Contacts of the strand formed by residues 58 - 67 (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 LYS 58 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9V ASP* 3.6 20.2 - - + +
10V TYR* 5.9 3.1 - - + -
54V GLN* 3.5 1.9 - - - +
55V VAL* 2.7 38.3 + - - +
56V ASP* 2.9 13.5 + - - +
57V GLY* 1.3 81.1 - - - +
59V THR* 1.3 62.2 + - - +
60V ILE* 3.6 6.5 + - + +
173V TYR* 3.5 24.0 - - + +
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Residues in contact with THR 59 (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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7V GLU 4.1 4.9 + - - +
8V TYR* 3.6 12.1 - - - +
9V ASP* 3.0 48.9 + - - +
10V TYR 3.7 0.2 + - - -
52V SER* 5.9 5.2 - - - -
53V ILE 3.4 6.5 - - - -
54V GLN* 3.0 31.6 - - - +
57V GLY 4.7 2.5 - - - +
58V LYS* 1.3 71.7 - - - +
60V ILE* 1.3 62.4 + - - +
61V LYS 4.2 0.3 + - - -
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Residues in contact with ILE 60 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8V TYR* 5.3 0.2 - - - -
9V ASP* 4.9 1.1 - - + -
10V TYR* 3.2 43.1 - - + +
12V PHE* 3.5 37.9 - - + -
51V ARG 3.9 0.2 - - - +
52V SER* 3.4 2.0 - - - -
53V ILE* 2.7 52.0 + - + +
55V VAL* 4.1 26.0 - - + +
58V LYS* 4.2 7.4 - - + +
59V THR* 1.3 78.6 - - - +
61V LYS* 1.3 65.6 + - - +
62V ALA 3.7 1.4 + - - +
169V LEU* 4.6 11.2 - - + +
173V TYR* 5.2 8.3 - - + -
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Residues in contact with LYS 61 (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* 4.2 34.6 - - + +
10V TYR 3.1 8.4 + - - +
11V LEU* 3.3 27.8 - - + +
12V PHE 3.2 21.8 + - - -
50V THR* 3.5 38.1 + - - +
51V ARG* 3.6 6.5 - - - +
52V SER* 3.4 21.3 - - - +
59V THR 4.2 1.2 + - - -
60V ILE* 1.3 71.9 - - - +
62V ALA* 1.3 59.9 + - - +
63V GLN* 6.1 0.6 - - - +
754X GLU* 5.4 2.2 + - - -
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Residues in contact with ALA 62 (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 3.6 5.4 - - - +
31V PHE* 4.6 6.3 - - + -
49V ALA 3.7 1.0 - - - +
50V THR* 3.1 28.5 - - - +
51V ARG 2.8 18.0 + - - +
60V ILE 3.7 1.2 + - - -
61V LYS* 1.3 73.0 - - - +
63V GLN* 1.3 60.7 + - - +
64V ILE* 3.8 18.5 + - + +
169V LEU* 3.7 39.0 - - + -
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Residues in contact with GLN 63 (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* 4.2 29.3 - - + +
12V PHE 2.7 18.0 + - - +
13V LYS* 4.0 12.9 - - - +
14V VAL 2.8 28.2 + - - +
48V PHE* 3.5 36.7 - - + -
49V ALA 3.7 1.6 - - - -
50V THR* 3.7 11.2 - - + +
61V LYS* 3.9 1.0 + - - +
62V ALA* 1.3 69.4 - - - +
64V ILE* 1.3 61.0 + - - +
65V TRP* 3.1 30.2 + - - +
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Residues in contact with ILE 64 (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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14V VAL* 3.3 26.5 - - + +
16V LEU* 3.6 34.1 - - + -
28V LEU* 3.6 21.8 - - + +
31V PHE* 4.1 17.3 - - + -
32V THR* 5.0 1.1 - - + -
48V PHE* 3.2 1.7 - - - -
49V ALA 2.8 38.3 + - - +
50V THR* 5.7 0.4 - - - -
62V ALA* 4.1 17.0 - - + +
63V GLN* 1.3 72.7 - - - +
65V TRP* 1.3 62.3 + - - +
165V PHE* 3.5 37.0 - - + -
169V LEU* 5.7 0.2 - - + -
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Residues in contact with TRP 65 (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* 3.4 37.2 - - + +
14V VAL 2.8 13.1 + - - +
15V VAL* 4.0 7.0 - - + -
16V LEU* 2.9 33.2 + - - +
46V VAL* 3.5 17.0 - - + -
47V GLU 3.4 15.0 - - - -
48V PHE* 3.4 38.7 - + + +
63V GLN* 3.1 40.6 + - - -
64V ILE* 1.3 74.3 - - - +
66V ASP* 1.3 60.5 + - - +
80V TYR* 3.0 17.4 + + + -
746X MET* 3.4 37.9 - - + -
750X PRO* 4.4 12.6 - - + -
753X LEU* 4.2 7.4 - - + -
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Residues in contact with ASP 66 (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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16V LEU* 4.4 7.0 - - + -
24V LYS* 4.1 9.0 - - - +
25V SER* 2.7 46.8 + - - -
28V LEU* 3.6 26.6 - - + +
43V THR* 3.8 12.2 - - - +
46V VAL* 3.9 0.3 - - - -
47V GLU* 3.0 40.1 + - + +
65V TRP* 1.3 75.7 - - - +
67V THR* 1.3 87.4 + - - +
80V TYR* 3.4 6.4 - - - -
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Residues in contact with THR 67 (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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16V LEU 4.5 5.4 + - - +
17V ILE* 5.9 0.9 - - + -
24V LYS* 3.4 20.2 - - - -
43V THR* 4.3 7.4 - - - -
45V GLY 3.1 20.3 + - - -
46V VAL* 3.6 9.7 - - - +
66V ASP* 1.3 87.8 + - - +
68V ALA* 1.3 80.1 + - - +
69V GLY 3.5 0.2 + - - -
80V TYR* 3.5 36.6 + - + +
200V GNP 3.5 5.9 + - - -
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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