Contacts of the strand formed by residues 58 - 67 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9G ASP* 3.3 22.3 + - + +
10G TYR* 3.6 30.3 - - + -
54G GLN* 3.3 3.9 - - - +
55G VAL 3.0 30.7 + - - +
56G ASP* 2.9 10.5 + - - +
57G GLY* 1.3 81.2 - - - +
59G THR* 1.3 62.5 + - - +
60G ILE* 3.6 2.6 + - + +
173G TYR* 3.0 27.4 - - + +
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Residues in contact with THR 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G GLU 3.6 22.4 + - - +
8G TYR* 3.6 17.6 - - + -
9G ASP* 2.8 40.4 + - - +
10G TYR 3.2 6.6 + - - -
52G SER* 4.4 12.8 - - - +
53G ILE 3.7 5.6 - - - +
54G GLN* 2.8 27.0 + - - +
57G GLY 4.0 1.3 + - - -
58G LYS* 1.3 69.7 - - - +
60G ILE* 1.3 67.5 + - - +
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Residues in contact with ILE 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G TYR* 3.4 42.0 - - + +
12G PHE* 3.4 35.0 - - + -
52G SER* 3.1 2.6 - - - -
53G ILE* 2.7 55.5 + - + +
55G VAL* 3.8 27.6 - - + -
58G LYS* 3.9 8.3 - - + +
59G THR* 1.3 75.7 - - - +
61G LYS* 1.3 66.5 + - - +
62G ALA 3.7 1.3 + - - +
169G LEU* 4.6 11.9 - - + -
173G TYR* 4.6 9.4 - - + -
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Residues in contact with LYS 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G ASP 5.4 3.6 + - - -
8G TYR* 3.5 33.5 - - + +
10G TYR 2.8 16.3 + - - +
11G LEU* 3.3 27.3 - - + +
12G PHE* 2.9 25.3 + - - +
50G THR* 4.1 28.4 + - - -
51G ARG 4.7 0.2 - - - +
52G SER* 3.6 23.5 + - - +
59G THR 4.0 1.2 + - - -
60G ILE* 1.3 72.3 - - - +
62G ALA* 1.3 67.4 + - - +
63G GLN* 5.5 2.2 - - - +
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Residues in contact with ALA 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G PHE 3.6 4.5 - - - -
31G PHE* 4.6 4.7 - - + -
50G THR* 3.1 9.9 - - - -
51G ARG 2.7 43.0 + - - +
60G ILE 3.7 1.0 + - - -
61G LYS* 1.3 71.7 - - - +
63G GLN* 1.3 60.7 + - - +
64G ILE* 3.8 20.0 + - + +
169G LEU* 3.6 36.8 - - + -
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Residues in contact with GLN 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G LEU* 4.0 30.5 - - + +
12G PHE 2.7 17.2 + - - +
13G LYS* 4.2 10.1 - - - +
14G VAL 3.0 24.4 + - - +
48G PHE* 3.5 27.8 - - + -
50G THR* 3.4 20.7 - - + +
61G LYS* 3.8 2.2 + - - +
62G ALA* 1.3 71.5 - - - +
64G ILE* 1.3 63.4 + - - +
65G TRP* 2.9 32.9 + - - +
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Residues in contact with ILE 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G VAL* 3.4 23.6 - - + +
16G LEU* 4.0 23.3 - - + -
28G LEU* 3.6 25.7 - - + +
31G PHE* 4.2 17.3 - - + -
32G THR* 4.6 1.6 - - + -
48G PHE* 2.9 22.8 - - - -
49G ALA 2.8 21.9 + - - +
50G THR* 5.5 0.7 - - - -
51G ARG 5.5 0.2 - - - +
62G ALA* 4.0 21.1 - - + +
63G GLN* 1.3 74.8 - - - +
65G TRP* 1.3 59.2 + - - +
66G ASP 4.0 0.2 + - - -
165G PHE* 3.8 36.1 - - + -
169G LEU* 5.6 0.7 - - + -
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Residues in contact with TRP 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G LYS* 3.4 33.0 - - + +
14G VAL 2.8 7.4 + - - -
15G VAL* 4.0 17.7 - - + -
16G LEU* 2.9 32.6 + - - +
46G VAL* 3.7 26.7 - - + -
47G GLU 3.3 9.0 - - - -
48G PHE* 3.5 36.5 - + + +
63G GLN* 2.9 43.2 + - - -
64G ILE* 1.3 73.4 - - - +
66G ASP* 1.3 61.3 + - - +
80G TYR* 3.2 10.0 + + + -
746I MET* 3.6 32.8 - - + -
750I PRO* 4.2 20.2 - - + -
753I LEU* 4.2 9.4 - - + -
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Residues in contact with ASP 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G LEU* 4.3 10.7 - - + +
24G LYS* 4.0 12.1 - - - +
25G SER* 3.2 31.9 + - - -
28G LEU* 3.7 26.9 - - + +
43G THR* 3.9 10.4 - - - +
46G VAL* 3.5 2.4 - - - +
47G GLU* 2.7 38.8 + - + +
65G TRP* 1.3 76.0 - - - +
67G THR* 1.3 87.1 + - - +
80G TYR* 3.4 4.0 - - - -
201G MG 3.3 9.9 - - - -
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Residues in contact with THR 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G LEU 4.7 4.1 + - - +
24G LYS* 3.8 7.6 - - - -
43G THR* 4.2 9.0 - - - -
45G GLY 3.0 20.5 + - - -
46G VAL* 3.3 11.9 - - - +
66G ASP* 1.3 92.1 + - - +
68G ALA* 1.3 76.9 + - - +
69G GLY 3.2 3.3 + - - -
71G GLU* 3.6 23.3 + - - +
76G ILE* 5.0 2.3 - - - +
80G TYR* 3.4 34.1 + - + +
201G MG 3.6 6.2 - - - -
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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