Contacts of the helix formed by residues 12 - 25 (chain F) in PDB entry 4CQM
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 ARG 12 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9F GLY 3.3 16.8 + - - +
10F GLY 3.5 1.0 - - - -
11F SER* 1.3 95.7 + - - +
13F GLY* 1.3 68.7 + - - +
14F ILE 3.5 1.2 + - - -
15F GLY 3.6 0.5 + - - -
16F ARG* 3.4 7.6 + - - +
34F ARG* 5.6 5.5 - - - +
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Residues in contact with GLY 13 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12F ARG* 1.3 74.7 - - - +
14F ILE* 1.3 62.7 + - - -
16F ARG* 3.1 14.0 + - - +
17F ALA* 3.2 13.4 + - - +
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Residues in contact with ILE 14 (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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12F ARG 3.5 0.8 + - - -
13F GLY* 1.3 71.6 - - - -
15F GLY* 1.3 59.7 + - - +
17F ALA* 3.2 7.3 + - - +
18F VAL* 2.9 40.4 + - + +
83F ALA* 4.7 7.6 - - + -
133F VAL* 4.2 31.2 - - + -
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Residues in contact with GLY 15 (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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7F VAL* 3.5 11.8 - - - +
9F GLY 3.3 15.2 + - - -
10F GLY* 3.3 15.3 - - - -
12F ARG 3.6 2.8 + - - -
13F GLY 3.4 0.6 - - - -
14F ILE* 1.3 78.3 - - - +
16F ARG* 1.3 56.2 + - - +
18F VAL* 3.7 3.8 - - - +
19F ALA* 3.0 24.4 + - - +
83F ALA* 3.7 20.8 + - - +
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Residues in contact with ARG 16 (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 GLY* 3.4 16.8 + - - -
11F SER 3.8 10.5 - - - +
12F ARG* 3.4 22.8 + - - +
13F GLY 3.1 12.4 + - - +
15F GLY* 1.3 77.6 - - - +
17F ALA* 1.3 58.9 + - - +
19F ALA* 3.4 4.8 + - - +
20F GLN* 2.6 54.7 + - + +
41F ALA 5.4 0.2 + - - -
42F ALA* 3.7 29.9 + - - +
45F ASP* 2.7 22.8 + - - +
46F LEU* 3.4 15.6 - - - +
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Residues in contact with ALA 17 (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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13F GLY 3.2 7.4 + - - +
14F ILE* 3.2 9.9 + - - +
16F ARG* 1.3 77.0 - - - +
18F VAL* 1.3 60.0 + - - +
20F GLN* 3.2 8.2 + - - +
21F LEU* 2.9 31.8 + - - +
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Residues in contact with VAL 18 (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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7F VAL* 4.0 15.3 - - + -
14F ILE* 2.9 36.4 + - + +
15F GLY* 3.7 7.9 - - - +
17F ALA* 1.3 77.0 - - + +
19F ALA* 1.3 62.7 + - - +
21F LEU* 3.4 3.9 + - - +
22F MET* 3.1 52.7 + - + +
81F VAL* 4.0 20.2 - - + -
133F VAL* 6.1 0.7 - - + -
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Residues in contact with ALA 19 (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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7F VAL* 4.7 6.5 - - + -
10F GLY 4.3 10.3 - - - +
15F GLY 3.0 17.9 + - - +
16F ARG* 3.6 7.6 - - - +
18F VAL* 1.3 75.8 - - - +
20F GLN* 1.3 61.3 + - - +
23F ALA* 3.2 8.5 + - - +
29F LEU* 3.1 38.3 - - + +
31F VAL* 4.4 8.5 - - + -
46F LEU* 3.6 20.8 - - + +
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Residues in contact with GLN 20 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16F ARG* 2.6 46.7 + - - +
17F ALA* 3.2 13.0 + - - +
19F ALA* 1.3 78.0 - - - +
21F LEU* 1.3 63.0 + - - +
23F ALA* 3.4 11.6 + - - +
24F ARG* 3.4 13.5 + - - +
45F ASP* 3.2 12.9 + - - +
46F LEU* 3.3 12.6 - - - +
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Residues in contact with LEU 21 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17F ALA 2.9 16.5 + - - +
18F VAL* 4.0 5.2 - - - +
20F GLN* 1.3 77.1 - - - +
22F MET* 1.3 64.5 + - + +
24F ARG* 3.3 18.7 + - + +
25F LYS* 3.3 44.5 + - + +
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Residues in contact with MET 22 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5F CYS* 3.6 33.9 - - + -
18F VAL* 3.1 35.2 + - + +
21F LEU* 1.3 77.4 - - + +
23F ALA* 1.3 63.3 + - - +
25F LYS* 3.1 11.5 + - + +
27F TYR* 3.0 73.6 + - + +
29F LEU* 3.6 15.3 - - + -
79F PHE* 4.7 6.7 - - + -
81F VAL* 4.5 4.5 - - + -
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Residues in contact with ALA 23 (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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19F ALA 3.2 20.5 + - - +
20F GLN* 3.6 5.4 - - - +
21F LEU 3.3 0.2 - - - -
22F MET* 1.3 77.9 - - - +
24F ARG* 1.3 60.9 + - - +
25F LYS 3.6 0.3 + - - -
26F GLY* 3.7 9.4 + - - -
27F TYR 3.9 7.5 - - - +
29F LEU* 3.3 12.0 - - + +
46F LEU* 3.9 20.4 - - + +
50F HIS* 4.0 21.5 + - + +
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Residues in contact with ARG 24 (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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20F GLN* 3.4 9.4 + - - +
21F LEU* 3.3 19.4 + - + +
22F MET 3.2 0.6 - - - -
23F ALA* 1.3 77.4 - - - +
25F LYS* 1.3 61.4 + - + +
26F GLY 3.2 4.5 + - - -
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Residues in contact with LYS 25 (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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4E GLN* 5.3 11.6 - - + +
5E LEU* 4.1 23.6 - - - +
244E ASP* 5.7 2.6 + - - -
21F LEU* 3.3 44.3 + - + +
22F MET* 3.1 12.3 + - + +
24F ARG* 1.3 81.6 - - + +
26F GLY* 1.3 57.5 + - - +
27F TYR* 3.4 26.8 + - + -
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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