Contacts of the strand formed by residues 59 - 63 (chain A) in PDB entry 3IO6
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 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A LEU* 4.7 4.7 - - + -
8A VAL 3.6 2.6 + - - -
9A ILE* 3.4 18.3 - - + +
10A TRP 2.8 27.0 + - - -
57A PRO* 3.9 4.1 - - - +
58A ASP* 1.3 86.9 - - + +
60A ILE* 1.3 62.9 + - - +
61A PHE* 3.7 26.2 - - + -
264A ALA* 3.9 15.7 - - + -
265A GLY 3.1 13.2 - - - +
266A ILE* 4.5 1.6 - - + -
276A ALA* 3.7 31.2 - - + -
279A PHE* 4.1 16.2 - - + -
280A LEU* 3.8 24.5 - - + -
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Residues in contact with ILE 60 (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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10A TRP* 3.4 11.0 - - + +
43A LEU* 3.7 31.6 - - + +
44A GLU* 5.1 0.2 - - - -
47A PHE* 3.6 65.5 - - + -
57A PRO* 4.5 3.8 - - + -
59A ILE* 1.3 73.4 - - - +
61A PHE* 1.3 66.5 + - - +
62A TRP* 4.7 6.1 - - + -
67A PHE* 3.3 17.4 - - + -
70A TYR* 4.7 8.3 - - + +
76A LEU* 4.4 10.5 - - + -
265A GLY 3.1 27.8 + - - +
267A ASN 5.8 1.1 - - - +
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Residues in contact with PHE 61 (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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9A ILE* 3.4 34.5 - - + -
10A TRP 2.8 14.3 + - - +
11A ILE* 3.6 37.7 - - + +
12A ASN* 4.4 1.6 + - - +
20A LEU* 3.8 13.0 - - + -
43A LEU* 4.2 5.4 - - - +
59A ILE* 3.7 10.3 - - + -
60A ILE* 1.3 71.5 - - - +
62A TRP* 1.3 73.9 + - - +
108A ILE* 3.8 17.9 - - + -
262A LEU* 4.5 11.7 - - + +
263A SER 3.2 9.4 - - - +
264A ALA* 3.1 27.4 - - + -
280A LEU* 3.7 6.1 - - + -
284A LEU* 3.3 32.8 - - + -
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Residues in contact with TRP 62 (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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12A ASN* 3.6 40.4 - - + -
43A LEU* 3.4 22.0 - - + -
44A GLU* 3.0 50.3 - - + +
60A ILE* 3.8 9.0 + - + -
61A PHE* 1.3 79.6 - - - +
63A ALA* 1.3 95.0 + - + +
65A ASP* 5.1 1.0 + - - -
66A ARG* 3.6 24.1 - - + +
67A PHE* 3.8 16.8 - + + -
70A TYR* 5.3 2.0 - - + -
262A LEU* 3.8 14.2 - - + +
263A SER* 2.9 33.2 + - - -
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Residues in contact with ALA 63 (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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62A TRP* 1.3 93.4 - - + +
64A HIS* 1.3 61.6 - - + +
65A ASP* 2.9 26.9 + - - +
66A ARG* 3.0 13.7 + - - +
67A PHE* 3.9 2.9 + - - -
111A GLU* 5.7 4.0 - - - +
260A GLY* 5.4 5.4 - - - -
261A VAL 3.7 8.7 - - - +
262A LEU* 4.1 8.1 - - + +
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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