Contacts of the strand formed by residues 9 - 14 (chain R) in PDB entry 5EEZ
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 9 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Q PHE* 5.5 0.9 - - - -
7R SER 4.6 5.8 - - - -
8R ASP* 1.3 87.2 + - - +
10R VAL* 1.3 72.4 + - - +
11R VAL* 3.8 8.3 - - + -
45R ILE* 3.5 22.2 - - + -
46R ALA 3.2 19.7 - - - +
47R GLN* 3.9 9.9 - - + -
48R PHE* 4.7 0.7 - - - +
64R GLN 4.6 0.3 - - - +
65R THR* 4.6 2.8 - - - -
66R ARG 5.1 0.2 + - - -
8S ASP* 3.6 31.0 - - + -
9S PHE 5.6 1.1 - - - -
10S VAL* 5.3 1.6 - - + -
48S PHE* 4.1 17.3 - + + -
65S THR* 3.7 29.2 - - + -
66S ARG* 4.2 9.4 - - + -
67S HIS* 3.2 50.5 + + - -
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Residues in contact with VAL 10 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Q PHE* 5.2 2.2 - - + -
45Q ILE* 4.1 28.0 - - + -
9R PHE* 1.3 80.8 - - - +
11R VAL* 1.3 63.3 + - - +
12R ILE* 3.8 25.8 - - + -
44R LEU 3.7 1.4 - - - +
45R ILE* 3.3 3.5 - - - +
46R ALA* 2.8 41.7 + - + +
48R PHE* 4.3 13.9 - - + -
55R ILE* 3.9 15.0 - - + -
63R ILE* 4.9 0.4 - - + -
64R GLN 3.6 8.5 - - - +
65R THR* 3.8 21.5 - - + -
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Residues in contact with VAL 11 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9R PHE* 3.8 23.8 - - + -
10R VAL* 1.3 75.3 - - - +
12R ILE* 1.3 65.5 + - - +
13R LYS 4.3 0.2 - - - -
43R VAL* 3.9 23.8 - - + -
44R LEU 3.6 3.1 - - - -
45R ILE* 4.3 7.9 - - + +
62R TYR 3.8 0.2 - - - +
63R ILE* 3.1 6.2 - - - +
64R GLN* 2.8 63.4 + - + +
65S THR* 3.9 20.0 - - + +
67S HIS* 4.6 1.6 - - + -
70S ILE* 4.0 20.6 - - + +
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Residues in contact with ILE 12 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45Q ILE* 5.4 0.4 - - + -
10R VAL* 3.8 26.0 - - + +
11R VAL* 1.3 80.0 - - - +
13R LYS* 1.3 59.6 - - - +
14R ALA 4.1 0.6 + - - +
19R VAL* 4.9 0.4 - - + -
21R VAL* 3.6 47.3 - - + -
38R LEU* 4.2 9.0 - - + +
42R GLU 3.8 1.2 - - - +
43R VAL* 3.3 5.2 - - - -
44R LEU* 2.9 43.8 + - + +
46R ALA* 5.2 1.8 - - + -
55R ILE* 4.6 1.6 - - + -
57R VAL* 4.1 15.5 - - + -
61R ALA* 3.8 23.8 - - + -
62R TYR 3.5 2.9 - - - -
63R ILE* 4.2 15.9 - - + -
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Residues in contact with LYS 13 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11R VAL 4.3 0.4 - - - -
12R ILE* 1.3 72.1 - - - +
14R ALA* 1.3 70.0 + - - +
15R LEU* 3.3 19.0 + - + +
41R GLY* 4.3 11.2 - - - +
42R GLU 3.4 5.4 - - - +
43R VAL* 3.9 12.8 - - + -
61R ALA* 3.2 5.0 - - - -
62R TYR* 2.8 44.1 + - + +
70S ILE* 3.7 28.2 - - + +
71S GLU* 2.6 34.0 + - - +
73S GLU* 2.9 34.7 + - - +
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Residues in contact with ALA 14 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12R ILE 4.1 1.4 + - - -
13R LYS* 1.3 76.1 - - - +
15R LEU* 1.3 58.5 - - - +
16R GLU 3.4 15.0 - - - +
19R VAL* 3.9 11.4 - - + -
38R LEU* 3.7 23.4 - - + +
39R ASP 3.3 24.0 - - - +
41R GLY* 2.7 28.1 + - - -
42R GLU 3.0 8.2 + - - +
60R LYS 4.0 4.9 - - - -
61R ALA* 4.4 2.2 - - - -
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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