Contacts of the helix formed by residues 23 - 34 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22I TYR* 1.3 86.9 - - - +
24I GLU* 1.3 75.1 + - - +
25I LEU* 3.0 15.6 + - - +
26I GLU* 2.6 31.7 + - - +
27I ALA* 3.3 7.6 + - - +
102I ARG 4.0 6.1 - - - -
103I ALA* 3.9 8.1 - - + -
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Residues in contact with GLU 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I THR* 1.3 80.7 - - - +
25I LEU* 1.3 52.1 + - - +
27I ALA* 3.1 6.7 + - - +
28I ILE* 2.7 42.2 + - + +
49I GLU* 3.9 28.0 - - + -
54I PHE* 3.6 21.5 - - + -
102I ARG* 3.1 45.4 + - - +
103I ALA* 4.3 5.7 - - - +
194J TRP* 5.9 1.8 - - + -
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Residues in contact with LEU 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I THR* 3.0 13.0 + - - +
24I GLU* 1.3 79.3 - - - +
26I GLU* 1.3 80.4 + - - +
27I ALA 3.0 0.3 + - - -
28I ILE* 3.1 2.7 + - - +
29I MET* 2.8 37.7 + - + +
29J MET* 4.6 6.7 - - + -
190J LEU* 3.4 55.6 - - + +
194J TRP* 3.7 24.7 - - + -
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Residues in contact with GLU 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I TYR* 4.2 16.8 - - + +
21I ALA 5.1 1.8 - - - +
22I TYR* 3.9 24.5 - - + -
23I THR* 2.6 43.2 + - - +
25I LEU* 1.3 93.8 - - - +
27I ALA* 1.3 61.6 + - - +
29I MET* 3.7 17.4 - - + +
30I TYR* 3.1 21.7 + - - +
60I PHE* 3.7 8.5 - - + -
191I SER* 4.7 2.3 + - - -
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Residues in contact with ALA 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I TYR* 5.0 3.4 - - + -
23I THR 3.3 9.4 + - - +
24I GLU* 3.1 12.7 + - - +
25I LEU 3.0 0.8 + - - -
26I GLU* 1.3 77.1 - - - +
28I ILE* 1.3 66.6 + - - +
30I TYR* 3.0 7.1 + - - +
31I ALA* 2.9 21.5 + - - +
46I PHE 5.0 0.7 - - - -
54I PHE* 4.4 12.3 - - + -
56I CYS* 4.1 28.3 - - + -
57I LEU 5.7 1.1 + - - +
60I PHE* 4.2 13.4 - - + -
102I ARG 5.3 1.3 - - - +
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Residues in contact with ILE 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I GLU 2.7 28.8 + - - +
25I LEU 3.7 3.4 - - - +
27I ALA* 1.3 72.1 - - - +
29I MET* 1.3 57.6 + - - +
31I ALA* 3.2 2.1 + - - +
32I LEU* 2.9 35.1 + - + +
46I PHE 3.8 8.5 - - - +
47I ILE* 3.2 45.5 - - + +
49I GLU* 3.6 28.3 - - + +
54I PHE* 3.7 18.6 - - + -
186J ALA 5.0 0.9 - - - +
189J ARG* 4.5 0.4 - - - +
190J LEU* 4.0 16.6 - - + -
194J TRP* 4.2 12.6 - - + -
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Residues in contact with MET 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I LEU* 2.8 24.9 + - + +
26I GLU* 3.7 28.3 - - + +
28I ILE* 1.3 76.3 - - - +
30I TYR* 1.3 62.5 + - - +
32I LEU* 3.5 3.4 + - - +
33I GLY* 3.0 19.8 + - - -
187I LEU* 4.7 16.0 - - + +
188I TYR* 5.9 0.2 - - - -
190I LEU* 4.0 32.8 - - + +
191I SER* 4.4 7.0 + - - +
25J LEU* 4.7 6.5 - - + -
29J MET* 3.2 41.7 - - + +
190J LEU* 3.7 20.1 - - + +
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Residues in contact with TYR 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26I GLU 3.1 13.0 + - - +
27I ALA 3.0 10.1 + - - +
29I MET* 1.3 75.4 - - - +
31I ALA* 1.3 71.4 + - - +
33I GLY* 3.0 4.3 + - - -
34I VAL* 2.8 49.2 + - + +
57I LEU* 4.3 11.2 - - + -
59I THR* 2.7 42.5 + - - -
60I PHE* 3.7 31.2 - + + -
62I VAL* 5.2 1.7 - - + +
63I ILE* 3.2 30.1 - - + -
188I TYR* 3.4 33.2 + + - -
191I SER* 3.7 10.9 + - - +
217I LEU 4.4 4.3 + - - -
220I PHE* 5.1 1.4 - - - -
221I GLY* 3.9 4.3 - - - -
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Residues in contact with ALA 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I ALA 2.9 10.5 + - - +
28I ILE 3.2 7.8 + - - +
30I TYR* 1.3 77.0 - - - +
32I LEU* 1.3 62.5 + - - +
34I VAL* 3.0 11.7 + - - +
35I GLY 3.2 0.5 + - - -
36I ALA* 3.1 30.7 + - + -
46I PHE* 3.5 25.6 - - + +
47I ILE* 5.1 1.3 - - + -
57I LEU* 3.9 28.5 - - + +
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Residues in contact with LEU 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I ILE* 2.9 24.5 + - + +
29I MET 3.8 4.3 - - - +
31I ALA* 1.3 74.7 - - - +
33I GLY* 1.3 61.2 + - - +
34I VAL 2.9 5.4 + - - -
35I GLY* 3.1 13.2 + - - -
36I ALA 3.6 19.8 - - - +
47I ILE* 4.2 21.3 - - + -
184I GLN* 3.7 5.9 + - - -
187I LEU* 3.7 16.2 - - + +
183J ASN* 4.3 15.7 - - + +
186J ALA* 3.6 31.6 - - + +
187J LEU* 4.0 22.0 - - + +
190J LEU* 4.2 11.2 - - + -
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Residues in contact with GLY 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I MET 3.0 7.8 + - - -
30I TYR 3.0 8.1 + - - -
32I LEU* 1.3 78.5 - - - +
34I VAL* 1.3 55.6 + - - +
184I GLN* 2.9 18.9 + - - -
187I LEU* 3.5 23.6 - - - +
188I TYR* 3.8 20.0 - - - +
218I CYS* 3.2 17.0 - - - -
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Residues in contact with VAL 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I TYR* 2.8 32.2 + - + +
31I ALA 3.4 10.8 - - - +
32I LEU 2.9 0.6 - - - -
33I GLY* 1.3 79.7 - - - +
35I GLY* 1.3 49.3 + - - +
57I LEU* 3.7 26.5 - - + -
59I THR* 5.5 0.2 - - - +
188I TYR* 4.3 11.7 - - + -
218I CYS* 3.6 9.6 - - - +
221I GLY* 3.2 36.3 - - - +
222I PHE* 3.2 19.7 - - - -
225I ARG* 2.5 32.6 + - - +
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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