Contacts of the helix formed by residues 35 - 48 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ASN* 6.0 2.2 - - + -
33A MET* 2.8 54.3 - - + +
34A THR* 1.3 75.1 + - + +
36A GLU* 1.3 73.9 + - - +
37A ASP* 3.0 13.1 + - - +
38A ASP* 3.8 1.0 + - - -
39A LEU* 4.6 2.9 + - - +
56A LYS* 5.9 0.3 + - - -
104A GLU* 4.8 0.2 - - - +
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Residues in contact with GLU 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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35A LEU* 1.3 89.2 - - - +
37A ASP* 1.3 79.5 + - - +
38A ASP 3.3 0.4 - - - -
40A ASN* 2.0 66.0 + - + +
41A GLU* 5.6 1.3 - - - +
56A LYS* 5.5 8.7 - - + +
89A TYR* 5.1 6.7 - - - +
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Residues in contact with ASP 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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34A THR 3.2 13.2 - - - +
35A LEU* 3.4 4.8 + - - +
36A GLU* 1.3 106.8 - - - +
38A ASP* 1.3 73.3 + - - +
41A GLU* 3.1 43.2 + - + +
186A ARG* 5.2 0.7 - - - +
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Residues in contact with ASP 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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32A GLY 5.3 1.2 - - - +
33A MET 3.2 7.4 - - - +
34A THR* 2.5 53.4 + - - +
35A LEU 3.8 0.2 + - - -
36A GLU 3.3 1.0 - - - -
37A ASP* 1.3 84.3 - - - +
39A LEU* 1.3 64.1 + - + +
42A THR* 3.6 9.7 + - - -
186A ARG* 3.9 14.3 - - - +
187A ILE* 3.7 24.0 - - + +
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Residues in contact with LEU 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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33A MET 3.4 21.9 + - - +
35A LEU 4.6 2.6 + - - +
36A GLU 3.6 2.0 + - - -
38A ASP* 1.3 78.0 - - + +
40A ASN* 1.3 55.1 - - - +
41A GLU 3.4 0.2 - - - -
42A THR* 3.1 7.4 + - - -
43A ASN* 1.9 43.8 + - - +
89A TYR* 3.9 24.0 - - + +
100A PHE* 4.3 14.1 - - + -
102A ALA* 3.7 29.2 - - + -
137A ILE* 4.3 16.8 - - + -
144A VAL* 6.2 0.9 - - + -
187A ILE* 4.0 25.1 - - + -
189A TYR* 5.1 4.2 - - + -
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Residues in contact with ASN 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 GLU* 2.0 53.9 + - + +
37A ASP* 4.5 0.4 - - - -
39A LEU* 1.3 77.5 - - - +
41A GLU* 1.3 66.9 + - + +
42A THR 3.0 0.2 - - - -
43A ASN* 2.8 13.6 + - - +
44A LYS* 2.8 45.9 + - - +
56A LYS* 5.8 7.1 - - - +
89A TYR* 4.4 7.6 + - - +
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Residues in contact with GLU 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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36A GLU* 5.6 1.2 - - - +
37A ASP* 3.1 42.1 + - + +
38A ASP 4.6 0.4 - - - +
40A ASN* 1.3 81.9 - - - +
42A THR* 1.3 67.2 + - - +
44A LYS* 3.2 30.1 + - - +
45A TYR* 3.0 23.2 + - - +
184A ALA 5.7 1.6 - - - +
186A ARG* 5.2 7.9 - - + -
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Residues in contact with THR 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 ASP 3.6 11.3 + - - -
39A LEU* 3.1 14.4 + - - -
40A ASN 3.0 0.4 - - - -
41A GLU* 1.3 80.5 - - - +
43A ASN* 1.3 57.1 + - - +
45A TYR* 3.2 5.0 + - - +
46A TYR* 2.9 37.7 + - - -
185A PRO 3.0 31.4 - - - -
186A ARG* 4.8 0.8 - - - +
187A ILE* 3.2 18.2 - - - -
189A TYR* 4.7 4.0 - - - -
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Residues in contact with ASN 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 LEU* 1.9 41.8 + - - +
40A ASN* 2.8 15.4 - - - +
42A THR* 1.3 73.6 - - - +
44A LYS* 1.3 55.0 + - - +
46A TYR* 3.1 9.3 + - - +
47A LEU* 2.6 35.7 + - - +
52A ALA 4.7 1.0 - - - +
54A ILE* 3.4 30.5 + - + +
55A HIS* 6.2 0.2 - - - -
89A TYR* 4.1 18.8 - - - -
100A PHE* 4.8 1.2 - - - -
189A TYR* 2.8 26.9 + - - -
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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 ASN* 2.8 37.0 + - - +
41A GLU* 3.6 32.0 + - - +
43A ASN* 1.3 75.9 - - - +
45A TYR* 1.3 65.8 + - - +
47A LEU* 2.9 20.2 + - + +
48A THR* 2.9 23.9 + - + +
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Residues in contact with TYR 45 (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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41A GLU 3.0 12.0 + - - +
42A THR* 3.2 13.2 - - - +
44A LYS* 1.3 77.1 - - - +
46A TYR* 1.3 77.0 + + - +
48A THR* 3.5 5.8 + - - -
49A ASN* 3.5 42.0 + - - +
51A ILE* 4.0 20.3 - - + +
184A ALA* 4.3 13.8 - - + +
185A PRO* 4.1 41.7 - - + +
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Residues in contact with TYR 46 (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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42A THR* 2.9 28.7 + - - -
43A ASN* 3.4 8.3 - - - +
45A TYR* 1.3 85.3 - + - +
47A LEU* 1.3 64.6 + - - +
49A ASN 3.6 2.3 + - - -
51A ILE* 3.1 56.2 + - + +
52A ALA* 3.7 20.6 - - + +
54A ILE* 6.0 2.2 - - + +
185A PRO* 4.8 7.2 - - + -
187A ILE 3.9 15.9 - - - -
188A ASP* 2.7 33.3 + - - -
189A TYR* 3.9 26.9 - + - +
190A ILE* 3.0 37.8 + - + +
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Residues in contact with LEU 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 ASN 2.6 19.0 + - - +
44A LYS* 2.9 14.3 + - + +
46A TYR* 1.3 71.2 - - - +
48A THR* 1.3 63.4 + - + +
50A GLN* 2.9 25.6 + - - +
52A ALA 3.6 14.5 + - - +
53A VAL* 4.3 15.5 - - + -
54A ILE 6.0 0.2 - - - +
55A HIS* 4.1 25.4 - - + +
123C HIS* 6.4 0.2 - - + -
126C GLN* 3.1 48.0 + - + +
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Residues in contact with THR 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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44A LYS* 2.9 21.6 + - + +
45A TYR* 3.5 8.3 + - - -
47A LEU* 1.3 75.9 - - + +
49A ASN* 1.3 67.0 + - - +
50A GLN* 3.5 5.6 - - - +
126C GLN* 5.4 2.0 - - - +
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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