Contacts of the helix formed by residues 27 - 45 (chain A) in PDB entry 1FLS
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 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A MET* 1.3 77.5 - - - +
28A HIS* 1.3 68.0 + - - +
29A SER* 3.8 7.6 + - - -
30A GLU* 3.2 35.5 + - - +
31A VAL* 3.1 19.2 + - - +
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Residues in contact with HIS 28 (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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22A TYR* 3.5 52.8 - + + +
23A THR 5.3 1.5 + - - -
26A MET 4.5 2.5 - - - -
27A THR* 1.3 77.7 - - - +
29A SER* 1.3 58.2 + - - +
31A VAL* 3.2 0.9 + - - +
32A GLU* 2.8 44.5 + - - +
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Residues in contact with SER 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A THR* 3.2 8.4 - - - -
28A HIS* 1.3 80.5 - - - +
30A GLU* 1.3 62.8 + - - +
32A GLU* 3.7 11.0 + - - +
33A LYS* 3.3 31.6 + - - +
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Residues in contact with GLU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A MET* 3.6 34.9 - - + +
27A THR* 3.2 30.2 + - - +
29A SER* 1.3 79.3 - - - +
31A VAL* 1.3 61.4 + - - +
33A LYS* 2.9 36.8 - - + +
34A ALA* 3.3 9.2 + - - +
106A SER* 4.9 14.6 + - - -
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 5.1 0.2 - - + -
21A ASN 5.1 1.6 - - - +
22A TYR* 3.5 47.6 - - + +
23A THR* 4.7 2.9 - - + -
26A MET* 3.9 27.4 - - + -
27A THR 3.1 14.1 + - - +
28A HIS 3.7 5.8 - - - +
30A GLU* 1.3 75.6 - - - +
32A GLU* 1.3 67.1 + - - +
34A ALA* 3.1 15.3 + - - +
35A PHE* 3.3 37.3 + - + -
64A PHE* 5.1 2.9 - - + -
113A LEU* 4.5 7.2 - - + -
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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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19A ILE* 4.5 4.7 - - + -
22A TYR* 3.6 24.0 - - + -
28A HIS* 2.8 33.6 + - - +
29A SER* 3.7 12.0 + - - +
31A VAL* 1.3 78.2 - - - +
33A LYS* 1.3 62.0 + - - +
34A ALA 3.2 0.2 + - - -
35A PHE* 3.3 7.3 + - - +
36A LYS* 3.1 33.0 + - - +
52A ARG* 2.8 41.6 + - - +
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Residues in contact with LYS 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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29A SER* 3.3 18.4 + - - +
30A GLU* 2.9 39.1 - - + +
32A GLU* 1.3 80.1 - - - +
34A ALA* 1.3 64.7 + - - +
36A LYS* 3.2 12.5 + - + +
37A LYS* 2.9 46.8 + - + +
106A SER* 5.5 6.5 - - - +
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Residues in contact with ALA 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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26A MET* 5.9 1.3 - - + -
30A GLU 3.7 9.0 - - - +
31A VAL 3.1 11.1 + - - +
33A LYS* 1.3 85.9 - - - +
35A PHE* 1.3 64.0 + - + +
37A LYS* 3.3 11.2 + - - +
38A ALA* 3.3 15.8 + - - +
106A SER* 5.4 6.7 - - - +
113A LEU* 3.9 28.7 - - + -
114A PHE* 3.8 19.2 - - + +
117A ALA* 5.4 1.2 - - - +
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Residues in contact with PHE 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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17A TYR* 5.5 4.7 - - + -
19A ILE* 4.0 26.7 - - + -
31A VAL* 3.3 42.1 + - + -
32A GLU 3.3 5.6 + - - +
34A ALA* 1.3 76.8 - - - +
36A LYS* 1.3 65.6 + - + +
38A ALA* 3.0 14.2 + - - +
39A PHE* 3.1 29.7 + - + -
62A ILE* 3.4 47.6 - - + -
64A PHE* 4.8 6.3 - + - -
98A PHE* 4.4 7.9 - + - -
113A LEU* 4.4 17.9 - - + -
117A ALA* 4.2 24.9 - - + -
120A GLU* 4.9 1.1 - - - -
121A PHE* 4.5 7.9 - + - -
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Residues in contact with LYS 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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17A TYR* 4.9 15.3 - - - +
32A GLU* 3.1 20.9 + - - +
33A LYS* 3.2 13.9 + - - +
35A PHE* 1.3 77.9 - - + +
37A LYS* 1.3 64.0 + - + +
39A PHE* 3.2 9.4 + - - +
40A LYS* 2.8 25.5 + - - +
