Contacts of the helix formed by residues 34 - 46 (chain F) in PDB entry 2CFX
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 PRO 34 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32F SER* 3.1 17.7 - - - +
33F PRO* 1.4 91.9 - - + +
35F SER* 1.3 60.6 + - - +
37F THR* 3.0 17.3 + - - +
38F GLU* 3.7 12.1 + - - +
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Residues in contact with SER 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F LEU* 3.3 20.9 - - - +
32F SER* 2.5 46.7 + - - -
34F PRO* 1.3 71.6 - - - +
36F VAL* 1.3 65.8 + - - -
38F GLU* 3.3 19.1 - - - +
39F ARG* 3.3 16.2 + - - +
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Residues in contact with VAL 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ILE* 3.9 9.6 - - + -
22F MET* 4.3 10.5 - - + +
25F LEU* 3.7 33.0 - - + -
26F GLY* 3.6 27.8 - - - +
29F ILE* 3.8 20.2 - - + -
31F LEU* 3.9 11.0 - - + -
32F SER 3.0 19.2 + - - +
33F PRO* 4.2 1.6 - - + -
35F SER* 1.3 70.4 + - - +
37F THR* 1.3 53.8 + - - +
38F GLU 2.6 16.9 + - - -
39F ARG* 2.9 18.0 + - - +
40F VAL* 3.1 14.5 + - + +
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Residues in contact with THR 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F MET* 3.3 39.6 - - + +
33F PRO 3.0 21.3 + - - +
34F PRO* 3.0 15.3 + - - +
36F VAL* 1.3 74.2 - - - +
38F GLU* 1.3 55.3 + - - +
40F VAL* 4.2 2.5 - - - +
41F ARG* 3.2 26.2 + - - +
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Residues in contact with GLU 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F PRO 3.7 10.2 + - - +
35F SER* 3.3 14.1 + - - +
36F VAL 2.6 5.7 + - - -
37F THR* 1.3 74.1 - - - +
39F ARG* 1.3 61.3 + - + +
41F ARG* 2.9 27.3 + - - +
42F GLN* 3.0 18.8 + - - +
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Residues in contact with ARG 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F ASP* 2.4 32.8 + - - -
6F ILE* 3.1 21.6 - - - +
7F ASP* 2.7 40.4 + - - +
10F ILE* 3.5 27.4 - - + -
31F LEU* 3.5 23.1 - - - +
35F SER 3.4 12.6 - - - +
36F VAL* 2.9 8.3 + - - +
38F GLU* 1.3 73.4 - - + +
40F VAL* 1.3 50.9 + - - +
42F GLN* 3.0 10.1 + - - +
43F LEU* 2.8 38.5 + - - +
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Residues in contact with VAL 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E ARG* 6.0 0.4 - - - +
10F ILE* 3.7 29.2 - - + -
14F LEU* 4.3 7.4 - - + -
22F MET* 4.1 18.8 - - + -
25F LEU* 3.8 18.2 - - + -
36F VAL 3.1 13.8 + - - +
37F THR 4.2 3.6 - - - +
39F ARG* 1.3 76.6 - - - +
41F ARG* 1.3 60.6 + - - +
43F LEU* 3.7 11.9 - - - +
44F GLU* 3.3 39.4 + - - +
49F ILE* 5.1 1.1 - - + -
52F TYR* 3.8 11.2 + - - +
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Residues in contact with ARG 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F THR 3.2 20.9 + - - +
38F GLU* 2.9 20.2 + - - +
40F VAL* 1.3 78.5 - - - +
42F GLN* 1.3 51.0 + - - +
44F GLU* 3.7 8.5 + - - +
45F SER* 2.8 33.5 + - - -
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Residues in contact with GLN 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MET* 3.3 29.5 - - + +
38F GLU* 3.0 17.5 + - + +
39F ARG* 3.0 10.6 + - - +
41F ARG* 1.3 76.7 - - - +
43F LEU* 1.3 61.9 + - - +
45F SER* 3.1 9.7 + - - +
46F PHE* 3.1 21.9 + - + +
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Residues in contact with LEU 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MET* 4.5 14.6 - - - -
3F LEU* 4.7 3.4 - - + -
7F ASP* 4.0 30.5 - - + +
10F ILE* 3.9 26.7 - - + -
11F ILE* 3.8 24.2 - - + -
39F ARG 2.8 19.0 + - - +
40F VAL* 3.8 9.2 - - - +
41F ARG 3.3 0.4 - - - -
42F GLN* 1.3 76.8 - - - +
44F GLU* 1.3 58.8 + - - +
47F GLY 3.2 3.6 + - - -
48F ILE* 3.1 52.7 + - + +
49F ILE* 3.3 21.6 + - + +
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Residues in contact with GLU 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E ARG* 3.8 11.5 + - - -
40F VAL* 3.3 25.8 + - - +
41F ARG* 3.9 8.7 - - - +
43F LEU* 1.3 75.7 - - - +
45F SER* 1.3 62.9 + - - +
47F GLY* 3.2 14.0 + - - -
49F ILE* 3.8 21.3 - - + +
52F TYR* 2.7 41.5 + - + +
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Residues in contact with SER 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F ARG 2.8 18.2 + - - -
42F GLN* 3.1 13.5 + - - -
44F GLU* 1.3 78.6 - - - +
46F PHE* 1.3 71.4 + - - +
47F GLY* 3.7 0.3 + - - -
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Residues in contact with PHE 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E LYS* 3.3 23.7 + - - -
1F MET* 3.1 58.3 - - + -
42F GLN* 3.1 11.7 + - + +
45F SER* 1.3 88.1 + - - +
47F GLY* 1.3 56.3 + - - +
48F ILE* 3.4 8.6 - - + +
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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