Contacts of the helix formed by residues 35 - 49 (chain D) in PDB entry 5FDK
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 LEU 35 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33D MET 3.4 6.6 + - - +
34D THR* 1.3 73.6 - - - +
36D GLU* 1.3 61.1 + - - +
37D ASP 2.9 1.8 - - - -
38D ASP* 2.7 26.1 + - + +
39D LEU* 2.3 53.2 + - + +
102D ALA* 5.0 14.1 - - + -
103D LYS 5.5 1.8 - - - +
104D GLU* 5.4 4.5 - - + -
137D ILE* 5.5 7.9 - - + +
138D ILE 5.3 0.2 - - - -
139D SER* 2.7 43.7 - - - +
144D VAL* 5.2 9.9 - - + -
181D LEU* 6.5 0.9 - - + -
187D ILE* 5.8 6.1 - - + -
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Residues in contact with GLU 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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34D THR* 5.5 1.3 - - - -
35D LEU* 1.3 80.0 - - - +
37D ASP* 1.3 62.5 + - - +
39D LEU* 3.6 9.9 - - - +
40D ASN* 2.9 28.0 + - + +
56D LYS* 3.1 27.9 + - + -
89D TYR* 3.8 16.6 + - - +
102D ALA* 5.9 3.5 - - + +
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Residues in contact with ASP 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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26D PRO* 5.0 7.3 - - - +
27D SER 4.6 8.0 + - - +
28D TYR 3.7 22.1 - - - +
29D SER* 4.6 7.1 - - - -
34D THR* 4.2 12.6 - - - -
35D LEU 2.7 3.6 + - - +
36D GLU* 1.3 81.6 - - - +
38D ASP* 1.3 69.2 + - - +
39D LEU 3.1 1.1 - - - -
40D ASN* 4.1 7.4 + - - +
41D GLU* 3.0 25.3 + - - +
186D ARG* 4.8 0.2 + - - -
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Residues in contact with ASP 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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29D SER* 3.7 7.9 - - - -
30D ASN* 3.2 30.5 + - - +
34D THR 2.5 28.0 - - - +
35D LEU* 2.7 30.1 + - + +
37D ASP* 1.3 70.8 - - - +
39D LEU* 1.3 56.8 + - - +
41D GLU* 3.5 2.9 + - - +
42D THR* 2.9 30.1 + - - +
181D LEU* 6.2 0.2 - - - +
186D ARG* 3.9 26.6 - - + +
187D ILE* 5.9 2.0 - - + -
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Residues in contact with LEU 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 LEU* 2.3 41.4 + - + +
36D GLU* 3.6 6.7 - - - +
38D ASP* 1.3 67.1 - - - +
40D ASN* 1.3 60.8 + - - +
42D THR* 2.8 38.6 - - + +
43D ASN* 2.8 21.4 + - - +
89D TYR* 3.5 35.7 - - + +
100D PHE* 5.9 4.3 - - + -
101D GLU 5.6 0.4 - - - -
102D ALA* 3.6 25.4 - - + -
137D ILE* 5.4 6.3 - - + -
187D ILE* 4.8 6.5 - - + -
189D TYR* 3.9 22.4 - - + +
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Residues in contact with ASN 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 GLU 2.9 19.8 + - - +
37D ASP* 3.5 8.6 + - - +
39D LEU* 1.3 68.2 - - - +
41D GLU* 1.3 75.1 + - - +
43D ASN* 3.3 9.3 + - - +
44D LYS* 2.9 30.1 + - - +
89D TYR* 5.0 3.0 + - + -
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Residues in contact with GLU 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 ASP 3.0 17.4 + - - +
38D ASP 3.7 1.8 - - - +
40D ASN* 1.3 85.9 - - - +
42D THR* 1.3 63.8 + - - +
44D LYS* 3.4 5.1 + - - +
45D TYR* 3.1 20.0 + - - +
186D ARG* 2.9 34.8 - - - +
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Residues in contact with THR 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 ASP 2.9 18.4 + - - +
39D LEU* 2.8 46.7 - - + +
