Contacts of the helix formed by residues 21 - 32 (chain B) in PDB entry 1F9N
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 THR 21 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B ILE* 3.2 20.4 - - - +
20B GLU* 1.3 89.9 - - + +
22B GLN* 1.3 58.9 + - - +
23B ASP* 2.9 15.3 + - - +
24B GLU* 2.9 51.0 + - - +
25B LEU 3.6 0.7 + - - -
62B TYR* 3.7 3.8 - - - -
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Residues in contact with GLN 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B THR* 1.3 72.5 - - - +
23B ASP* 1.3 57.5 + - - +
25B LEU* 4.3 3.6 - - - -
26B VAL* 3.2 22.7 + - - +
38B GLN* 4.3 9.5 - - - +
41B VAL* 4.2 7.0 - - + +
42B SER* 3.5 36.3 + - - +
45B ILE* 3.4 28.4 - - + +
62B TYR* 3.5 20.0 + - - +
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Residues in contact with ASP 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B THR* 2.9 9.6 - - - +
22B GLN* 1.3 79.1 - - - +
24B GLU* 1.3 67.0 + - + +
25B LEU 3.0 1.8 - - - -
26B VAL* 3.0 19.9 + - - +
27B ASP* 3.0 17.0 + - - +
38B GLN* 5.5 4.1 - - - +
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLU 3.8 18.2 - - - +
19B ILE* 4.2 13.1 - - + +
20B GLU* 3.9 9.4 + - - +
21B THR* 2.9 49.5 + - - +
23B ASP* 1.3 76.4 - - + +
25B LEU* 1.3 61.0 + - - +
27B ASP* 3.6 7.3 + - - +
28B MET* 3.1 23.6 + - - +
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ILE* 4.3 24.9 - - + -
13B ILE* 3.8 29.8 - - + -
14B ILE* 3.8 19.1 - - + -
19B ILE* 3.8 17.9 - - + +
21B THR 3.6 6.2 + - - +
22B GLN* 4.3 6.5 - - - +
23B ASP 3.0 0.4 - - - -
24B GLU* 1.3 77.3 - - - +
26B VAL* 1.3 59.1 + - - +
28B MET* 3.0 6.9 + - - +
29B LEU* 2.9 34.6 + - + +
41B VAL* 3.6 24.2 - - + -
45B ILE* 4.1 20.6 - - + -
50B LEU* 4.9 4.3 - - + -
62B TYR* 5.1 3.1 - - + -
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Residues in contact with VAL 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B GLN 3.2 20.9 - - - +
23B ASP* 3.0 12.5 + - - +
25B LEU* 1.3 77.2 - - - +
27B ASP* 1.3 57.7 + - - +
28B MET 3.1 0.2 + - - -
29B LEU* 3.1 5.2 + - - +
30B LYS* 2.9 59.9 + - + +
36B VAL* 3.8 11.2 - - + -
37B THR 4.9 5.8 - - - -
38B GLN* 4.5 17.5 - - + +
41B VAL* 3.4 29.4 - - + -
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Residues in contact with ASP 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ASP* 3.0 20.0 + - - +
24B GLU* 4.0 7.9 - - - +
26B VAL* 1.3 77.3 - - - +
28B MET* 1.3 60.6 + - - +
30B LYS* 4.2 7.9 - - - +
31B GLN* 3.1 26.0 + - - +
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Residues in contact with MET 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ILE* 3.5 33.2 - - + -
17B ASN* 4.0 26.0 - - - +
19B ILE* 5.2 4.5 - - + -
24B GLU 3.1 14.3 + - - +
25B LEU* 3.0 14.7 + - - +
26B VAL 3.0 0.8 - - - -
27B ASP* 1.3 75.9 - - - +
29B LEU* 1.3 62.9 + - - +
31B GLN* 3.2 11.3 + - + +
32B ASP* 2.5 46.5 + - - +
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ARG* 4.0 35.0 - - + +
9B LYS* 4.3 13.0 - - + -
10B ILE* 4.2 23.3 - - + -
13B ILE* 3.6 22.7 - - + -
25B LEU* 2.9 22.7 + - + +
26B VAL 3.7 4.9 - - - +
28B MET* 1.3 76.5 - - - +
30B LYS* 1.3 58.0 + - - +
32B ASP* 2.8 24.6 + - - +
34B TYR* 3.2 28.7 + - + +
36B VAL* 4.4 7.2 - - + -
41B VAL* 4.1 24.0 - - + -
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Residues in contact with LYS 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B VAL* 2.9 38.8 + - + +
27B ASP* 4.2 7.0 - - - +
29B LEU* 1.3 75.7 - - - +
31B GLN* 1.3 63.3 + - - +
33B GLY* 3.1 12.5 + - - -
34B TYR 3.0 23.5 + - - +
35B LYS* 5.1 0.9 - - - +
36B VAL* 3.2 33.4 + - + +
38B GLN* 4.9 11.5 + - - +
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Residues in contact with GLN 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ASP* 3.1 24.0 + - - +
28B MET* 3.2 15.5 + - + +
30B LYS* 1.3 77.4 - - - +
32B ASP* 1.3 61.7 + - - +
33B GLY 3.3 1.5 + - - -
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Residues in contact with ASP 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LYS* 4.4 22.8 + - + +
13B ILE* 4.8 9.2 - - - +
28B MET* 2.5 39.6 - - - +
29B LEU* 2.8 14.5 + - - +
31B GLN* 1.3 80.2 - - - +
33B GLY* 1.3 59.0 + - - +
34B TYR* 3.5 16.4 - - + -
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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