Contacts of the helix formed by residues 42 - 54 (chain G) in PDB entry 5TJ4
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 42 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12G ASN* 5.9 0.6 + - - -
40G PRO 4.0 0.2 + - - -
41G ASP* 1.3 75.3 - - + +
43G LEU* 1.3 50.8 + - - +
44G GLU* 3.5 15.9 - - - +
45G GLU* 3.1 16.8 + - + +
46G LYS* 2.8 30.7 + - - +
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Residues in contact with LEU 43 (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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10G TRP* 3.5 35.2 - - + -
11G ILE 3.9 15.9 - - - +
12G ASN* 4.6 8.2 + - - +
40G PRO* 3.5 37.5 - - + +
41G ASP 2.9 4.4 + - - -
42G LYS* 1.3 73.5 - - - +
44G GLU* 1.3 66.5 + - - +
46G LYS* 3.8 6.7 - - - +
47G PHE* 2.9 32.1 + - - +
60G ILE* 4.3 15.7 - - + -
61G PHE 4.1 11.0 - - - +
62G TRP* 3.9 24.9 - - + -
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Residues in contact with GLU 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G ASN* 5.1 0.7 - - - +
42G LYS* 3.6 11.7 - - - +
43G LEU* 1.3 88.6 + - - +
45G GLU* 1.3 65.7 + - + +
48G PRO* 3.1 14.6 - - - +
60G ILE* 5.4 0.4 - - - -
62G TRP* 3.3 49.9 - - + +
66G ARG* 3.7 35.0 + - + +
70G TYR* 2.6 31.2 + - - +
153G GLU* 5.5 2.6 - - - +
344G ARG* 5.5 3.6 + - - -
2Q GLC 5.6 1.1 + - - -
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Residues in contact with GLU 45 (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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42G LYS* 3.1 18.4 + - + +
44G GLU* 1.3 90.4 - - + +
46G LYS* 1.3 65.7 + - - +
47G PHE 3.5 0.2 - - - -
48G PRO* 3.2 15.4 - - - +
49G GLN* 4.0 7.6 + - - +
66G ARG* 4.6 9.4 - - - +
1368G GLN* 4.9 8.7 - - + -
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Residues in contact with LYS 46 (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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10G TRP* 4.2 15.9 - - + -
40G PRO* 5.1 4.0 - - + -
41G ASP 4.5 5.6 - - - +
42G LYS 2.8 16.6 + - - +
43G LEU* 3.3 9.8 + - - +
45G GLU* 1.3 74.7 - - - +
47G PHE* 1.3 65.6 + - - +
49G GLN* 3.2 10.0 + - - +
50G VAL* 3.1 21.4 + - + +
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Residues in contact with PHE 47 (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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10G TRP* 3.9 10.9 - - + -
43G LEU 2.9 15.6 + - - +
46G LYS* 1.3 71.2 - - - +
48G PRO* 1.3 63.9 - - + +
50G VAL* 3.3 1.5 + - - +
51G ALA* 2.7 60.9 + - + +
57G PRO* 3.8 27.1 - - + -
60G ILE* 3.3 44.9 - - + -
70G TYR* 3.9 37.0 - + + +
75G LEU* 3.9 25.1 - - + -
76G LEU* 4.5 2.9 - - + -
267G ASN* 4.1 19.1 - - + -
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Residues in contact with PRO 48 (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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44G GLU 3.1 22.9 - - - +
45G GLU* 3.2 17.7 - - - +
47G PHE* 1.3 96.7 - - + +
49G GLN* 1.3 59.7 + - - +
52G ALA* 3.2 25.3 + - - +
70G TYR* 4.0 15.3 - - + -
75G LEU* 3.6 25.5 - - + +
1368G GLN* 4.5 18.1 - - + +
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Residues in contact with GLN 49 (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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45G GLU 4.2 7.9 - - - +
46G LYS* 3.2 10.8 + - - +
48G PRO* 1.3 83.3 - - - +
50G VAL* 1.3 62.8 + - - +
52G ALA* 3.5 11.7 + - - +
53G THR* 3.7 12.1 + - - +
1367G GLU 4.7 4.9 - - - +
1368G GLN* 3.6 25.4 + - - +
1370G TRP* 5.0 11.2 - - + -
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Residues in contact with VAL 50 (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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10G TRP* 4.6 13.0 - - + -
46G LYS 3.1 14.3 + - - +
47G PHE* 3.8 3.1 - - - +
49G GLN* 1.3 75.3 - - - +
51G ALA* 1.3 62.2 + - - +
53G THR* 2.7 28.9 + - - -
55G ASP* 3.3 14.1 + - + +
56G GLY* 4.1 20.6 - - - +
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Residues in contact with ALA 51 (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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47G PHE* 2.7 54.2 + - + +
50G VAL* 1.3 71.5 - - - +
52G ALA* 1.3 60.8 + - - +
54G GLY* 3.2 13.2 + - - -
55G ASP 3.3 12.3 - - - +
56G GLY* 4.8 0.6 - - - -
75G LEU* 4.0 20.1 - - + +
267G ASN* 4.1 9.7 - - - +
269G ALA* 4.7 6.2 - - - +
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Residues in contact with ALA 52 (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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48G PRO 3.2 21.0 + - - +
49G GLN* 3.6 6.7 - - - +
50G VAL 3.2 0.4 - - - -
51G ALA* 1.3 75.3 - - - +
53G THR* 1.3 64.4 + - + +
54G GLY* 3.4 0.7 + - - -
75G LEU* 4.4 14.1 - - + +
1368G GLN 5.7 2.0 - - - +
1369G ASN* 6.3 1.8 - - - +
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Residues in contact with THR 53 (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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49G GLN 3.9 12.3 - - - +
50G VAL* 2.7 19.5 + - - -
52G ALA* 1.3 78.0 - - + +
54G GLY* 1.3 55.5 + - - +
55G ASP* 3.3 15.5 + - - +
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Residues in contact with GLY 54 (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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2G ILE* 4.3 16.1 - - - +
50G VAL 3.6 0.2 + - - -
51G ALA 3.2 9.9 + - - -
52G ALA 3.2 4.6 + - - -
53G THR* 1.3 77.3 - - - +
55G ASP* 1.3 64.5 + - - +
269G ALA* 3.3 28.0 - - - +
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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