52A ARG* 4.4 21.9 - - - +
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Residues in contact with LYS 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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33A LYS* 2.9 41.8 + - + +
34A ALA* 3.6 8.1 - - - +
35A PHE 3.2 0.2 - - - -
36A LYS* 1.3 75.8 - - + +
38A ALA* 1.3 64.2 + - - +
40A LYS* 3.2 7.5 + - - +
41A VAL* 2.9 29.6 + - + +
114A PHE* 3.6 21.8 - - + -
146A LYS* 5.7 10.3 - - + +
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Residues in contact with ALA 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 ALA 3.3 9.1 + - - +
35A PHE* 3.0 11.8 + - - +
37A LYS* 1.3 81.0 - - - +
39A PHE* 1.3 63.2 + - - +
41A VAL* 3.3 1.1 + - - +
42A TRP* 3.0 32.9 + - + -
114A PHE* 3.5 17.5 - - + -
117A ALA* 4.7 2.9 - - + -
118A ALA* 4.6 12.6 - - - +
121A PHE* 3.9 28.5 - - + -
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Residues in contact with PHE 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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17A TYR* 3.9 44.9 - + + -
35A PHE* 3.1 36.6 + + + -
36A LYS* 3.8 8.1 - - - +
38A ALA* 1.3 79.1 - - - +
40A LYS* 1.3 54.5 + - - +
42A TRP* 4.6 4.7 - + + -
43A SER* 2.5 41.5 + - - -
50A PHE* 3.2 56.3 - + + -
60A ILE* 5.2 1.6 - - + -
62A ILE* 5.3 1.6 - - + -
121A PHE* 3.1 44.9 - + - -
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Residues in contact with LYS 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 LYS 2.8 17.4 + - - +
37A LYS* 3.4 9.2 - - - +
39A PHE* 1.3 78.6 - - - +
41A VAL* 1.3 56.8 + - + +
43A SER* 3.3 8.2 + - - +
44A ASP* 2.6 60.7 + - - +
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Residues in contact with VAL 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 LYS* 2.9 24.2 + - + +
38A ALA* 3.7 5.4 - - - +
40A LYS* 1.3 75.8 - - + +
42A TRP* 1.3 66.4 + - + +
44A ASP* 3.4 21.4 - - - +
45A VAL 4.3 0.2 + - - -
114A PHE* 4.1 20.2 - - + -
136A LEU* 5.3 5.8 - - + -
149A PHE* 4.6 18.2 - - + +
150A MET* 5.2 1.1 - - - -
151A LEU* 3.2 46.6 - - + +
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Residues in contact with TRP 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 ALA* 3.0 30.8 + - - +
39A PHE* 3.9 5.2 - + + +
41A VAL* 1.3 77.9 - - + +
43A SER* 1.3 59.7 + - - +
44A ASP 3.1 2.7 + - - -
45A VAL* 3.4 3.8 + - - +
46A THR* 2.3 36.3 + - + +
48A LEU* 6.2 0.2 - - + -
50A PHE* 5.2 8.5 - - + -
118A ALA* 3.5 35.1 + - + +
121A PHE* 3.8 17.4 - + + +
122A GLY* 4.0 10.3 - - - -
125A LEU* 3.7 25.8 - - + -
127A LEU* 3.8 31.2 - - + -
136A LEU* 4.8 10.8 - - + -
137A MET* 5.1 5.8 - - + -
151A LEU* 3.5 38.1 - - + -
155A ASP* 5.0 10.8 - - + -
159A ILE* 4.2 15.0 - - + -
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Residues in contact with SER 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 PHE* 2.5 28.6 + - - -
40A LYS* 3.0 19.1 + - - +
42A TRP* 1.3 69.6 - - - +
44A ASP* 1.3 67.7 + - - +
45A VAL 3.2 0.4 - - - -
46A THR* 3.2 23.9 + - - +
48A LEU 4.4 7.0 - - - -
50A PHE* 4.2 19.2 - - - -
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Residues in contact with ASP 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 LYS* 2.6 60.5 + - - +
41A VAL* 3.4 19.5 - - - +
42A TRP 3.1 0.6 - - - -
43A SER* 1.3 80.5 + - - +
45A VAL* 1.3 67.9 + - + +
46A THR 4.0 0.2 + - - -
150A MET* 5.7 5.6 - - - +
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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
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42A TRP 3.9 6.1 - - - +
44A ASP* 1.3 86.7 - - + +
46A THR* 1.3 63.5 + - + +
47A PRO* 4.4 3.1 - - - +
151A LEU* 3.5 30.3 - - + -
156A VAL* 4.6 19.5 - - + -
159A ILE* 4.2 19.3 - - + +
160A GLN* 4.6 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
------------------------------------------------------------
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