Contacts of the helix formed by residues 17 - 28 (chain F) in PDB entry 3KZ1
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 17 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15F ALA 3.2 4.6 + - - -
16F CYS* 1.3 78.3 - - - +
18F LYS* 1.3 61.5 + - - +
20F CYS* 4.3 0.7 - - - +
21F LEU* 3.3 19.6 + - - +
117F ASN* 3.3 17.6 + - - -
118F LYS* 4.4 0.4 - - - -
161F ALA* 5.5 0.5 - - - +
538F GSP 3.1 43.2 + - - -
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Residues in contact with LYS 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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10F ILE* 3.6 31.9 - - + +
11F VAL* 3.3 15.5 - - - +
12F GLY* 2.8 46.3 + - - +
13F ASP 3.1 10.5 + - - -
16F CYS* 3.7 13.2 - - - -
17F GLY* 1.3 72.8 - - - +
19F THR* 1.3 65.7 + - - +
21F LEU* 3.8 0.2 - - - +
22F LEU* 3.4 19.4 + - - +
59F ASP* 4.0 8.7 - - - +
60F THR* 3.5 27.8 - - - -
62F GLY* 3.7 4.1 - - - +
83F CYS* 4.4 3.6 - - + -
117F ASN* 4.7 0.4 - - - +
538F GSP 2.6 41.4 + - - +
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Residues in contact with THR 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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18F LYS* 1.3 72.9 - - - +
20F CYS* 1.3 63.9 + - - +
22F LEU* 3.2 5.9 + - - +
23F ILE* 3.1 33.6 + - + +
31F PRO* 5.7 2.2 - - + -
35F VAL 5.1 5.6 - - - +
37F THR* 2.4 15.3 + - + +
40F GLU* 6.1 0.2 - - + -
42F TYR* 4.2 15.0 - - - +
59F ASP* 2.9 18.3 + - - +
538F GSP 2.5 21.9 + - - +
550F MG 2.0 33.5 - - - -
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Residues in contact with CYS 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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17F GLY 4.5 0.7 - - - +
19F THR* 1.3 72.2 - - - +
21F LEU* 1.3 56.9 + - - +
23F ILE* 3.3 1.3 + - - +
24F VAL* 3.0 35.0 + - - +
30F PHE* 3.9 20.2 - - + -
31F PRO* 4.0 26.5 - - + -
33F VAL 6.1 0.4 - - - -
161F ALA* 4.2 2.9 - - + -
538F GSP 2.8 74.6 + - + +
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Residues in contact with LEU 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ILE* 4.0 21.1 - - + -
17F GLY 3.3 16.6 + - - +
18F LYS 3.8 2.9 - - - +
19F THR 3.3 0.8 - - - -
20F CYS* 1.3 77.2 - - - +
22F LEU* 1.3 60.9 + - - +
24F VAL* 4.0 1.9 + - - +
25F PHE* 3.4 21.0 + - - +
81F LEU* 4.8 5.2 - - + -
83F CYS* 4.4 1.6 - - - -
115F VAL* 4.4 9.0 - - + -
117F ASN* 3.8 23.1 - - - +
159F CYS* 3.7 24.5 - - - -
161F ALA* 4.2 11.6 - - + +
167F VAL* 3.9 27.7 - - + +
170F VAL* 4.9 3.1 - - + -
171F PHE* 4.0 18.3 - - + -
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Residues in contact with LEU 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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8F LEU* 5.2 3.4 - - + -
10F ILE* 3.4 48.9 - - + -
18F LYS 3.4 5.8 + - - +
19F THR 3.2 6.8 + - - +
21F LEU* 1.3 78.3 - - - +
23F ILE* 1.3 59.1 + - - +
25F PHE* 3.4 4.0 + - - +
26F SER* 2.8 34.7 + - - -
42F TYR* 4.4 15.7 - - + -
57F LEU* 4.0 24.1 - - + +
58F TRP 4.7 0.4 - - - -
59F ASP* 3.6 32.5 - - + +
171F PHE* 4.0 24.0 - - + -
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Residues in contact with ILE 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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719B THR* 6.6 0.4 - - + -
19F THR* 3.1 22.6 + - + +
20F CYS 3.3 0.9 + - - +
22F LEU* 1.3 73.4 - - - +
24F VAL* 1.3 59.9 + - - +
26F SER* 3.8 5.4 - - - +
27F LYS* 2.6 55.4 + - + -
28F ASP 3.1 4.0 + - - -
29F GLN* 3.2 18.6 - - + +
31F PRO* 3.5 34.3 - - + -
42F TYR* 4.3 31.0 - - + +
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Residues in contact with VAL 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 CYS 3.0 20.0 + - - +
21F LEU 4.2 2.7 - - - +
23F ILE* 1.3 77.2 - - - +
25F PHE* 1.3 58.9 + - - +
28F ASP* 2.7 30.4 + - - +
29F GLN 3.5 17.9 - - - +
30F PHE* 3.7 19.7 - - + -
161F ALA* 3.4 27.1 - - + +
164F LYS* 3.6 30.0 - - + +
167F VAL* 4.1 22.9 - - + -
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Residues in contact with PHE 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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21F LEU 3.4 8.3 + - - +
22F LEU 3.4 3.3 + - - +
23F ILE 3.2 0.6 - - - -
24F VAL* 1.3 84.4 - - - +
26F SER* 1.3 61.6 + - - +
28F ASP* 4.4 2.9 + - - +
44F ALA* 3.9 26.1 - - + +
45F ASP 4.8 4.3 - - - -
46F ILE* 4.0 24.0 - - + -
55F LEU* 3.9 9.2 - - + -
57F LEU* 4.5 5.6 - - + -
167F VAL* 4.2 10.5 - - + -
168F ARG* 4.5 21.1 - - + -
171F PHE* 3.5 68.6 - + + -
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Residues in contact with SER 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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22F LEU 2.8 29.0 + - - -
23F ILE* 3.8 4.5 - - - -
25F PHE* 1.3 76.5 - - - +
27F LYS* 1.3 67.3 + - - +
42F TYR* 4.3 15.5 - - - +
43F VAL 3.6 23.4 - - - +
44F ALA* 4.2 8.2 - - - +
57F LEU* 4.0 14.1 - - - -
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Residues in contact with LYS 27 (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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23F ILE* 2.6 40.7 + - + +
26F SER* 1.3 80.7 - - - +
28F ASP* 1.3 61.4 + - - +
29F GLN* 3.2 37.6 + - + +
42F TYR* 4.9 20.8 - - - -
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Residues in contact with ASP 28 (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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23F ILE 3.1 0.8 + - - -
24F VAL* 2.7 30.1 + - - +
25F PHE 5.2 2.9 - - - +
26F SER 3.6 1.0 - - - -
27F LYS* 1.3 74.8 - - - +
29F GLN* 1.3 57.8 + - - +
164F LYS* 3.1 39.6 + - - +
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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