41D GLU* 1.3 71.9 - - - +
43D ASN* 1.3 58.8 + - - +
45D TYR* 2.8 27.5 + - - +
46D TYR* 3.1 20.7 + - - -
185D PRO 2.5 28.9 + - - -
186D ARG* 4.4 5.0 - - - +
187D ILE* 2.8 24.3 + - + -
189D TYR* 4.2 9.0 - - + -
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Residues in contact with ASN 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 LEU* 2.8 22.4 + - - +
40D ASN* 3.6 7.8 - - - +
42D THR* 1.3 73.8 - - - +
44D LYS* 1.3 57.9 + - - +
46D TYR* 3.3 11.6 + - - +
47D LEU* 3.0 26.7 + - - +
52D ALA 4.8 0.7 - - - +
54D ILE* 3.5 36.1 + - - +
55D HIS* 4.8 3.7 - - - +
89D TYR* 3.3 38.6 - - - -
189D TYR* 2.9 24.3 + - - -
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Residues in contact with LYS 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 ASN* 2.9 23.3 + - - +
41D GLU* 3.8 5.4 - - - +
43D ASN* 1.3 73.8 - - - +
45D TYR* 1.3 66.7 + - - +
47D LEU* 3.2 27.3 + - + +
48D THR* 3.0 39.5 + - - +
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Residues in contact with TYR 45 (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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41D GLU 3.1 11.9 + - - +
42D THR* 2.8 18.8 + - - +
44D LYS* 1.3 72.5 - - - +
46D TYR* 1.3 69.1 + + - +
48D THR* 3.6 2.6 + - - -
49D ASN* 3.1 55.5 + - - +
51D ILE* 3.9 20.8 - - + +
184D ALA* 3.9 15.8 + - + -
185D PRO* 3.4 45.1 - - + +
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Residues in contact with TYR 46 (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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42D THR* 3.1 24.2 + - - -
43D ASN* 3.4 15.9 - - - +
44D LYS 3.2 0.2 - - - -
45D TYR* 1.3 90.7 - + - +
47D LEU* 1.3 66.0 + - - +
49D ASN 3.4 0.5 + - - -
50D GLN 3.3 2.9 + - - -
51D ILE* 3.1 47.9 + - + +
52D ALA* 3.5 17.7 - - + +
54D ILE* 5.3 3.1 - - + +
185D PRO* 4.2 7.6 - - + -
187D ILE 2.8 23.0 + - - -
188D ASP* 3.3 13.2 + - - -
189D TYR* 3.6 19.1 + + - -
190D ILE* 3.2 49.4 - - + +
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Residues in contact with LEU 47 (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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126B GLN* 3.3 42.2 + - - +
43D ASN 3.0 10.8 + - - +
44D LYS* 3.2 33.4 + - + +
46D TYR* 1.3 80.7 - - - +
48D THR* 1.3 66.3 + - - +
49D ASN 3.1 1.0 + - - -
50D GLN* 3.2 13.5 + - - +
52D ALA 3.5 7.5 + - - +
53D VAL* 3.8 27.2 - - + +
54D ILE 5.8 0.4 - - - +
55D HIS* 3.6 28.0 - - + -
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Residues in contact with THR 48 (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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126B GLN* 6.0 0.2 - - - +
44D LYS* 3.0 37.2 + - - +
45D TYR* 4.2 4.0 - - - -
47D LEU* 1.3 78.1 - - - +
49D ASN* 1.3 65.0 + - - +
50D GLN* 3.3 10.4 + - - +
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Residues in contact with ASN 49 (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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45D TYR* 3.1 52.8 + - + +
46D TYR 3.4 0.4 + - - +
47D LEU 3.1 1.2 - - - -
48D THR* 1.3 86.2 - - - +
50D GLN* 1.3 74.1 + - - +
51D ILE* 3.3 24.3 + - + +
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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