Contacts of the strand formed by residues 59 - 66 (chain I) in PDB entry 1IBM
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 59 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4I TYR* 3.7 26.9 - + - -
19I LEU* 3.6 36.6 - - + -
20I ARG 3.1 19.3 - - - -
21I PRO* 4.2 5.6 - - + -
22I GLY 2.7 23.6 - - - +
24I GLY 3.1 6.9 + - - -
50I LEU* 5.1 4.3 - - + -
55I ALA* 4.1 20.6 - - + -
56I LEU* 3.3 13.9 + - - +
58I ARG* 1.3 103.4 - - + +
60I ASP* 1.3 71.0 + - - +
85I LEU* 4.4 7.4 - - + -
88I TYR* 3.1 38.1 - + - -
92I TYR* 5.2 2.7 - + - -
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Residues in contact with ASP 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I LEU* 3.4 3.6 - - - +
20I ARG* 2.9 39.4 + - + +
21I PRO 5.0 0.4 - - - +
22I GLY* 4.2 7.2 - - - -
23I ASN* 4.1 5.7 + - - +
24I GLY* 3.6 11.0 + - - +
25I LYS* 2.5 54.0 + - - +
26I VAL* 5.2 1.3 - - - -
27I THR 5.5 0.2 + - - -
50I LEU* 6.3 0.4 - - - +
59I PHE* 1.3 81.1 - - - +
61I ALA* 1.3 76.3 + - - +
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Residues in contact with ALA 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I VAL* 4.8 1.6 - - + -
18I PHE 2.9 17.3 - - - +
19I LEU* 3.6 17.5 - - + -
20I ARG* 5.8 1.1 - - - +
25I LYS 3.2 6.6 + - - +
26I VAL* 3.1 23.9 - - + +
27I THR* 3.0 24.4 + - - -
50I LEU* 6.4 1.3 - - + -
60I ASP* 1.3 84.0 + - - +
62I TYR* 1.3 59.0 + - - +
63I ILE* 4.3 12.1 - - + -
81I ILE* 5.8 2.0 - - + -
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Residues in contact with TYR 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1128A C 3.9 2.6 + - - -
1129A C 2.5 38.6 + - - -
1130A A 4.0 14.6 - - - -
16I ARG 3.9 0.2 - - - +
18I PHE* 2.9 65.8 + + + +
20I ARG* 4.5 17.2 - - - +
27I THR* 3.8 30.1 - - + +
29I ASN* 5.2 6.6 - - - -
30I GLY 5.3 1.3 - - - -
61I ALA* 1.3 73.6 - - - +
63I ILE* 1.3 64.4 + - - +
64I THR* 4.2 18.8 + - - -
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Residues in contact with ILE 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I ALA* 4.9 1.3 - - + -
16I ARG 3.3 11.7 - - - +
17I VAL* 4.0 15.5 - - + -
26I VAL* 3.8 22.4 - - + -
27I THR 2.8 15.4 + - - +
28I VAL* 3.2 8.6 - - + -
29I ASN* 2.7 32.6 + - - -
33I PHE* 5.9 0.7 - - + -
47I LEU* 5.6 0.9 - - + -
61I ALA* 4.3 4.5 - - + -
62I TYR* 1.3 84.9 - - - +
64I THR* 1.3 60.6 + - - +
65I VAL* 3.3 28.7 - - + -
77I ILE* 3.7 34.3 - - + -
81I ILE* 4.0 13.5 - - + -
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Residues in contact with THR 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1128A C 4.9 8.2 + - - -
14I VAL 3.6 2.1 - - - +
15I ALA* 3.4 0.9 - - - -
16I ARG* 2.6 65.2 + - - +
18I PHE* 5.4 2.5 - - - -
29I ASN* 2.7 17.6 + - - +
62I TYR* 4.2 21.0 + - - -
63I ILE* 1.3 70.4 + - - +
65I VAL* 1.3 59.9 + - - +
66I ARG* 3.4 34.8 - - + +
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Residues in contact with VAL 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1249A C 6.1 0.2 - - - +
13I ALA* 5.5 0.2 - - + -
14I VAL 3.3 9.4 - - - +
15I ALA* 3.7 9.0 - - + -
28I VAL* 4.6 6.3 - - + -
29I ASN* 2.5 31.0 + - - +
36I TYR* 4.4 3.6 + - + -
63I ILE* 3.3 15.7 - - + -
64I THR* 1.3 71.4 - - - +
66I ARG* 1.3 65.3 + - - +
67I GLY 5.3 0.4 - - - +
73I GLN* 3.1 52.7 + - + +
77I ILE* 3.3 36.8 - - + -
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Residues in contact with ARG 66 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1127A G 4.3 7.5 + - - -
1128A C 3.7 20.0 + - - -
1148A U 4.9 13.4 + - - +
1250A A 4.1 10.3 - - - +
13I ALA* 4.0 0.2 - - - -
14I VAL* 3.0 38.1 + - + +
16I ARG* 3.2 30.5 - - - +
29I ASN* 5.2 3.4 + - - +
64I THR* 3.4 26.8 - - - +
65I VAL* 1.3 73.9 + - - +
67I GLY* 1.3 64.2 + - - +
73I GLN* 4.2 1.8 - - - +
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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