Contacts of the strand formed by residues 46 - 55 (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 VAL 46 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43V THR* 6.0 0.2 - - - -
44V ILE 3.8 0.8 + - - -
45V GLY* 1.3 80.2 - - - +
47V GLU* 1.3 72.8 + - - +
65V TRP* 3.5 35.4 - - + -
66V ASP 3.9 8.7 - - - +
67V THR* 3.6 12.6 - - - +
76V ILE* 5.5 5.8 - - + +
80V TYR* 4.1 13.9 - - + -
742X ILE* 3.9 31.3 - - + +
746X MET* 4.2 8.1 - - + -
753X LEU* 3.8 23.1 - - + +
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Residues in contact with GLU 47 (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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28V LEU* 4.7 5.6 - - + +
43V THR* 4.3 18.3 - - + +
44V ILE* 4.9 9.3 - - - +
46V VAL* 1.3 81.4 - - - +
48V PHE* 1.3 67.1 + - - +
65V TRP* 3.4 9.7 - - - -
66V ASP* 3.0 45.3 + - + +
753X LEU* 3.5 8.7 - - - +
755X VAL* 3.7 27.9 - - + +
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Residues in contact with PHE 48 (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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28V LEU* 5.2 1.8 - - - -
47V GLU* 1.3 77.9 - - - +
49V ALA* 1.3 64.5 + - - +
50V THR* 4.6 2.9 - - + -
63V GLN* 3.5 37.5 - - + -
64V ILE 3.2 13.2 - - - +
65V TRP* 3.4 44.0 - + + -
66V ASP 4.7 0.2 - - - +
750X PRO* 3.3 25.8 - - + -
751X SER* 4.5 6.7 - - - -
753X LEU* 3.3 11.6 + - + -
754X GLU* 3.4 45.0 - - + +
755X VAL* 3.0 25.7 + - - -
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Residues in contact with ALA 49 (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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28V LEU* 3.7 14.7 - - + +
32V THR* 3.6 28.5 - - + +
33V ARG* 5.1 3.6 - - - +
48V PHE* 1.3 76.7 - - - +
50V THR* 1.3 65.0 + - - +
62V ALA 3.7 0.3 - - - +
63V GLN 3.7 1.2 - - - -
64V ILE* 2.8 35.9 + - - +
754X GLU* 4.9 2.9 - - - -
755X VAL* 4.5 14.4 - - + +
756X LYS* 5.0 6.5 - - + +
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Residues in contact with THR 50 (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* 5.3 0.7 - - + -
32V THR* 4.3 13.7 - - - +
48V PHE* 4.6 4.5 - - + -
49V ALA* 1.3 78.6 - - - +
51V ARG* 1.3 64.1 + - - +
61V LYS* 3.5 34.7 - - + +
62V ALA 3.1 14.8 - - - +
63V GLN* 3.7 26.5 - - + +
64V ILE* 5.7 0.2 - - - -
754X GLU* 3.3 21.9 + - - +
756X LYS* 5.0 9.5 - - - +
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Residues in contact with ARG 51 (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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30V ARG 5.2 1.0 + - - -
31V PHE* 3.0 63.7 + - + +
32V THR* 4.5 13.0 - - - +
50V THR* 1.3 77.4 - - - +
52V SER* 1.3 77.5 + - - +
53V ILE* 4.0 9.9 + - - +
60V ILE 3.9 0.3 - - - +
61V LYS* 4.4 1.6 - - - +
62V ALA* 2.8 32.5 + - - +
162V GLU* 2.9 39.6 + - - -
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Residues in contact with SER 52 (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* 5.4 3.1 - - - +
51V ARG* 1.3 87.2 + - - +
53V ILE* 1.3 62.7 + - - +
54V GLN* 5.9 2.0 - - - -
59V THR* 5.9 5.2 - - - -
60V ILE 3.4 7.9 - - - -
61V LYS* 3.4 27.8 - - - +
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Residues in contact with ILE 53 (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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31V PHE* 4.6 15.7 - - + -
51V ARG* 5.1 9.6 - - + +
52V SER* 1.3 76.3 - - - +
54V GLN* 1.3 70.4 + - - +
55V VAL* 3.9 17.5 - - + -
59V THR* 3.4 3.1 - - - -
60V ILE* 2.7 50.0 + - + +
162V GLU* 4.3 12.3 - - - +
166V GLN* 3.0 50.9 - - + +
169V LEU* 3.8 23.6 - - + -
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Residues in contact with GLN 54 (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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52V SER* 5.9 1.6 - - - -
53V ILE* 1.3 81.2 + - - +
55V VAL* 1.3 65.9 + - - +
56V ASP 4.2 0.8 + - - -
57V GLY* 3.5 21.7 - - - +
58V LYS 3.6 0.4 - - - -
59V THR* 3.0 41.7 + - - +
166V GLN* 3.8 14.7 + - - +
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Residues in contact with VAL 55 (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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53V ILE* 3.9 20.2 + - + -
54V GLN* 1.3 79.7 - - - +
56V ASP* 1.3 71.5 + - + +
57V GLY 3.2 0.2 - - - -
58V LYS* 2.7 21.8 + - - +
60V ILE* 4.1 16.1 - - + +
166V GLN* 4.7 3.6 - - - +
169V LEU* 4.6 5.6 - - + -
170V THR* 3.2 48.0 - - + +
173V TYR* 3.3 33.9 - - + -
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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