Contacts of the strand formed by residues 58 - 67 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9P ASP* 3.0 27.1 - - + +
10P TYR* 5.6 2.2 - - + -
54P GLN* 3.6 1.1 - - - -
55P VAL 2.9 31.9 + - - +
56P ASP 3.0 6.9 + - - +
57P GLY* 1.3 77.1 - - - +
59P THR* 1.3 61.3 + - - +
60P ILE* 3.6 9.5 + - + +
173P TYR* 4.5 12.3 - - + +
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Residues in contact with THR 59 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7P GLU 3.7 19.4 + - - -
8P TYR* 3.9 4.7 - - - +
9P ASP* 3.1 31.3 + - - +
52P SER* 5.4 6.8 - - - -
53P ILE 3.1 12.3 - - - +
54P GLN* 4.3 8.3 - - + +
57P GLY 4.8 4.7 - - - +
58P LYS* 1.3 72.8 - - - +
60P ILE* 1.3 63.0 + - - +
61P LYS 4.2 0.2 - - - -
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Residues in contact with ILE 60 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9P ASP* 4.3 2.9 - - + -
10P TYR* 3.1 51.6 - - + +
12P PHE* 3.6 35.2 - - + -
52P SER* 3.6 1.5 - - - -
53P ILE* 2.6 56.6 + - + +
55P VAL* 4.6 11.0 - - + +
58P LYS* 4.1 13.2 - - + +
59P THR* 1.3 77.8 - - - +
61P LYS* 1.3 68.1 + - - +
62P ALA 3.7 1.6 + - - +
169P LEU* 5.2 5.6 - - + +
173P TYR* 5.2 10.5 - - + -
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Residues in contact with LYS 61 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6P ASP* 4.4 15.3 - - - +
8P TYR* 3.7 45.1 - - + +
10P TYR 3.3 10.2 + - - +
11P LEU* 3.7 13.6 - - + +
12P PHE 3.4 19.6 + - - -
50P THR* 3.4 37.4 + - + +
51P ARG 3.6 10.1 - - - +
52P SER* 3.7 21.3 + - - +
60P ILE* 1.3 71.6 - - - +
62P ALA* 1.3 65.9 + - - +
63P GLN* 5.8 1.4 - - - +
754R GLU* 5.3 3.2 + - - -
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Residues in contact with ALA 62 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P PHE* 3.7 5.8 - - - +
14P VAL* 5.1 2.5 - - + -
31P PHE* 5.2 6.5 - - + -
49P ALA 3.9 0.2 - - - +
50P THR* 3.6 7.8 - - - +
51P ARG 3.1 31.0 + - - +
60P ILE 3.7 1.8 + - - +
61P LYS* 1.3 74.0 - - - +
63P GLN* 1.3 60.7 + - - +
64P ILE* 3.8 14.8 + - + +
165P PHE* 6.2 0.4 - - + -
169P LEU* 3.6 43.1 - - + -
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Residues in contact with GLN 63 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11P LEU* 4.1 29.5 - - + +
12P PHE 2.7 18.3 + - - +
13P LYS* 4.2 10.9 - - - +
14P VAL* 2.8 27.4 + - - +
48P PHE* 3.8 35.7 - - + -
49P ALA 4.1 2.0 - - - -
50P THR* 4.0 12.4 - - + +
61P LYS* 3.9 2.0 + - - +
62P ALA* 1.3 71.5 - - - +
64P ILE* 1.3 62.1 + - - +
65P TRP* 3.1 29.7 + - - +
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Residues in contact with ILE 64 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14P VAL* 3.3 13.5 - - + +
16P LEU* 3.4 31.0 - - + -
28P LEU* 3.4 30.3 - - + +
31P PHE* 3.3 29.8 - - + -
32P THR* 4.5 2.5 - - + -
48P PHE* 3.0 23.3 - - - -
49P ALA 3.0 15.9 + - - +
51P ARG 6.2 0.2 - - - +
62P ALA* 4.5 12.6 - - + +
63P GLN* 1.3 70.7 - - - +
65P TRP* 1.3 60.1 + - - +
66P ASP 4.1 0.2 + - - -
165P PHE* 3.1 35.9 - - + -
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Residues in contact with TRP 65 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13P LYS* 3.7 31.7 - - + +
14P VAL 3.0 9.7 + - - +
15P VAL* 4.4 8.3 - - + -
16P LEU* 3.2 30.3 + - - +
46P VAL* 3.5 24.2 - - + -
47P GLU 3.3 5.6 - - - -
48P PHE* 3.6 34.4 - + + +
63P GLN* 3.1 40.8 + - - -
64P ILE* 1.3 73.9 - - - +
66P ASP* 1.3 61.0 + - - +
80P TYR* 3.2 16.1 + + + -
746R MET* 3.3 41.1 - - + -
750R PRO* 3.9 23.8 - - + -
753R LEU* 4.2 7.0 - - + -
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Residues in contact with ASP 66 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16P LEU* 4.2 9.1 - - + +
24P LYS* 4.1 10.9 - - - +
25P SER* 2.9 36.8 + - - -
28P LEU* 3.7 24.5 - - + +
43P THR* 3.9 10.0 + - - +
46P VAL* 3.6 2.6 - - - +
47P GLU* 2.9 40.1 + - + +
65P TRP* 1.3 76.4 - - - +
67P THR* 1.3 89.4 + - - +
80P TYR* 3.4 4.9 - - - -
201P MG 3.3 7.1 - - - -
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Residues in contact with THR 67 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16P LEU 4.9 1.5 + - - +
24P LYS* 3.9 7.6 - - - -
43P THR* 4.5 5.8 - - - -
45P GLY 2.5 25.9 + - - -
46P VAL* 3.3 10.4 - - + +
66P ASP* 1.3 91.9 + - - +
68P ALA* 1.3 70.7 + - - +
69P GLY 3.3 2.3 + - - -
71P GLU* 3.7 23.3 - - - +
80P TYR* 3.4 36.4 + - + +
200P GNP 3.7 1.0 + - - -
201P MG 3.5 7.3 - - - -
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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