Contacts of the helix formed by residues 15 - 26 (chain F) in PDB entry 4K81
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 GLY 15 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13F GLY* 3.3 5.0 - - - -
14F VAL* 1.3 79.9 - - - +
16F LYS* 1.3 67.5 + - - +
17F SER 3.2 3.1 - - - -
18F ALA* 3.7 13.7 - - - -
19F LEU* 2.8 32.9 + - - +
81F VAL* 5.1 0.2 - - - -
116F ASN* 3.6 10.3 - - - -
117F LYS* 5.3 2.0 - - - -
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Residues in contact with LYS 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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8F VAL* 3.7 26.5 - - + +
9F VAL* 3.3 35.0 - - - +
10F GLY 2.9 13.9 + - - +
11F ALA 2.8 30.9 + - - -
12F VAL* 4.6 1.4 - - - +
13F GLY 4.7 2.8 - - - +
14F VAL* 3.7 13.1 - - + +
15F GLY* 1.3 76.5 - - - +
17F SER* 1.3 53.5 + - - +
19F LEU* 3.9 6.1 - - - +
20F THR* 2.8 35.9 + - - -
57F ASP* 3.4 12.6 - - - +
58F THR* 3.3 23.8 - - - +
59F ALA 4.2 0.4 - - - -
60F GLY* 3.9 10.6 - - - +
81F VAL* 4.3 3.1 - - + +
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Residues in contact with SER 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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15F GLY* 3.2 0.6 - - - -
16F LYS* 1.3 75.7 - - - +
18F ALA* 1.3 60.6 + - - +
20F THR* 4.4 1.6 - - - +
21F ILE* 2.8 47.1 + - - +
29F VAL* 6.0 0.7 - - - -
33F ASP 4.9 4.2 + - - -
35F THR* 2.7 21.5 + - - -
38F ASP* 5.3 0.2 + - - -
40F TYR* 5.5 0.9 - - - -
57F ASP* 2.4 30.6 + - - -
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Residues in contact with ALA 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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15F GLY* 3.2 17.5 + - - +
17F SER* 1.3 78.6 - - - +
19F LEU* 1.3 56.6 + - - +
21F ILE* 4.0 3.7 - - - +
22F GLN* 2.9 32.2 + - - +
27F HIS 4.9 1.2 - - - +
28F PHE* 4.2 19.8 - - + -
29F VAL* 4.7 15.2 + - + +
116F ASN* 5.3 0.4 - - - +
146F ALA* 3.5 18.8 - - + +
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Residues in contact with LEU 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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8F VAL* 5.6 0.7 - - + -
15F GLY 2.8 21.4 + - - +
16F LYS* 3.9 3.4 - - - +
18F ALA* 1.3 73.5 - - - +
20F THR* 1.3 63.9 + - - +
22F GLN* 3.5 4.2 - - + +
23F LEU* 3.0 22.9 + - - +
79F LEU* 5.0 11.0 - - + -
81F VAL* 4.0 26.5 - - + -
114F VAL* 4.1 4.7 - - + -
116F ASN* 3.4 42.2 - - + +
144F THR* 3.5 25.6 - - + +
145F SER 4.7 0.9 - - - -
146F ALA* 3.9 13.9 - - + +
152F VAL* 4.8 12.1 - - - -
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Residues in contact with THR 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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8F VAL* 3.6 21.0 - - - +
16F LYS 2.8 22.6 + - - -
17F SER* 3.8 5.4 - - - -
19F LEU* 1.3 76.3 - - - +
21F ILE* 1.3 59.5 + - - +
23F LEU* 3.1 7.0 + - - +
24F ILE* 2.9 38.5 + - + +
40F TYR* 3.5 40.2 - - + -
55F ILE* 3.8 21.3 - - + +
57F ASP* 4.4 5.1 - - + +
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Residues in contact with ILE 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 SER* 2.8 30.5 + - - +
18F ALA 4.1 1.8 - - - +
20F THR* 1.3 68.5 - - - +
22F GLN* 1.3 60.0 + - - +
24F ILE* 3.1 4.4 + - - +
25F GLN* 2.6 61.6 + - - +
26F ASN 3.5 0.2 + - - -
27F HIS* 3.7 24.0 - - + +
29F VAL* 3.8 25.1 - - + +
40F TYR* 3.7 31.0 - - + +
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Residues in contact with GLN 22 (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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18F ALA 2.9 20.0 + - - +
19F LEU* 3.5 8.1 - - + +
21F ILE* 1.3 77.0 - - - +
23F LEU* 1.3 57.1 + - - +
26F ASN* 3.0 24.5 + - - +
27F HIS* 3.0 32.1 + - - +
28F PHE* 3.5 19.8 - - - +
146F ALA* 2.5 35.2 + - + +
147F LYS 4.3 4.4 + - - -
149F ARG* 2.5 59.5 + - + +
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Residues in contact with LEU 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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6F LEU* 6.2 0.7 - - + -
19F LEU 3.0 14.8 + - - +
20F THR* 3.1 9.2 + - - +
22F GLN* 1.3 76.9 - - - +
24F ILE* 1.3 64.1 + - + +
26F ASN* 4.8 0.5 + - - +
42F LYS* 2.7 41.7 + - + +
44F VAL* 6.3 2.5 - - + -
53F LEU* 4.9 12.8 - - + -
55F ILE* 3.7 29.8 - - + -
149F ARG* 4.3 12.2 + - - +
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Residues in contact with ILE 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 THR* 2.9 19.8 + - + +
21F ILE* 4.1 0.4 - - - +
23F LEU* 1.3 85.4 - - + +
25F GLN* 1.3 72.4 + - + +
26F ASN 3.8 0.2 - - - -
40F TYR* 3.9 34.1 - - + -
41F ARG 3.9 17.0 - - - +
42F LYS* 4.0 32.4 - - + +
55F ILE* 3.9 26.2 - - + -
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Residues in contact with GLN 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F ILE* 2.6 32.4 + - - +
24F ILE* 1.3 87.2 - - + +
26F ASN* 1.3 68.6 + - - +
27F HIS* 3.1 33.9 + - + +
40F TYR* 4.2 23.0 - - - -
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Residues in contact with ASN 26 (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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21F ILE 3.5 0.8 + - - -
22F GLN* 3.0 21.0 + - - +
23F LEU 4.7 0.8 + - - +
24F ILE 3.8 0.4 - - - -
25F GLN* 1.3 80.6 - - - +
27F HIS* 1.3 60.4 + - - +
149F ARG* 3.2 37.1 + - - +
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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