Contacts of the helix formed by residues 30 - 44 (chain D) in PDB entry 4LLL
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D ASP* 4.0 11.7 - - - +
24D LEU* 4.1 3.1 - - - -
29D ILE* 1.3 77.8 - - - +
31D ASN* 1.3 52.1 + - - +
32D GLU* 3.3 11.7 + - - -
33D GLN* 2.7 21.3 + - - +
34D GLY* 2.4 33.6 + - - -
12E T 3.7 19.1 - - - +
13E A 2.4 35.4 + - - +
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Residues in contact with ASN 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ARG* 5.4 6.0 - - - +
16D MET 4.8 0.4 - - - -
17D LYS* 3.3 35.0 - - - +
20D ALA* 3.8 19.6 - - + +
21D ASP* 3.1 17.4 + - - +
24D LEU* 3.5 14.8 - - + +
30D THR* 1.3 71.6 - - - +
32D GLU* 1.3 96.4 + - - +
34D GLY* 3.8 0.9 - - - +
35D HIS* 2.5 52.7 + - + +
108D PHE* 4.3 8.3 - - + -
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Residues in contact with GLU 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ARG* 6.1 5.1 - - - -
17D LYS* 5.0 6.6 - - - +
21D ASP* 4.8 3.3 - - - +
30D THR* 3.3 11.9 + - - +
31D ASN* 1.3 110.6 + - - +
33D GLN* 1.3 55.8 + - - +
35D HIS* 4.0 7.0 - - - +
36D THR* 2.5 36.2 + - - -
57D LEU* 5.2 0.3 - - - +
67D LEU* 3.9 15.7 - - + -
13E A 3.2 44.6 - - - +
14E T 3.9 10.9 + - - +
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Residues in contact with GLN 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ILE* 3.3 15.4 - - + +
30D THR* 2.7 31.8 + - - +
32D GLU* 1.3 78.2 - - - +
34D GLY* 1.3 61.5 + - - +
36D THR* 3.5 3.9 + - - -
37D LEU* 3.1 33.1 + - - +
67D LEU* 4.0 10.5 - - + -
70D ASN* 4.0 18.4 - - - +
71D LEU* 3.7 25.1 - - + +
74D LYS* 3.4 19.1 + - - +
12E T 3.6 9.3 + - - -
13E A 3.1 35.1 + - - +
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Residues in contact with GLY 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D ILE* 3.7 21.0 - - - +
30D THR 2.4 17.2 + - - -
31D ASN* 2.9 7.6 + - - -
33D GLN* 1.3 74.4 - - - +
35D HIS* 1.3 55.5 + - - +
38D GLY* 3.1 21.8 + - - -
104D PHE* 3.2 20.2 - - - -
108D PHE* 3.9 12.2 - - - -
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Residues in contact with HIS 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C SER* 3.7 17.3 + - - -
10C ARG* 3.2 52.2 + - - +
31D ASN* 2.5 37.6 + - + +
32D GLU* 4.1 5.7 - - - +
34D GLY* 1.3 69.9 - - - +
36D THR* 1.3 62.0 + - - +
38D GLY* 3.3 2.5 + - - -
39D TYR* 2.8 28.2 + - - +
57D LEU* 4.6 9.5 - - + +
108D PHE* 3.1 46.2 - + - -
111D MET* 6.1 1.1 - - + -
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Residues in contact with THR 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D GLU 2.5 25.0 + - - -
33D GLN 3.8 2.9 - - - -
35D HIS* 1.3 72.5 - - - +
37D LEU* 1.3 62.1 + - - +
39D TYR* 2.9 9.5 + - + +
40D LEU* 2.8 33.7 + - + +
53D ILE* 4.2 15.0 - - + -
57D LEU* 3.6 27.6 - - + +
67D LEU* 3.1 30.9 - - + +
68D LEU* 4.2 12.8 - - + -
71D LEU* 4.3 4.3 - - + -
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Residues in contact with LEU 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ILE* 4.7 2.7 - - + -
33D GLN 3.1 20.0 + - - +
34D GLY 4.1 2.2 - - - +
