Contacts of the helix formed by residues 41 - 57 (chain A) in PDB entry 5TSQ
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 THR 41 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A VAL* 4.2 7.6 - - - -
40A GLN* 1.3 87.4 + - - +
42A LEU* 1.3 65.5 + - - +
43A GLU* 3.8 8.5 + - - +
44A LYS* 3.1 31.7 + - + +
45A VAL* 3.0 20.3 + - - +
75A VAL* 5.5 5.6 - - + -
77A THR* 3.8 9.6 - - + +
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Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A THR* 3.6 42.8 - - - +
36A VAL* 3.9 4.9 - - - +
37A VAL* 4.0 9.2 - - - +
40A GLN 3.7 0.4 + - - -
41A THR* 1.3 73.8 - - - +
43A GLU* 1.3 61.5 + - - +
45A VAL* 3.4 5.7 - - + +
46A THR* 2.7 39.2 + - - +
65A ALA* 4.3 10.3 - - + -
66A GLY 3.2 25.1 - - - +
67A CYS 3.8 9.9 - - - +
68A CYS* 3.7 35.5 + - + +
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Residues in contact with GLU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 3.2 8.5 + - - +
42A LEU* 1.3 78.6 - - - +
44A LYS* 1.3 63.7 + - - +
46A THR* 3.8 3.9 - - - -
47A ARG* 3.1 59.0 + - + +
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Residues in contact with LYS 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A GLN* 3.4 27.1 + - + +
41A THR* 3.1 21.0 + - - +
43A GLU* 1.3 78.5 - - + +
45A VAL* 1.3 59.7 + - - +
47A ARG* 3.3 26.7 + - - +
48A ASN* 2.9 34.5 + - - +
84A GLU* 2.8 43.1 + - - +
85A THR* 3.8 15.9 - - - +
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Residues in contact with VAL 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASP* 3.7 21.8 - - + +
11A PRO* 3.4 30.9 - - - +
35A THR* 4.2 12.7 - - - +
36A VAL 3.4 24.0 - - - +
40A GLN* 3.5 35.2 - - + +
41A THR 3.0 15.5 + - - +
42A LEU* 3.4 14.8 - - - +
44A LYS* 1.3 76.9 - - - +
46A THR* 1.3 60.4 + - - +
48A ASN* 3.3 2.4 + - - +
49A ALA* 2.9 23.2 + - - +
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Residues in contact with THR 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A THR* 2.9 29.0 + - - +
42A LEU* 2.7 30.8 + - - +
43A GLU* 3.8 5.2 - - - -
45A VAL* 1.3 74.0 - - - +
47A ARG* 1.3 66.5 + - - +
49A ALA* 3.1 3.6 + - - +
50A GLN* 3.0 24.4 + - - +
63A ILE* 4.8 4.0 - - + -
65A ALA* 3.8 9.9 - - + +
100A LEU* 3.5 41.7 - - + +
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Residues in contact with ARG 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A GLU* 3.1 53.5 + - + +
44A LYS* 3.6 31.8 - - - +
46A THR* 1.3 75.8 - - + +
48A ASN* 1.3 60.8 + - - +
50A GLN* 3.2 12.9 + - - +
51A LEU* 2.9 24.8 + - - +
92A TYR* 4.8 9.1 - - + -
96A PHE* 3.5 34.5 - - + -
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Residues in contact with ASN 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PRO* 2.8 33.5 + - + +
44A LYS 2.9 19.0 + - - +
45A VAL* 3.5 1.7 - - - +
46A THR 3.1 0.2 - - - -
47A ARG* 1.3 74.7 - - - +
49A ALA* 1.3 64.6 + - - +
51A LEU* 3.2 5.3 + - - +
52A VAL* 3.0 29.1 + - - +
85A THR 2.9 22.5 + - - +
86A GLY* 3.4 13.7 - - - -
87A LEU* 3.6 18.9 - - + +
92A TYR* 2.6 30.5 + - - -
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PRO* 4.2 14.7 - - + +
19A ILE* 4.6 4.2 - - + +
33A ILE* 4.3 12.7 - - + +
35A THR* 3.9 20.6 - - + -
45A VAL 2.9 14.1 + - - +
46A THR 3.5 7.9 - - - +
48A ASN* 1.3 75.5 - - - +
50A GLN* 1.3 63.6 - - - +
