Contacts of the helix formed by residues 30 - 43 (chain A) in PDB entry 4L9T
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 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A LEU* 4.4 3.2 - - - +
29A ILE* 1.3 76.8 - - - +
31A ASN* 1.3 66.0 + - - +
32A GLU* 3.6 7.1 + - - +
33A GLN* 3.0 42.7 + - - +
34A GLY* 2.9 19.6 + - - -
67A LEU* 5.0 1.2 - - - +
201A SO4 3.7 17.9 - - - +
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Residues in contact with ASN 31 (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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21A ASP* 3.2 28.9 + - - -
24A LEU* 3.3 22.6 - - - +
30A THR* 1.3 72.7 - - - +
32A GLU* 1.3 58.2 + - - +
34A GLY* 3.2 2.8 + - - -
35A HIS* 2.9 56.5 + - + -
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Residues in contact with GLU 32 (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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30A THR* 3.2 6.1 + - - +
31A ASN* 1.3 79.6 - - - +
33A GLN* 1.3 57.7 + - - +
35A HIS* 3.3 11.6 + - - +
36A THR* 2.9 31.9 + - - -
57A LEU* 5.1 1.9 - - + +
59A ARG* 4.4 19.7 - - - +
67A LEU* 4.0 19.9 - - + +
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Residues in contact with GLN 33 (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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28A ASP 4.2 3.1 - - - +
29A ILE* 3.4 17.5 - - + +
30A THR* 3.0 47.9 + - - +
32A GLU* 1.3 74.6 - - - +
34A GLY* 1.3 59.1 + - - +
36A THR* 3.2 7.4 + - - -
37A LEU* 2.9 34.7 + - - +
67A LEU* 4.1 17.6 - - + +
70A ASN* 4.0 28.8 - - - +
71A LEU* 4.0 27.8 - - + +
74A LYS* 5.2 3.4 + - - +
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Residues in contact with GLY 34 (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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24A LEU* 4.5 7.9 - - - -
29A ILE* 4.0 19.6 - - - +
30A THR 2.9 14.3 + - - -
31A ASN 3.2 3.8 + - - -
33A GLN* 1.3 75.3 - - - +
35A HIS* 1.3 57.2 + - - +
37A LEU* 3.4 4.2 + - - +
38A GLY* 2.9 26.3 + - - -
101A VAL* 5.5 0.5 - - - +
104A PHE* 6.4 2.5 - - - -
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Residues in contact with HIS 35 (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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31A ASN* 2.9 43.3 + - + -
32A GLU* 3.6 11.7 - - - +
34A GLY* 1.3 75.8 - - - +
36A THR* 1.3 58.2 + - - +
38A GLY* 3.5 1.4 + - - -
39A TYR* 3.0 29.1 + - - +
57A LEU* 4.6 12.9 - - + +
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Residues in contact with THR 36 (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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32A GLU 2.9 16.2 + - - -
33A GLN* 3.5 8.6 - - - -
34A GLY 3.2 0.2 - - - -
35A HIS* 1.3 75.9 - - - +
37A LEU* 1.3 63.1 + - - +
39A TYR* 3.3 5.9 + - - +
40A LEU* 3.0 29.5 + - + +
53A ILE* 4.2 17.2 - - + +
57A LEU* 3.5 21.7 - - + +
64A VAL* 6.0 0.2 - - + -
67A LEU* 4.0 12.5 - - + +
68A LEU* 4.1 20.0 - - + -
71A LEU* 3.9 21.5 - - + -
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Residues in contact with LEU 37 (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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29A ILE* 4.2 23.3 - - + -
33A GLN 2.9 22.3 + - - +
34A GLY* 3.8 3.8 - - - +
36A THR* 1.3 76.2 - - - +
38A GLY* 1.3 58.2 + - - +
40A LEU* 3.4 6.3 + - + +
41A TYR* 2.8 29.6 + - - +
71A LEU* 3.9 29.8 - - + -
76A LEU* 4.2 23.8 - - + -
77A ILE* 4.0 9.4 - - + -
93A LEU* 3.7 24.8 - - + +
97A GLY* 4.9 3.4 - - - +
100A LEU* 4.4 7.9 - - + -
101A VAL* 3.6 22.8 - - + +
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Residues in contact with GLY 38 (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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34A GLY 2.9 16.9 + - - -
35A HIS* 3.8 2.0 - - - -
37A LEU* 1.3 74.5 - - - +
39A TYR* 1.3 60.2 + - - +
41A TYR* 3.4 9.3 + - - +
42A ALA* 3.0 28.1 + - - +
101A VAL* 4.3 9.1 - - - +
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Residues in contact with TYR 39 (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 HIS 3.0 18.9 + - - +
36A THR* 3.7 4.3 - - - +
37A LEU 3.3 0.2 - - - -
38A GLY* 1.3 74.0 - - - +
40A LEU* 1.3 65.9 + - - +
42A ALA* 3.2 4.6 + - + -
43A HIS* 3.1 59.9 + + - +
48A LEU* 4.2 25.1 - - + +
52A ASP* 4.6 6.7 + - + +
53A ILE* 4.7 15.3 - - + -
56A ALA* 3.3 34.9 - - + +
57A LEU* 4.5 11.7 - - + -
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Residues in contact with LEU 40 (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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36A THR* 3.0 31.9 + - + +
37A LEU* 3.6 7.6 - - + +
39A TYR* 1.3 77.4 - - - +
41A TYR* 1.3 58.1 + - - +
43A HIS 3.1 1.6 + - - -
44A GLN* 2.9 35.0 + - - +
48A LEU* 3.8 21.3 - - + +
53A ILE* 3.7 26.0 - - + -
68A LEU* 5.0 1.1 - - + -
77A ILE* 3.6 30.3 - - + -
91A ILE* 3.8 28.7 - - + +
92A GLY* 5.1 2.5 - - - +
93A LEU* 3.9 17.0 - - + +
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Residues in contact with TYR 41 (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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37A LEU 2.8 17.6 + - - +
38A GLY* 3.5 6.7 - - - +
40A LEU* 1.3 75.3 - - - +
42A ALA* 1.3 64.5 + - + +
44A GLN* 3.2 31.7 + - - +
93A LEU* 3.7 15.4 - - + +
98A ILE* 4.2 11.9 - - + -
101A VAL* 3.7 29.6 - - + -
102A GLU* 2.7 44.3 + - + +
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Residues in contact with ALA 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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38A GLY 3.0 16.4 + - - +
39A TYR* 3.2 6.9 + - + +
41A TYR* 1.3 81.2 - - + +
43A HIS* 1.3 80.4 + - + +
44A GLN 3.6 0.4 - - - -
45A GLN* 3.5 11.7 + - - +
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Residues in contact with HIS 43 (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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39A TYR* 3.1 59.3 + + - +
40A LEU 3.4 3.8 - - - -
42A ALA* 1.3 93.9 + - + +
44A GLN* 1.3 53.0 + - - +
45A GLN* 2.8 26.6 + - - +
46A ASP* 3.3 28.3 + - - +
47A GLY 4.7 0.3 + - - -
48A LEU* 3.7 33.3 - - + +
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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