Contacts of the helix formed by residues 23 - 34 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C TYR* 1.3 85.5 - - - +
24C GLU* 1.3 74.9 + - - +
25C LEU* 3.0 16.5 + - - +
26C GLU* 2.6 32.7 + - - +
27C ALA* 3.3 8.0 + - - +
102C ARG 3.7 5.6 - - - -
103C ALA* 3.5 10.1 - - + -
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Residues in contact with GLU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C THR* 1.3 81.2 - - - +
25C LEU* 1.3 57.3 + - - +
27C ALA* 3.2 6.5 + - - +
28C ILE* 2.8 38.6 + - + +
49C GLU* 3.9 16.2 - - + -
54C PHE* 3.6 24.9 - - + -
102C ARG* 2.7 56.1 + - - +
103C ALA* 4.0 5.4 - - - +
194D TRP* 6.0 1.6 - - + -
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Residues in contact with LEU 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C THR* 3.0 13.5 + - - +
24C GLU* 1.3 78.8 - - - +
26C GLU* 1.3 80.8 + - - +
28C ILE* 3.1 3.5 + - - +
29C MET* 2.8 38.4 + - + +
29D MET* 4.8 5.6 - - + -
190D LEU* 3.4 50.7 - - + +
194D TRP* 3.5 27.6 - - + -
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Residues in contact with GLU 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C TYR* 4.4 9.9 - - + +
21C ALA 5.1 2.2 - - - +
22C TYR* 3.6 21.7 - - + -
23C THR* 2.6 46.2 + - - +
25C LEU* 1.3 94.8 - - - +
27C ALA* 1.3 62.2 + - - +
29C MET* 3.5 18.1 + - + +
30C TYR* 3.1 21.3 + - - +
60C PHE* 3.8 11.6 - - + -
191C SER* 4.7 2.3 + - - -
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Residues in contact with ALA 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C TYR* 4.9 4.5 - - + -
23C THR 3.3 9.8 + - - +
24C GLU* 3.2 13.0 + - - +
25C LEU 3.0 0.4 - - - -
26C GLU* 1.3 76.8 - - - +
28C ILE* 1.3 65.9 + - - +
30C TYR* 2.9 8.2 + - - +
31C ALA* 2.9 21.6 + - - +
46C PHE 5.1 0.7 - - - -
54C PHE* 4.4 12.3 - - + -
56C CYS* 4.0 28.0 - - + -
57C LEU 5.7 1.1 + - - +
60C PHE* 4.2 11.6 - - - -
102C ARG 5.0 2.0 - - - +
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Residues in contact with ILE 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C GLU* 2.8 28.9 + - + +
25C LEU 3.6 3.1 - - - +
27C ALA* 1.3 71.6 - - - +
29C MET* 1.3 64.1 + - - +
31C ALA* 3.1 1.4 + - - +
32C LEU* 2.9 29.8 + - + +
46C PHE 3.9 8.7 - - - +
47C ILE* 3.3 43.7 - - + +
49C GLU* 3.5 31.0 - - + +
54C PHE* 3.8 18.8 - - + -
186D ALA 4.9 1.8 - - - +
189D ARG* 4.6 1.1 - - - +
190D LEU* 4.0 16.2 - - + -
194D TRP* 4.5 10.8 - - + -
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Residues in contact with MET 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C LEU* 2.8 29.9 + - + +
26C GLU* 3.6 29.4 - - + +
28C ILE* 1.3 77.4 - - - +
30C TYR* 1.3 61.8 + - - +
32C LEU* 3.5 3.0 + - - +
33C GLY* 3.0 19.9 + - - -
187C LEU* 4.9 11.6 - - + +
188C TYR* 6.0 0.2 - - - -
190C LEU* 4.2 33.4 - - + +
191C SER* 4.3 8.0 + - - +
25D LEU* 4.8 5.8 - - + -
29D MET* 3.3 37.2 - - + +
190D LEU* 3.7 21.9 - - + +
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Residues in contact with TYR 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C GLU 3.1 12.8 + - - +
27C ALA 2.9 11.0 + - - +
29C MET* 1.3 76.9 - - - +
31C ALA* 1.3 67.8 + - - +
33C GLY* 3.1 3.2 + - - -
34C VAL* 2.9 48.7 + - + +
57C LEU* 4.4 11.7 - - + -
59C THR* 2.7 42.5 + - - -
60C PHE* 3.7 32.3 - + + -
62C VAL* 5.2 1.4 - - + +
63C ILE* 3.2 30.7 - - + -
188C TYR* 3.4 31.2 + + - -
191C SER* 3.6 10.5 - - - +
217C LEU 4.4 4.7 + - - -
220C PHE* 5.1 1.4 - - - -
221C GLY* 4.0 3.8 - - - -
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Residues in contact with ALA 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ALA 2.9 10.5 + - - +
28C ILE 3.5 7.6 - - - +
30C TYR* 1.3 78.1 - - - +
32C LEU* 1.3 62.1 + - - +
34C VAL* 3.1 10.1 + - - +
35C GLY 3.2 0.7 + - - -
36C ALA* 3.1 28.1 + - + -
46C PHE* 3.6 30.1 - - + +
47C ILE* 5.1 1.6 - - + -
57C LEU* 3.9 29.6 - - + +
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Residues in contact with LEU 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ILE* 2.9 26.6 + - + +
29C MET* 3.9 3.6 - - - +
31C ALA* 1.3 74.7 - - - +
33C GLY* 1.3 61.1 + - - +
34C VAL 2.9 5.9 + - - -
35C GLY* 3.0 14.6 + - - -
36C ALA 3.7 18.9 - - - +
47C ILE* 4.1 23.1 - - + -
184C GLN* 4.0 5.0 + - - -
187C LEU* 3.8 15.8 - - + +
183D ASN* 4.3 17.0 - - + +
186D ALA* 3.8 24.9 - - + +
187D LEU* 4.0 27.1 - - + +
190D LEU* 4.3 8.5 - - + -
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Residues in contact with GLY 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C MET 3.0 12.2 + - - -
30C TYR 3.5 4.7 - - - -
32C LEU* 1.3 77.4 - - - +
34C VAL* 1.3 57.6 + - - +
35C GLY 3.5 0.4 - - - -
184C GLN* 3.1 16.6 + - - -
187C LEU* 3.5 23.9 - - - +
188C TYR* 3.6 20.6 - - - +
218C CYS* 3.3 16.5 - - - -
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Residues in contact with VAL 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C TYR* 2.9 32.0 + - + +
31C ALA* 3.1 11.0 + - - +
32C LEU 2.9 0.6 + - - -
33C GLY* 1.3 77.2 - - - +
35C GLY* 1.3 50.8 + - - +
57C LEU* 3.7 25.4 - - + -
59C THR* 5.5 0.4 - - - +
188C TYR* 4.2 11.7 - - + -
218C CYS* 3.7 10.1 - - - +
221C GLY* 3.3 35.0 - - - +
222C PHE* 3.2 20.2 - - - -
225C ARG* 2.6 32.4 + - - +
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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