Contacts of the helix formed by residues 22 - 35 (chain A) in PDB entry 1CF7
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 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A LYS 4.1 0.6 + - - -
21A SER* 1.3 71.3 - - - +
23A GLY* 1.3 51.8 + - - +
25A LEU* 3.0 18.0 + - + +
26A THR* 2.7 41.3 + - - +
57A ARG* 4.4 10.3 - - - +
60A ASP* 3.8 33.2 - - + +
61A ILE* 3.7 27.8 - - + -
125B ASP* 3.7 33.9 - - + +
128B ASN* 5.0 9.4 - - + +
129B VAL* 4.0 18.4 - - + -
506C G 3.1 18.1 + - - +
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Residues in contact with GLY 23 (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 SER* 3.0 5.8 + - - -
22A LEU* 1.3 80.5 - - - +
24A LEU* 1.3 65.0 + - - +
26A THR* 3.1 11.8 - - - -
27A THR* 3.1 23.6 + - - -
128B ASN* 4.1 22.5 + - - +
132B ALA* 3.5 7.3 - - - +
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Residues in contact with LEU 24 (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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18A HIS* 3.3 47.8 - - + +
19A GLU* 3.9 22.0 - - - +
21A SER* 2.8 25.3 + - - +
23A GLY* 1.3 70.3 - - - -
25A LEU* 1.3 69.9 + - - +
27A THR* 2.9 22.3 + - - +
28A LYS* 3.2 26.1 + - - +
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Residues in contact with LEU 25 (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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20A LYS* 6.0 2.2 - - - -
21A SER 3.1 12.6 + - - +
22A LEU* 3.0 17.2 + - + +
24A LEU* 1.3 76.3 - - + +
26A THR* 1.3 63.2 + - - +
28A LYS* 3.2 15.9 + - - +
29A PHE* 2.9 20.6 + - - +
50A LEU* 3.2 49.1 - - + +
51A ALA* 4.4 6.5 - - + -
53A ARG* 4.9 9.9 - - + -
57A ARG* 3.9 36.1 - - + -
58A ILE* 6.2 2.5 - - + -
61A ILE* 4.0 12.6 - - + -
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Residues in contact with THR 26 (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 LEU 2.7 28.5 + - - -
23A GLY* 3.1 12.9 - - - -
24A LEU 2.9 0.2 + - - -
25A LEU* 1.3 72.8 - - - +
27A THR* 1.3 66.0 + - - +
29A PHE* 2.9 5.8 + - + +
30A VAL* 2.8 22.9 + - + +
61A ILE* 3.9 23.6 - - + +
65A LEU* 6.1 1.1 - - + -
129B VAL* 3.9 31.4 - - + +
132B ALA* 3.7 20.2 - - + +
133B MET* 4.5 16.8 - - + -
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Residues in contact with THR 27 (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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23A GLY 3.1 10.2 + - - -
24A LEU* 2.9 14.3 + - - +
26A THR* 1.3 79.6 - - - +
28A LYS* 1.3 64.7 + - + +
30A VAL* 3.3 9.1 + - + +
31A SER* 3.1 28.3 + - - +
132B ALA* 4.4 13.5 + - - +
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Residues in contact with LYS 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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19A GLU 5.5 4.9 + - - -
24A LEU* 3.7 24.1 - - - +
25A LEU* 3.5 16.4 - - + +
26A THR 3.1 0.8 - - - -
27A THR* 1.3 78.9 - - + +
29A PHE* 1.3 56.5 + - - +
31A SER* 3.1 6.8 + - - -
32A LEU* 2.7 36.6 + - - +
49A THR* 5.1 4.5 - - + +
50A LEU* 3.2 30.1 - - + -
51A ALA* 4.3 16.0 - - - +
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Residues in contact with PHE 29 (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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25A LEU 2.9 13.4 + - - +
26A THR* 2.9 9.8 + - - +
28A LYS* 1.3 74.0 - - - +
30A VAL* 1.3 54.6 + - + +
32A LEU* 3.4 6.8 + - - +
33A LEU* 2.7 50.9 + - + +
41A LEU* 4.0 20.0 - - + +
43A LEU* 4.6 9.4 - - + -
46A ALA* 4.2 18.4 - - + -
50A LEU* 3.5 6.7 - - + +
58A ILE* 4.1 33.7 - - + -
61A ILE* 3.8 37.9 - - + -
62A THR* 4.1 19.3 - - + -
65A LEU* 4.6 9.2 - - + -
71A ILE* 4.6 7.2 - - + -
79A ILE* 4.7 3.8 - - + -
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Residues in contact with VAL 30 (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 THR* 2.8 17.4 + - + +
27A THR* 3.5 12.8 - - + +
29A PHE* 1.3 75.8 - - + +
31A SER* 1.3 65.8 + - - +
33A LEU* 3.0 17.0 + - + +
34A GLN* 2.7 46.0 + - + +
65A LEU* 5.4 4.0 - - + -
81A TRP* 6.0 0.2 - - + -
132B ALA 5.8 1.6 - - - +
133B MET* 3.4 35.4 - - + -
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Residues in contact with SER 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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27A THR* 3.1 18.5 + - - +
28A LYS* 3.6 8.5 - - - -
30A VAL* 1.3 78.6 - - - +
32A LEU* 1.3 65.5 + - - +
34A GLN* 3.3 20.9 + - - +
35A GLU* 2.9 26.6 + - - +
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Residues in contact with LEU 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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28A LYS 2.7 19.5 + - - +
29A PHE* 3.4 5.6 - - - +
31A SER* 1.3 72.9 - - - +
33A LEU* 1.3 67.0 + - - +
35A GLU* 3.3 6.0 + - + +
36A ALA* 3.1 22.0 + - + +
41A LEU* 4.4 11.2 - - + -
45A LEU* 3.7 26.5 - - + -
46A ALA* 3.2 26.5 - - + -
49A THR* 3.7 20.0 - - + +
50A LEU* 3.1 33.0 - - + -
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Residues in contact with LEU 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 PHE* 2.7 28.7 + - + +
30A VAL* 3.0 17.5 + - + +
32A LEU* 1.3 75.3 - - - +
34A GLN* 1.3 61.6 + - + +
35A GLU 2.8 7.3 + - - -
36A ALA* 3.0 20.3 + - - +
39A GLY* 4.7 6.3 - - - +
40A VAL 5.6 0.2 - - - -
41A LEU* 3.6 34.0 - - + +
65A LEU* 5.0 4.9 - - + -
71A ILE* 4.2 10.1 - - + -
79A ILE* 4.3 11.4 - - + -
81A TRP* 3.5 51.6 - - + -
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Residues in contact with GLN 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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30A VAL* 2.7 36.0 + - + +
31A SER* 3.3 25.7 + - - +
33A LEU* 1.3 74.6 - - + +
35A GLU* 1.3 62.5 + - + +
36A ALA 4.4 1.9 - - - +
37A LYS* 5.2 4.3 + - - -
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Residues in contact with GLU 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 SER 2.9 19.4 + - - +
32A LEU* 3.6 6.3 - - + +
33A LEU 2.8 1.6 + - - -
34A GLN* 1.3 79.0 - - - +
36A ALA* 1.3 53.5 - - - +
37A LYS* 2.7 33.6 + - - +
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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