Contacts of the helix formed by residues 23 - 34 (chain F) in PDB entry 1S9C
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 23 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22F TYR* 1.3 86.8 - - - +
24F GLU* 1.3 73.2 + - - +
25F LEU* 3.0 16.2 + - - +
26F GLU* 2.6 32.9 + - - +
27F ALA* 3.3 8.0 + - - +
102F ARG 3.7 5.2 - - - -
103F ALA* 3.5 10.3 - - + -
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Residues in contact with GLU 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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194E TRP* 6.0 0.9 - - + -
23F THR* 1.3 80.8 - - - +
25F LEU* 1.3 53.2 + - - +
27F ALA* 3.1 6.5 + - - +
28F ILE* 2.8 42.9 + - + +
49F GLU* 3.9 16.4 - - + -
54F PHE* 3.5 25.6 - - + -
102F ARG* 2.7 56.8 + - - +
103F ALA* 4.0 6.7 - - - +
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Residues in contact with LEU 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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29E MET* 4.9 5.4 - - + -
190E LEU* 3.6 36.8 - - + +
194E TRP* 3.5 37.7 - - + -
23F THR* 3.0 13.4 + - - +
24F GLU* 1.3 76.9 - - - +
26F GLU* 1.3 74.1 + - - +
28F ILE* 3.0 5.3 + - - +
29F MET* 2.8 45.5 + - + +
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Residues in contact with GLU 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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20F TYR* 3.9 15.3 - - + +
21F ALA 5.1 2.0 - - - +
22F TYR* 3.8 23.5 - - + -
23F THR* 2.6 44.4 + - - +
25F LEU* 1.3 93.9 - - - +
27F ALA* 1.3 62.4 + - - +
29F MET* 3.5 18.4 + - + +
30F TYR* 3.0 22.2 + - - +
60F PHE* 3.8 5.9 - - + -
191F SER* 4.6 2.6 + - - -
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Residues in contact with ALA 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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22F TYR* 5.0 2.7 - - + -
23F THR 3.3 9.3 + - - +
24F GLU* 3.1 13.7 + - - +
25F LEU 3.0 0.8 - - - -
26F GLU* 1.3 76.2 - - - +
28F ILE* 1.3 66.2 + - - +
30F TYR* 3.0 7.7 + - - +
31F ALA* 2.9 21.9 + - - +
46F PHE 5.0 0.9 - - - -
54F PHE* 4.4 11.7 - - + -
56F CYS* 4.0 28.9 - - + -
57F LEU 5.9 1.3 + - - -
60F PHE* 4.3 13.4 - - + -
102F ARG 5.1 1.3 - - - +
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Residues in contact with ILE 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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186E ALA 5.0 0.7 - - - +
189E ARG* 4.5 0.7 - - - +
190E LEU* 3.9 17.7 - - + -
194E TRP* 4.1 14.6 - - + -
24F GLU 2.8 26.8 + - - +
25F LEU 3.6 3.1 - - - +
27F ALA* 1.3 71.6 - - - +
29F MET* 1.3 62.8 + - - +
31F ALA* 3.1 1.9 + - - +
32F LEU* 2.9 28.7 + - + +
46F PHE 3.9 8.7 - - - +
47F ILE* 3.3 43.5 - - + +
49F GLU* 3.5 30.7 - - + +
54F PHE* 3.7 18.6 - - + -
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Residues in contact with MET 29 (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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25E LEU* 4.7 6.1 - - + -
29E MET* 3.3 33.7 - - + +
190E LEU* 3.8 23.3 - - + +
25F LEU* 2.8 31.0 + - + +
26F GLU* 3.6 29.2 - - + +
28F ILE* 1.3 77.5 - - - +
30F TYR* 1.3 64.0 + - - +
32F LEU* 3.5 3.3 + - - +
33F GLY* 3.0 19.6 + - - -
187F LEU* 4.9 11.4 - - + +
190F LEU* 4.1 34.1 - - + +
191F SER* 4.3 8.3 + - - +
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Residues in contact with TYR 30 (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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26F GLU 3.0 13.0 + - - +
27F ALA 3.0 10.3 + - - +
29F MET* 1.3 77.2 - - - +
31F ALA* 1.3 61.0 - - - +
33F GLY* 3.1 3.9 + - - -
34F VAL* 2.8 45.9 + - + +
57F LEU* 4.3 13.7 - - + -
59F THR* 2.7 42.1 + - - -
60F PHE* 3.8 32.8 - + + -
62F VAL* 5.2 2.0 - - + +
63F ILE* 3.2 27.8 - - + -
188F TYR* 3.4 35.0 + + - -
191F SER* 3.6 10.7 + - - +
217F LEU 4.4 4.9 + - - -
220F PHE* 5.2 1.0 - - - -
221F GLY* 3.9 11.3 - - - -
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Residues in contact with ALA 31 (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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27F ALA 2.9 9.7 + - - +
28F ILE 3.5 7.4 - - - +
30F TYR* 1.3 77.6 - - - +
32F LEU* 1.3 62.7 + - - +
34F VAL* 3.1 9.3 + - - +
35F GLY 3.2 0.7 + - - -
36F ALA* 3.1 29.1 + - + +
46F PHE* 3.6 30.1 - - + +
47F ILE* 5.1 1.3 - - + -
57F LEU* 3.8 28.9 - - + +
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Residues in contact with LEU 32 (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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183E ASN* 4.5 14.1 - - + +
186E ALA* 3.6 27.6 - - + +
187E LEU* 3.9 21.5 - - + +
190E LEU* 4.1 16.2 - - + -
28F ILE* 2.9 24.3 + - + +
29F MET* 3.8 3.8 - - - +
31F ALA* 1.3 74.4 - - - +
33F GLY* 1.3 65.4 + - - +
34F VAL 2.9 1.4 + - - -
35F GLY* 3.0 14.4 + - - -
36F ALA 3.6 19.0 - - - +
47F ILE* 4.1 22.9 - - + -
184F GLN* 3.9 5.2 + - - -
187F LEU* 3.9 15.2 - - + +
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Residues in contact with GLY 33 (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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29F MET 3.0 12.2 + - - -
30F TYR* 3.5 4.5 - - - -
32F LEU* 1.3 80.2 - - - +
34F VAL* 1.3 57.8 + - - +
35F GLY 3.5 0.4 - - - -
184F GLN* 2.9 19.3 + - - -
187F LEU* 3.6 23.7 - - - +
188F TYR* 3.8 19.0 - - - +
218F CYS* 3.4 15.6 - - - -
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Residues in contact with VAL 34 (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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30F TYR* 2.8 31.2 + - + +
31F ALA 3.1 10.5 + - - +
32F LEU 3.0 0.4 - - - -
33F GLY* 1.3 79.7 - - - +
35F GLY* 1.3 48.4 + - - +
57F LEU* 3.8 25.8 - - + -
59F THR* 5.5 0.2 - - - +
188F TYR* 4.2 11.0 - - + -
218F CYS* 3.6 10.5 - - - +
221F GLY* 3.3 36.1 - - - +
222F PHE* 3.2 20.2 - - - -
225F ARG* 2.4 33.7 + - - +
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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