Contacts of the strand formed by residues 67 - 72 (chain J) in PDB entry 1I5L
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 VAL 67 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J VAL* 4.3 1.6 - - + -
20J ARG 3.9 6.1 - - - +
21J LEU* 4.1 12.1 - - + -
22J LYS* 4.6 1.7 + - - +
38J MET* 4.3 7.2 - - + +
40J LEU* 4.1 21.5 - - + -
62J ILE* 4.3 4.7 - - + -
63J ARG 4.1 4.0 - - - +
64J GLY* 2.7 33.4 + - - +
65J ASP 4.6 2.8 - - - +
66J THR* 1.3 73.5 - - - +
68J VAL* 1.3 65.4 + - - +
69J PHE* 3.3 28.9 - - - +
70J VAL* 4.0 10.5 - - + -
61K VAL 5.7 0.2 - - - +
63K ARG* 3.6 30.9 + - + +
66K THR* 4.0 6.2 + - - -
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Residues in contact with VAL 68 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J ARG* 3.1 24.0 + - + +
21J LEU 3.7 17.5 - - - +
22J LYS* 3.6 30.3 - - + -
67J VAL* 1.3 76.9 - - - +
69J PHE* 1.3 79.8 + - + +
21K LEU* 4.5 13.0 - - + -
62K ILE* 3.7 6.3 - - + +
63K ARG* 3.2 22.3 + - - +
66K THR* 3.9 27.4 - - + +
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Residues in contact with PHE 69 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J ILE* 4.6 11.7 - - + -
19J VAL* 3.4 1.0 - - - -
20J ARG* 3.0 64.4 + - + +
26J GLU* 4.6 0.2 - - - -
67J VAL* 3.3 4.6 - - - +
68J VAL* 1.3 93.7 - - + +
70J VAL* 1.3 77.5 + - - +
71J SER* 4.0 19.7 - - - -
27K PHE* 3.8 28.7 - + - -
47K GLU* 4.2 8.5 - - - -
55K ARG* 3.9 26.7 - - - -
57K VAL* 5.6 3.8 - - + -
60K VAL* 4.4 9.0 - - + -
61K VAL 3.2 15.9 - - - +
62K ILE* 4.5 9.0 - - + -
63K ARG 4.9 0.2 - - - +
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Residues in contact with VAL 70 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J LEU* 3.9 28.7 - - + -
12J SER* 6.6 0.2 - - - -
17J VAL* 4.1 26.5 - - + -
18J ILE 3.2 8.7 - - - +
19J VAL* 4.3 6.3 - - + -
31J LEU* 5.3 2.5 - - + -
38J MET* 5.8 5.6 - - - -
40J LEU* 3.7 29.4 - - + -
67J VAL* 4.0 9.9 - - + -
69J PHE* 1.3 83.8 - - - +
71J SER* 1.3 62.9 + - - +
72J PRO* 4.4 2.1 - - - +
60K VAL* 3.7 0.5 - - - -
61K VAL* 3.2 33.9 + - + +
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Residues in contact with SER 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J VAL* 3.4 2.9 - - - -
18J ILE* 2.7 46.4 + - - +
69J PHE* 4.0 13.0 - - - -
70J VAL* 1.3 76.3 - - - +
72J PRO* 1.3 74.1 + - - +
73J ALA 3.3 0.2 + - - -
57K VAL* 3.5 21.5 - - - +
59K SER 2.8 19.6 + - - -
60K VAL* 3.5 12.8 - - - -
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Residues in contact with PRO 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J VAL* 6.3 2.7 - - + -
12J SER* 4.5 16.4 - - - +
15J SER* 5.9 0.7 - - - +
16J PRO 3.9 10.3 - - - +
17J VAL* 4.2 4.9 - - + -
70J VAL* 4.4 2.4 - - + +
71J SER* 1.3 89.7 + - - +
73J ALA* 1.3 59.5 + - - +
74J PRO* 3.7 9.7 - - + +
57K VAL* 5.7 0.5 - - - +
58K GLY* 5.6 3.1 + - - +
59K SER* 3.2 39.9 - - - +
60K VAL* 4.9 0.4 - - - -
61K VAL* 6.5 0.4 - - + -
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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