Contacts of the helix formed by residues 10 - 21 (chain F) in PDB entry 6XAV
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 10 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8F ASN 3.8 2.4 - - - +
9F THR* 1.3 93.5 + - + +
11F VAL* 1.3 64.3 + - + +
12F SER* 4.0 11.7 - - - +
13F GLU* 3.6 37.4 + - + +
14F LEU* 3.4 20.7 + - - +
31F LYS* 5.2 0.4 - - - +
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Residues in contact with VAL 11 (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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130E LYS 6.1 0.9 - - - +
131E ILE* 5.9 8.3 - - + -
135E ASN* 4.2 25.8 - - + +
10F PRO* 1.3 74.1 - - + +
12F SER* 1.3 66.4 + - - +
14F LEU* 3.3 6.8 + - - +
15F ILE* 3.0 42.2 + - + +
29F MET 5.5 4.3 - - - +
31F LYS* 4.3 28.5 - - + +
34F ILE* 4.7 9.9 - - + -
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Residues in contact with SER 12 (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 PRO* 4.0 13.9 - - - +
11F VAL* 1.3 79.3 - - - +
13F GLU* 1.3 66.7 + - - +
15F ILE* 3.4 8.1 + - - +
16F THR* 3.0 29.1 + - - -
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Residues in contact with GLU 13 (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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9F THR* 4.4 12.1 - - - +
10F PRO* 3.6 37.1 + - + +
11F VAL 3.3 0.4 - - - -
12F SER* 1.3 84.9 + - - +
14F LEU* 1.3 59.5 + - + +
16F THR* 4.0 5.0 - - - -
17F LEU* 2.9 31.9 + - - +
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Residues in contact with LEU 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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6F LEU* 3.9 13.7 - - + +
9F THR* 3.3 25.6 - - + +
10F PRO 3.4 14.6 + - - +
11F VAL* 3.3 9.7 + - + +
13F GLU* 1.3 79.6 - - + +
15F ILE* 1.3 61.0 + - - +
17F LEU* 4.6 4.3 - - + -
18F GLY* 3.1 18.4 + - - -
26F LEU* 4.3 0.3 - - - +
31F LYS* 3.8 34.1 - - + -
34F ILE* 3.7 27.3 - - + +
35F ILE* 3.9 20.2 - - + -
38F ILE* 4.1 19.0 - - + +
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Residues in contact with ILE 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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129E ASN* 4.5 13.7 - - - +
11F VAL* 3.0 32.9 + - + +
12F SER* 3.9 7.2 - - - +
14F LEU* 1.3 74.6 - - - +
16F THR* 1.3 66.4 + - - +
18F GLY 3.4 0.3 + - - -
19F GLU* 3.1 45.1 + - - +
26F LEU* 3.6 21.3 - - + +
27F ALA* 3.7 38.6 - - + +
29F MET 6.0 0.2 - - - +
34F ILE* 3.8 9.2 - - + -
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Residues in contact with THR 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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12F SER 3.0 18.3 + - - -
13F GLU* 4.0 5.4 - - - -
15F ILE* 1.3 80.2 - - - +
17F LEU* 1.3 57.8 + - - +
19F GLU* 3.4 8.8 + - - +
20F ASN* 2.3 45.6 + - - +
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Residues in contact with LEU 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 GLU 2.9 19.4 + - - +
14F LEU* 4.1 6.5 - - + +
16F THR* 1.3 78.4 - - - +
18F GLY* 1.3 61.7 + - - +
20F ASN* 3.5 13.0 + - + +
21F MET* 3.3 44.9 + - + +
38F ILE* 3.9 24.7 - - + -
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Residues in contact with GLY 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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14F LEU 3.1 14.1 + - - -
15F ILE 3.4 0.2 + - - -
16F THR 3.2 0.2 - - - -
17F LEU* 1.3 77.3 - - - +
19F GLU* 1.3 62.9 + - - +
21F MET* 3.2 17.7 + - - +
22F GLY 3.5 7.1 + - - -
23F LEU* 3.8 13.3 + - - +
26F LEU* 3.5 25.5 - - - +
38F ILE* 4.6 10.3 - - - -
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Residues in contact with GLU 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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15F ILE* 3.1 35.6 + - - +
16F THR* 3.4 7.9 + - - +
18F GLY* 1.3 76.3 - - - +
20F ASN* 1.3 61.9 + - - +
22F GLY* 3.4 11.0 + - - -
23F LEU 5.1 4.3 - - - +
24F GLU 5.5 0.7 - - - +
25F ASN* 5.4 5.7 - - - +
26F LEU* 3.8 16.0 + - + +
27F ALA* 4.7 9.9 + - - +
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Residues in contact with ASN 20 (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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16F THR* 2.3 48.0 + - - +
17F LEU* 3.9 12.2 - - + +
18F GLY 3.2 0.8 - - - -
19F GLU* 1.3 78.6 - - - +
21F MET* 1.3 60.7 + - + +
22F GLY 3.4 0.9 + - - -
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Residues in contact with MET 21 (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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17F LEU* 3.3 40.2 - - + +
18F GLY* 3.2 10.8 + - - +
20F ASN* 1.3 78.7 - - + +
22F GLY* 1.3 63.5 + - - +
23F LEU* 4.6 11.5 - - + +
38F ILE* 4.4 14.6 - - - +
41F GLN* 3.7 40.4 + - + +
42F HIS* 4.5 19.7 - - + +
45F SER* 5.6 2.5 - - - +
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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