Contacts of the helix formed by residues 10 - 20 (chain F) in PDB entry 2F9K
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 TYR 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 ASP 4.6 1.3 - - - +
9F VAL* 1.3 98.8 - - + +
11F ALA* 1.3 51.9 + - - +
13F GLU* 2.7 24.0 + - - +
14F LYS* 2.7 20.2 + - - +
59F ASN* 3.7 11.7 - - + -
62F LEU* 3.6 26.8 - - + +
63F THR* 3.0 44.1 + - - +
66F VAL* 4.1 18.6 - - + +
340F VAL 5.2 1.7 + - - -
343F GLY* 4.0 22.4 - - - -
344F LEU* 3.2 23.3 + - + +
347F LYS* 3.6 42.2 - - + +
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Residues in contact with ALA 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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8F ASP* 3.1 19.0 + - - +
10F TYR* 1.3 78.6 - - - +
12F GLN* 1.3 58.8 + - - +
13F GLU 3.2 1.0 + - - -
14F LYS* 3.7 19.9 + - - +
15F GLN* 4.6 8.3 + - - +
347F LYS* 4.9 2.8 - - - +
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Residues in contact with GLN 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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8F ASP* 2.9 28.9 + - - +
9F VAL* 3.3 28.5 - - + +
10F TYR 3.1 0.4 - - - -
11F ALA* 1.3 75.2 - - - +
13F GLU* 1.3 67.4 + - + +
15F GLN 5.5 0.2 - - - -
16F ASP* 5.7 1.9 - - - +
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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 VAL* 3.1 23.6 + - + +
10F TYR 2.7 8.1 + - - +
12F GLN* 1.3 89.7 - - + +
14F LYS* 1.3 63.9 + - - +
15F GLN 3.6 1.3 - - - -
16F ASP* 3.6 16.9 + - - +
17F PHE* 3.1 19.9 + - - +
62F LEU* 4.0 10.3 - - + -
65F VAL* 3.8 21.6 - - + +
66F VAL* 4.2 15.8 - - + -
69F ARG* 2.9 55.1 + - - +
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Residues in contact with LYS 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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10F TYR 2.7 12.4 + - - +
11F ALA* 3.7 15.2 + - - +
12F GLN 3.6 0.8 - - - -
13F GLU* 1.3 77.9 - - - +
15F GLN* 1.3 75.4 + - - +
17F PHE* 2.7 24.4 + - - +
18F VAL* 2.8 26.1 + - + +
56F GLY 4.9 2.0 + - - -
57F LYS* 3.9 27.4 + - - +
58F TYR* 4.2 14.8 - - + -
62F LEU* 3.5 27.6 - - + -
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Residues in contact with GLN 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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11F ALA 4.6 6.8 + - - +
12F GLN 5.5 0.4 - - - -
13F GLU 3.6 0.2 - - - -
14F LYS* 1.3 104.5 - - + +
16F ASP* 1.3 57.5 + - - +
18F VAL* 3.9 12.3 - - - +
19F GLN* 3.0 33.0 + - - +
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Residues in contact with ASP 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 GLN 5.7 1.8 - - - +
13F GLU* 3.6 19.9 + - - +
15F GLN* 1.3 78.8 - - - +
17F PHE* 1.3 57.3 + - - +
19F GLN* 3.3 13.6 + - - +
20F HIS* 2.6 49.5 + - + -
69F ARG* 5.4 3.8 + - - -
86F TRP* 6.4 0.2 - - + -
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Residues in contact with PHE 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 3.1 4.5 + - - +
14F LYS* 2.7 17.9 + - + +
16F ASP* 1.3 75.6 - - - +
18F VAL* 1.3 62.4 + - + -
20F HIS* 3.2 13.9 + - - +
58F TYR* 3.8 26.9 - + + -
61F GLY* 4.0 11.4 - - - -
62F LEU* 3.5 28.5 - - + -
65F VAL* 3.9 11.7 - - + -
86F TRP* 3.6 27.1 - - + -
89F GLY* 3.8 12.6 - - - -
90F TRP* 3.0 84.8 + + - -
93F GLU* 4.1 3.8 - - + -
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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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14F LYS* 2.8 33.6 + - + +
15F GLN* 3.9 13.9 - - - +
17F PHE* 1.3 77.0 - - + +
19F GLN* 1.3 63.8 + - - +
21F PHE* 3.1 20.3 + - - +
22F SER* 4.5 0.9 + - - -
54F ILE* 5.3 7.6 - - + -
58F TYR* 3.8 39.0 - - + +
90F TRP* 4.2 7.2 - - - -
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Residues in contact with GLN 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 GLN 3.0 20.1 + - - +
16F ASP* 3.6 16.7 - - - +
17F PHE 3.2 0.2 - - - -
18F VAL* 1.3 77.7 - - - +
20F HIS* 1.3 65.0 + - + +
21F PHE 3.2 1.3 + - - -
22F SER* 3.6 18.6 + - - -
23F GLN 4.7 0.2 + - - -
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Residues in contact with HIS 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 ASP* 2.6 41.8 + - + -
17F PHE 3.2 7.3 + - - +
18F VAL 3.1 1.4 - - - -
19F GLN* 1.3 80.8 - - + +
21F PHE* 1.3 64.3 + - - +
22F SER 3.2 1.8 - - - -
23F GLN* 3.3 15.3 + - + +
24F ILE* 3.2 23.3 + - - +
86F TRP* 3.2 66.1 + + + -
90F TRP* 4.4 0.9 - - - -
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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