A ILE* 3.7 23.8 - - + -
274A LEU* 4.1 14.9 - - + +
275A SER 3.3 7.9 - - - -
276A ALA* 3.5 21.5 - - + -
291A PHE* 5.4 0.4 - + - -
292A LEU* 4.0 3.1 - - + -
296A LEU* 3.5 26.2 - - + -
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Residues in contact with TRP 74 (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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24A ASN* 3.5 46.0 - - + -
27A LYS* 6.0 2.9 - - - +
55A LEU* 3.4 27.1 - - + -
56A GLU* 3.4 46.5 - - + +
72A ILE* 4.7 5.2 - - + -
73A PHE* 1.3 81.4 - - - +
75A ALA* 1.3 89.7 + - + +
77A ASP* 5.8 0.6 + - - -
78A ARG* 3.8 23.5 - - + +
79A PHE* 3.5 21.4 - - + -
82A TYR* 5.0 2.5 - - + -
274A LEU* 3.6 11.3 - - - +
275A SER* 2.8 31.0 + - - +
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Residues in contact with ALA 75 (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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74A TRP* 1.3 98.9 - - + +
76A HIS* 1.3 65.7 + - - +
77A ASP* 3.3 21.5 + - - +
78A ARG 3.5 8.1 + - - -
79A PHE* 3.9 8.3 - - - -
272A GLY* 6.0 2.5 - - - -
273A VAL 3.6 9.9 - - - +
274A LEU* 4.3 5.2 - - - +
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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