36D THR* 1.3 78.6 - - - +
38D GLY* 1.3 52.1 + - - +
40D LEU* 3.0 9.6 + - + +
41D TYR* 2.6 35.9 + - - +
71D LEU* 3.7 36.6 - - + -
76D LEU* 4.0 10.5 - - + -
77D ILE* 3.7 22.4 - - + -
93D LEU* 3.9 11.5 - - + +
97D GLY 5.0 1.3 - - - +
100D LEU* 3.7 30.1 - - + -
101D VAL* 4.1 17.1 - - + +
104D PHE* 4.2 9.2 - - + -
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Residues in contact with GLY 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D GLY 3.1 17.8 + - - -
35D HIS* 3.6 4.5 - - - -
36D THR 3.2 0.4 - - - -
37D LEU* 1.3 74.6 - - - +
39D TYR* 1.3 59.7 + - - +
41D TYR* 3.1 12.1 + - - +
42D ALA* 3.0 21.7 + - - +
101D VAL* 4.4 9.6 - - - -
104D PHE* 4.3 3.5 - - - -
108D PHE* 6.5 0.2 - - - -
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Residues in contact with TYR 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D HIS 2.8 16.1 + - - +
36D THR* 3.2 12.3 - - + +
38D GLY* 1.3 72.3 - - - +
40D LEU* 1.3 53.1 + - + +
42D ALA* 2.8 6.7 + - - -
43D HIS* 2.7 84.0 + + - +
48D LEU* 3.9 30.4 - - + +
52D ASP 5.2 0.6 + - - -
53D ILE* 4.7 18.2 - - + -
56D ALA* 3.3 33.0 - - + +
57D LEU* 4.6 16.2 - - + -
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Residues in contact with LEU 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D THR* 2.8 28.4 + - + +
37D LEU* 3.3 15.3 - - + +
39D TYR* 1.3 68.8 - - + +
41D TYR* 1.3 65.5 + - - +
44D GLN* 2.9 37.7 + - + +
48D LEU* 3.7 22.4 - - + -
53D ILE* 3.9 15.3 - - + -
68D LEU* 4.9 3.6 - - + -
77D ILE* 3.7 23.1 - - + -
91D ILE* 3.7 40.4 - - + +
92D GLY 4.8 2.9 - - - +
93D LEU* 4.1 13.5 - - + +
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Residues in contact with TYR 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LEU 2.6 13.2 + - - +
38D GLY 3.2 10.3 - - - +
40D LEU* 1.3 73.5 - - - +
42D ALA* 1.3 65.6 + - + +
44D GLN* 4.6 7.9 + - - +
93D LEU* 3.5 21.0 - - + +
98D ILE* 3.8 23.3 - - + -
101D VAL* 3.3 38.6 - - + -
102D GLU* 3.0 26.5 + - + +
105D THR* 6.3 2.0 - - + -
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Residues in contact with ALA 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D GLY 3.0 9.7 + - - +
39D TYR* 2.8 7.4 + - - +
41D TYR* 1.3 85.0 - - + +
43D HIS* 1.3 78.7 + - + +
44D GLN* 3.8 0.4 - - - -
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Residues in contact with HIS 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D TYR* 2.7 56.9 + + + +
42D ALA* 1.3 94.8 - - + +
44D GLN* 1.3 59.4 + - - +
45D GLN 3.4 2.7 - - - -
46D ASP* 2.8 36.2 - - + +
48D LEU* 3.4 27.8 - - + +
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Residues in contact with GLN 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D LEU* 2.9 23.0 + - + +
41D TYR* 4.6 7.8 + - - +
42D ALA 3.8 0.8 - - - -
43D HIS* 1.3 70.3 - - - +
45D GLN* 1.3 63.1 + - + +
46D ASP 2.7 12.1 + - - -
47D GLY* 3.5 9.0 + - - -
48D LEU* 3.6 16.6 + - + +
91D ILE 4.4 6.8 - - - +
92D GLY* 3.8 12.8 - - - -
93D LEU* 2.9 49.0 + - - +
98D ILE* 4.8 10.7 - - - +
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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