Contacts of the helix formed by residues 23 - 34 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22G TYR* 1.3 86.0 - - - +
24G GLU* 1.3 73.5 + - - +
25G LEU* 3.0 15.8 + - - +
26G GLU* 2.7 31.5 + - - +
27G ALA* 3.4 7.6 + - - +
102G ARG 3.9 5.6 - - - -
103G ALA* 3.8 10.1 - - + -
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Residues in contact with GLU 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G THR* 1.3 82.1 - - - +
25G LEU* 1.3 52.4 + - - +
27G ALA* 3.2 7.1 + - - +
28G ILE* 2.8 42.6 + - + +
49G GLU* 3.8 23.8 - - + -
54G PHE* 3.6 24.2 - - + -
102G ARG* 3.0 48.5 + - - +
103G ALA* 4.2 6.2 - - - +
194H TRP* 5.9 1.6 - - + -
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Residues in contact with LEU 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G THR* 3.0 12.6 + - - +
24G GLU* 1.3 79.8 - - - +
26G GLU* 1.3 82.4 + - - +
27G ALA 3.0 0.9 + - - -
28G ILE* 3.0 2.9 + - - +
29G MET* 2.9 38.3 + - + +
29H MET* 4.7 5.8 - - + -
190H LEU* 3.3 52.5 - - + +
194H TRP* 3.4 28.9 - - + -
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Residues in contact with GLU 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G TYR* 3.8 24.2 - - + +
21G ALA 5.1 1.3 - - - +
22G TYR* 3.9 15.9 - - + -
23G THR* 2.7 43.2 + - - +
25G LEU* 1.3 92.6 - - - +
27G ALA* 1.3 61.6 + - - +
29G MET* 3.5 19.0 + - + +
30G TYR* 3.1 21.8 + - - +
60G PHE* 3.8 5.6 - - + -
191G SER* 4.7 2.4 + - - -
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Residues in contact with ALA 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G TYR* 4.9 5.8 - - + -
23G THR 3.4 9.4 + - - +
24G GLU* 3.2 13.4 + - - +
25G LEU 3.0 0.6 - - - -
26G GLU* 1.3 76.0 - - - +
28G ILE* 1.3 66.2 + - - +
30G TYR* 3.0 7.1 + - - +
31G ALA* 2.9 21.2 + - - +
46G PHE 5.0 0.7 - - - -
54G PHE* 4.4 11.9 - - + -
56G CYS* 4.0 27.6 - - + -
57G LEU 5.8 1.6 + - - +
60G PHE* 4.3 11.8 - - - -
102G ARG 5.2 1.1 - - - +
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Residues in contact with ILE 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G GLU 2.8 27.3 + - - +
25G LEU 3.6 2.5 - - - +
27G ALA* 1.3 71.4 - - - +
29G MET* 1.3 58.1 + - - +
31G ALA* 3.1 2.4 + - - +
32G LEU* 2.9 34.9 + - + +
46G PHE 3.9 9.0 - - - +
47G ILE* 3.2 46.4 - - + +
49G GLU* 3.5 29.2 - - + +
54G PHE* 3.7 18.2 - - + -
186H ALA 4.9 1.3 - - - +
189H ARG* 4.4 0.9 - - - +
190H LEU* 3.9 16.4 - - + -
194H TRP* 4.2 13.9 - - + -
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Residues in contact with MET 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G LEU* 2.9 34.1 + - + +
26G GLU* 3.6 20.6 - - + +
28G ILE* 1.3 76.3 - - - +
30G TYR* 1.3 62.6 + - - +
32G LEU* 3.6 3.1 + - - +
33G GLY* 3.1 20.1 + - - -
187G LEU* 4.8 11.1 - - + +
188G TYR* 5.9 0.3 - - - -
190G LEU* 4.0 36.3 - - + +
191G SER* 4.3 7.8 + - - +
25H LEU* 4.8 4.5 - - + -
29H MET* 3.3 40.6 - - + +
190H LEU* 3.5 23.5 - - + +
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Residues in contact with TYR 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G GLU 3.1 13.0 + - - +
27G ALA 3.0 9.7 + - - +
29G MET* 1.3 77.6 - - - +
31G ALA* 1.3 68.7 + - - +
33G GLY* 3.2 3.4 + - - -
34G VAL* 2.9 42.1 + - + +
57G LEU* 4.3 11.4 - - + -
59G THR* 2.8 42.8 + - - -
60G PHE* 3.7 31.9 - + + -
62G VAL* 5.3 1.8 - - + +
63G ILE* 3.1 30.3 - - + -
188G TYR* 3.4 32.5 + + - -
191G SER* 3.7 10.7 + - - +
217G LEU 4.3 4.7 + - - -
220G PHE* 5.0 1.4 - - - -
221G GLY* 3.8 12.3 - - - -
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Residues in contact with ALA 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G ALA 2.9 10.7 + - - +
28G ILE 3.1 8.5 + - - +
30G TYR* 1.3 77.7 - - - +
32G LEU* 1.3 62.0 + - - +
34G VAL* 3.1 9.4 + - - +
35G GLY 3.2 0.7 + - - -
36G ALA* 3.0 32.9 + - + -
46G PHE* 3.6 25.4 - - + +
47G ILE* 5.1 1.3 - - + -
57G LEU* 3.8 29.2 - - + +
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Residues in contact with LEU 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G ILE* 2.9 21.5 + - + +
29G MET* 3.9 3.8 - - - +
31G ALA* 1.3 76.0 - - - +
33G GLY* 1.3 60.4 + - - +
34G VAL 2.9 5.4 + - - -
35G GLY* 3.0 13.7 + - - -
36G ALA 3.6 19.4 - - - +
47G ILE* 4.1 26.9 - - + -
184G GLN* 3.8 5.7 + - - -
187G LEU* 3.8 14.4 - - + +
183H ASN* 4.2 16.4 - - + +
186H ALA* 3.4 34.1 - - + +
187H LEU* 3.9 20.0 - - + +
190H LEU* 4.3 8.3 - - + -
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Residues in contact with GLY 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G MET 3.1 12.2 + - - -
30G TYR* 3.5 3.8 - - - -
32G LEU* 1.3 79.2 - - - +
34G VAL* 1.3 57.7 + - - +
184G GLN* 2.9 18.1 + - - -
187G LEU* 3.5 23.9 - - - +
188G TYR* 3.7 19.7 - - - +
218G CYS* 3.3 16.6 - - - -
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Residues in contact with VAL 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G TYR* 2.9 33.5 + - + +
31G ALA* 3.4 11.2 - - - +
32G LEU 2.9 0.6 - - - -
33G GLY* 1.3 79.0 - - - +
35G GLY* 1.3 49.4 + - - +
57G LEU* 3.7 24.2 - - + -
59G THR* 5.5 0.2 - - - +
188G TYR* 4.2 10.8 - - + -
218G CYS* 3.6 11.4 - - - +
221G GLY* 3.3 35.4 - - - +
222G PHE* 3.1 20.3 - - - -
225G ARG* 2.5 32.5 + - - +
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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