Contacts of the strand formed by residues 10 - 18 (chain V) in PDB entry 4UJ3
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 TYR 10 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8V TYR* 3.5 10.1 - - - -
9V ASP* 1.3 111.9 - - + +
11V LEU* 1.3 59.3 + - - +
12V PHE* 3.7 29.6 - + + -
58V LYS* 5.9 3.1 - - + -
59V THR 3.7 2.6 + - - -
60V ILE* 3.2 25.2 - - + +
61V LYS 3.1 25.1 + - - +
173V TYR* 4.6 20.5 - + - -
176V VAL* 3.9 28.7 + - + -
177V SER* 4.7 5.4 + - - -
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Residues in contact with LEU 11 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8V TYR* 3.6 29.7 - - + +
10V TYR* 1.3 73.7 - - - +
12V PHE* 1.3 68.0 + - - +
13V LYS 4.0 1.6 + - - +
61V LYS* 3.3 43.1 - - + +
62V ALA 5.1 0.2 - - - -
63V GLN* 4.2 32.3 - - + +
85V VAL* 6.0 0.5 - - - +
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Residues in contact with PHE 12 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10V TYR* 3.7 33.8 - + + -
11V LEU* 1.3 80.4 - - - +
13V LYS* 1.3 55.3 + - - +
14V VAL* 3.8 3.7 + - + +
60V ILE* 3.5 33.2 - - + -
61V LYS 3.2 7.6 + - - +
62V ALA* 3.6 2.4 - - - +
63V GLN* 2.7 34.6 + - - +
85V VAL* 3.9 17.7 - - + -
169V LEU* 3.9 27.1 - - + -
172V ILE* 3.5 40.4 - - + -
173V TYR* 3.8 16.4 - - - -
176V VAL* 4.1 9.0 - - + -
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Residues in contact with LYS 13 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11V LEU 4.0 2.6 + - - -
12V PHE* 1.3 71.4 - - - +
14V VAL* 1.3 62.8 + - - +
15V VAL* 4.1 4.0 - - - -
63V GLN* 3.5 14.6 - - + +
65V TRP* 3.4 50.4 - - + +
79V ALA 3.6 10.3 + - - -
80V TYR* 2.8 30.0 + - - +
82V ARG 2.8 26.4 + - - +
83V GLY* 3.8 13.0 + - - +
84V ALA* 3.6 10.6 - - + +
85V VAL* 3.0 32.3 + - - +
86V GLY 3.3 5.0 + - - -
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Residues in contact with VAL 14 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12V PHE 3.8 4.7 + - - +
13V LYS* 1.3 79.2 - - - +
15V VAL* 1.3 71.6 + - - +
63V GLN 2.8 10.8 + - - +
64V ILE* 3.3 26.8 - - + +
65V TRP* 2.8 26.5 + - - +
86V GLY* 3.1 25.4 - - - +
87V ALA 3.9 2.5 - - - +
88V LEU* 4.1 22.2 - - + -
165V PHE* 5.3 0.2 - - + -
168V ILE* 4.2 9.9 - - + -
169V LEU* 4.3 22.2 - - + -
172V ILE* 4.3 8.3 - - + -
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Residues in contact with VAL 15 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13V LYS* 4.1 4.3 - - - -
14V VAL* 1.3 77.1 - - - +
16V LEU* 1.3 57.5 + - - +
17V ILE* 3.9 3.3 + - + -
65V TRP* 3.9 14.6 - - + -
80V TYR* 3.4 46.2 - - + +
81V TYR* 4.2 22.9 - - + -
84V ALA* 4.0 15.0 - - + -
86V GLY 2.9 12.9 + - - +
87V ALA* 3.2 15.1 - - + +
88V LEU 2.8 31.7 + - - -
117V ILE* 5.0 0.4 - - + -
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Residues in contact with LEU 16 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15V VAL* 1.3 71.0 - - - +
17V ILE* 1.3 63.5 + - - +
24V LYS* 3.6 45.1 - - + +
27V LEU* 5.1 5.2 - - + -
28V LEU* 4.1 15.0 - - + +
64V ILE* 3.6 26.7 - - + -
65V TRP 2.9 19.6 + - - +
66V ASP* 4.4 7.2 - - + -
67V THR* 4.5 5.9 + - - +
80V TYR* 2.7 20.9 + - - +
88V LEU* 3.3 45.1 - - + +
90V VAL* 4.6 9.4 - - + -
165V PHE* 4.8 2.7 - - + -
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Residues in contact with ILE 17 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15V VAL* 3.9 6.5 + - + -
16V LEU* 1.3 79.7 - - - +
18V GLY* 1.3 58.9 + - - +
24V LYS* 3.5 10.7 - - - +
67V THR* 5.9 1.1 - - + -
80V TYR* 3.8 17.9 - - + -
81V TYR* 3.5 32.1 - - + +
87V ALA* 5.2 2.9 - - + -
88V LEU 3.1 7.5 + - - +
89V LEU* 3.5 15.9 - - + -
90V VAL* 2.9 25.1 + - - -
105V TRP* 4.0 34.5 - - + +
109V LEU* 3.8 29.6 - - + -
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Residues in contact with GLY 18 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17V ILE* 1.3 78.7 - - - +
19V ASP* 1.3 63.7 + - - -
24V LYS* 2.8 22.4 + - - +
69V GLY* 3.5 10.2 - - - -
90V VAL 3.5 13.7 - - - -
105V TRP* 3.5 31.2 - - - -
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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