Contacts of the strand formed by residues 59 - 65 (chain C) in PDB entry 1I2M
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C VAL* 3.6 13.7 - - + +
11C PHE* 3.8 28.9 - - + -
50C LEU 3.7 1.0 - - - +
51C VAL* 3.7 2.4 - - - -
52C PHE* 2.8 41.9 + - + +
54C THR* 4.0 14.1 - - + +
56C ARG* 5.6 2.5 - - + +
57C GLY 3.8 6.7 - - - +
58C PRO* 1.3 79.6 - - - +
60C LYS* 1.3 63.6 + - - +
61C PHE* 4.2 19.7 - - + -
165C ALA* 4.2 7.9 - - + -
169C ILE* 4.4 15.7 - - + -
174C LEU* 3.9 31.4 - - + -
176C PHE* 5.2 0.7 - - + -
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Residues in contact with LYS 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C GLN* 4.6 18.5 + - - +
9C VAL 2.9 15.7 + - - +
10C GLN* 3.1 34.8 - - + +
11C PHE* 2.8 30.5 + - - +
38C LYS* 5.5 6.9 - - - +
49C PRO* 3.8 18.4 - - + +
50C LEU 3.5 4.3 - - - +
51C VAL* 3.7 29.2 - - + +
58C PRO 4.2 0.2 - - - -
59C ILE* 1.3 74.1 - - - +
61C PHE* 1.3 65.3 + - - +
62C ASN* 3.1 23.2 - - - +
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Residues in contact with PHE 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C PHE* 3.3 18.4 - + + -
13C LEU* 3.8 16.8 - - + -
48C HIS 3.3 0.7 - - - +
50C LEU* 2.7 44.8 + - + +
52C PHE* 3.8 18.2 - + - -
59C ILE* 4.2 16.8 - - + -
60C LYS* 1.3 73.5 - - - +
62C ASN* 1.3 62.1 + - - +
63C VAL* 3.2 19.7 + - + -
85C CYS* 3.9 9.6 - - - -
161C PHE* 3.7 49.6 - + + -
164C LEU* 4.3 3.8 - - + -
165C ALA* 4.1 19.1 - - + -
168C LEU* 3.8 22.9 - - + -
176C PHE* 5.0 2.0 - + - -
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Residues in contact with ASN 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C GLN* 3.6 25.9 + - - +
11C PHE 2.8 13.9 + - - +
12C LYS* 3.5 18.9 - - + +
13C LEU 2.9 22.3 + - - +
38C LYS* 5.9 3.6 - - - +
47C VAL* 3.5 22.9 - - + +
48C HIS 4.2 0.4 - - - -
49C PRO* 3.8 13.5 - - - +
60C LYS* 3.1 31.6 - - - +
61C PHE* 1.3 68.4 - - - +
63C VAL* 1.3 61.5 - - - +
64C TRP* 3.7 7.2 - - + -
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Residues in contact with VAL 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LEU* 3.2 39.9 - - + +
15C LEU* 4.2 10.1 - - + -
27C VAL* 4.5 17.9 - - + -
47C VAL* 3.3 2.2 - - - -
48C HIS* 2.6 50.1 + - + +
50C LEU* 3.6 27.8 - - + -
61C PHE* 3.7 13.9 - - + +
62C ASN* 1.3 74.5 - - - +
64C TRP* 1.3 72.1 + - - +
65C ASP 4.9 0.2 - - - +
161C PHE* 4.5 1.6 - - + -
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Residues in contact with TRP 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LYS* 3.5 28.7 - - + -
13C LEU 3.1 13.7 + - - -
14C VAL* 3.5 22.4 - - + +
15C LEU* 2.9 24.7 + - - +
40C VAL* 4.1 22.0 - - + -
43C LEU* 3.5 30.7 - - + +
45C VAL* 4.0 8.3 - - + -
46C GLU 3.9 15.7 - - - +
47C VAL* 4.7 4.0 - - + -
48C HIS* 4.7 1.3 - - - -
62C ASN* 3.7 17.5 - - + -
63C VAL* 1.3 79.9 - - - +
65C ASP* 1.3 60.9 + - - +
66C THR* 4.4 3.8 - - + -
78C GLY 5.5 0.2 - - - -
79C TYR 3.0 29.1 + - - -
80C TYR 4.5 0.4 - - - -
82C GLN* 3.6 17.7 - - + -
83C ALA* 3.4 35.4 - - + -
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Residues in contact with ASP 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B ARG* 3.0 27.9 + - - +
15C LEU* 3.4 21.4 - - + +
23C LYS* 3.0 39.9 + - - +
24C THR* 4.8 0.9 + - - -
27C VAL* 5.6 4.5 - - + -
45C VAL* 4.1 21.0 - - - +
46C GLU 5.0 0.6 + - - -
48C HIS* 5.2 8.6 + - + +
63C VAL* 4.9 0.2 - - - +
64C TRP* 1.3 72.5 - - - +
66C THR* 1.3 63.8 + - - +
67C ALA* 2.7 32.5 + - + +
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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