52A VAL* 3.3 6.9 + - - +
53A ALA* 3.0 23.2 + - - +
63A ILE* 3.8 15.9 - - + +
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Residues in contact with GLN 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A THR* 3.0 21.4 + - - +
47A ARG* 3.5 19.7 + - - +
49A ALA* 1.3 77.1 - - - +
51A LEU* 1.3 56.8 + - - +
53A ALA* 3.3 2.4 + - - +
54A ASP* 2.8 32.7 + - - +
63A ILE* 4.0 13.5 - - + -
96A PHE* 3.6 32.5 - - + +
98A THR* 3.0 28.4 + - - +
99A LYS* 4.3 2.6 - - - +
100A LEU* 3.6 40.5 - - + +
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Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ARG 2.9 14.0 + - - +
48A ASN* 3.2 8.7 + - - +
50A GLN* 1.3 76.3 - - - +
52A VAL* 1.3 58.4 + - - +
54A ASP* 3.2 7.2 + - + +
55A VAL* 2.8 48.0 + - + +
87A LEU* 3.9 10.5 - - + -
90A VAL* 3.7 30.1 - - + -
91A SER 4.1 8.5 - - - +
92A TYR* 3.8 16.8 - - + -
93A PRO* 3.8 30.3 - - + -
96A PHE* 3.7 10.0 - - + -
217A PHE* 4.1 8.1 - - + -
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Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PRO* 5.2 1.6 - - + -
16A ALA* 3.6 32.5 - - + +
19A ILE* 3.7 29.2 - - + -
20A LEU* 3.6 27.1 - - + +
48A ASN 3.0 17.2 + - - +
49A ALA 3.7 6.1 - - - +
50A GLN 3.3 0.2 - - - -
51A LEU* 1.3 73.5 - - - +
53A ALA* 1.3 63.4 + - - +
55A VAL* 3.2 8.0 + - - +
56A ALA* 3.0 23.2 + - - +
87A LEU* 4.6 4.0 - - + -
217A PHE* 4.0 19.5 - - + -
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 5.5 0.2 - - - +
33A ILE* 5.3 1.8 - - + -
49A ALA 3.0 17.0 + - - +
50A GLN 3.6 2.5 - - - +
52A VAL* 1.3 77.8 - - - +
54A ASP* 1.3 57.2 + - - +
57A GLY* 2.9 24.4 + - - -
58A ILE* 3.0 39.7 + - + +
63A ILE* 3.8 18.2 - - + -
98A THR* 3.5 20.1 + - + +
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Residues in contact with ASP 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLN 2.8 20.4 + - - +
51A LEU* 3.6 11.4 - - + +
53A ALA* 1.3 72.4 - - - +
55A VAL* 1.3 65.6 + - + +
56A ALA 3.4 0.3 + - - -
57A GLY* 3.4 8.2 + - - -
93A PRO* 4.6 4.8 - - + +
95A GLU 4.4 2.1 - - - +
96A PHE* 3.4 15.2 - - + +
97A LYS* 2.7 33.3 + - - +
98A THR* 2.7 42.2 + - - -
313A PRO* 5.7 0.2 - - - +
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Residues in contact with VAL 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU* 5.6 1.3 - - + -
51A LEU* 2.8 33.8 + - + +
52A VAL* 3.2 6.5 + - - +
54A ASP* 1.3 79.1 - - + +
56A ALA* 1.3 62.5 + - + +
57A GLY 3.7 0.3 + - - -
213A LYS* 4.6 3.4 - - + +
214A PRO* 3.6 40.5 - - + +
217A PHE* 3.9 38.4 - - + -
313A PRO* 3.8 7.3 - - - +
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU* 3.5 35.0 - - + -
23A TYR* 3.7 15.0 + - + -
52A VAL 3.0 9.7 + - - +
55A VAL* 1.3 76.5 - - + +
57A GLY* 1.3 64.0 + - - +
58A ILE* 3.5 11.6 + - + -
214A PRO* 4.3 6.1 - - + -
310A ILE* 4.0 15.5 - - + +
313A PRO* 3.5 17.6 - - - +
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Residues in contact with GLY 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TYR* 3.3 10.6 + - - -
53A ALA 2.9 7.9 + - - -
54A ASP* 3.4 7.4 + - - -
55A VAL 3.4 3.8 + - - -
56A ALA* 1.3 78.8 - - - +
58A ILE* 1.3 62.8 + - - +
59A VAL* 3.2 17.9 + - - +
313A PRO* 4.0 12.3 - - - +
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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