Contacts of the helix formed by residues 23 - 34 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22E TYR* 1.3 87.2 - - - +
24E GLU* 1.3 74.1 + - - +
25E LEU* 3.0 16.0 + - - +
26E GLU* 2.6 33.3 + - - +
27E ALA* 3.3 8.1 + - - +
102E ARG 3.8 5.6 - - - -
103E ALA* 3.7 9.6 - - + -
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Residues in contact with GLU 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E THR* 1.3 80.9 - - - +
25E LEU* 1.3 56.3 + - - +
27E ALA* 3.1 6.3 + - - +
28E ILE* 2.8 38.2 + - + +
49E GLU* 3.9 25.8 - - + -
54E PHE* 3.7 21.3 - - + -
102E ARG* 2.8 49.6 + - - +
103E ALA* 4.0 6.6 - - - +
194F TRP* 6.1 1.3 - - + -
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Residues in contact with LEU 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E THR* 3.0 12.6 + - - +
24E GLU* 1.3 76.7 - - - +
26E GLU* 1.3 82.2 + - - +
27E ALA 3.0 0.7 + - - -
28E ILE* 3.0 5.9 + - - +
29E MET* 2.8 40.0 + - + +
29F MET* 4.7 6.1 - - + -
190F LEU* 3.4 50.9 - - + +
194F TRP* 3.7 25.6 - - + -
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Residues in contact with GLU 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E TYR* 3.8 24.7 - - + +
21E ALA 5.1 1.8 - - - +
22E TYR* 3.9 16.2 - - + -
23E THR* 2.6 43.0 + - - +
25E LEU* 1.3 93.3 - - - +
27E ALA* 1.3 62.0 + - - +
29E MET* 3.6 18.5 + - + +
30E TYR* 3.1 21.8 + - - +
60E PHE* 3.8 6.5 - - + -
191E SER* 4.6 2.4 + - - -
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Residues in contact with ALA 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E TYR* 5.0 4.7 - - + -
23E THR 3.3 10.0 + - - +
24E GLU* 3.1 12.9 + - - +
25E LEU 3.0 0.6 - - - -
26E GLU* 1.3 75.0 - - - +
28E ILE* 1.3 66.8 + - - +
30E TYR* 3.0 7.4 + - - +
31E ALA* 2.9 21.6 + - - +
46E PHE 5.1 1.1 - - - -
54E PHE* 4.4 12.6 - - + -
55E SER 5.6 0.2 - - - +
56E CYS* 4.0 28.0 - - + -
57E LEU 5.7 1.7 + - - +
60E PHE* 4.2 12.4 - - - -
102E ARG 5.1 1.3 - - - +
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Residues in contact with ILE 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E GLU* 2.8 28.9 + - + +
25E LEU 3.6 2.9 - - - +
27E ALA* 1.3 72.0 - - - +
29E MET* 1.3 58.2 + - - +
31E ALA* 3.0 3.1 + - - +
32E LEU* 2.8 35.6 + - + +
46E PHE 3.9 9.6 - - - +
47E ILE* 3.2 43.7 - - + +
49E GLU* 3.6 31.2 - - + +
54E PHE* 3.7 17.9 - - + -
186F ALA 4.9 1.6 - - - +
189F ARG* 4.7 1.1 - - - +
190F LEU* 4.0 15.9 - - + -
194F TRP* 4.5 10.5 - - + -
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Residues in contact with MET 29 (chain E).
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* 2.8 38.8 + - + +
26E GLU* 3.6 21.8 - - + +
28E ILE* 1.3 78.2 - - - +
30E TYR* 1.3 62.7 + - - +
32E LEU* 3.9 4.3 - - - +
33E GLY* 3.0 19.9 + - - -
187E LEU* 4.9 11.5 - - + +
188E TYR* 5.9 0.2 - - - -
190E LEU* 4.1 37.0 - - + +
191E SER* 4.3 6.6 + - - +
25F LEU* 4.9 5.8 - - + -
29F MET* 3.3 35.0 - - + +
190F LEU* 3.8 19.9 - - + +
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Residues in contact with TYR 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E GLU 3.1 11.9 + - - +
27E ALA 3.0 11.2 + - - +
29E MET* 1.3 77.4 - - - +
31E ALA* 1.3 61.9 + - - +
33E GLY* 3.0 4.3 + - - -
34E VAL* 2.8 55.8 + - + +
57E LEU* 4.4 11.7 - - + -
59E THR* 2.8 41.8 + - - -
60E PHE* 3.7 31.2 - + + -
62E VAL* 5.2 2.4 - - + +
63E ILE* 3.2 30.7 - - + -
188E TYR* 3.5 30.5 + + - -
191E SER* 3.6 10.5 + - - +
217E LEU 4.3 4.9 + - - -
220E PHE* 5.1 1.2 - - - -
221E GLY* 4.0 4.3 - - - -
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Residues in contact with ALA 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E ALA 2.9 10.9 + - - +
28E ILE 3.4 7.2 - - - +
30E TYR* 1.3 76.0 - - - +
32E LEU* 1.3 62.5 + - - +
34E VAL* 3.2 8.8 + - - +
35E GLY 3.2 0.5 + - - -
36E ALA* 3.1 28.8 + - + +
46E PHE* 3.5 30.5 - - + +
47E ILE* 5.1 1.3 - - + -
57E LEU* 3.9 28.3 - - + +
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Residues in contact with LEU 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E ILE* 2.8 30.1 + - + +
29E MET* 3.9 3.8 - - - +
31E ALA* 1.3 73.5 - - - +
33E GLY* 1.3 64.0 + - - +
34E VAL 3.0 1.6 + - - -
35E GLY* 3.1 14.0 + - - -
36E ALA 3.6 18.8 - - - +
47E ILE* 4.1 22.2 - - + -
184E GLN* 4.0 4.2 + - - -
187E LEU* 3.8 16.9 - - + +
183F ASN* 4.3 17.0 - - + +
186F ALA* 3.8 25.6 - - + +
187F LEU* 4.0 26.2 - - + +
190F LEU* 4.3 8.5 - - + -
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Residues in contact with GLY 33 (chain E).
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 3.0 14.0 + - - -
30E TYR 3.0 4.5 + - - -
32E LEU* 1.3 75.6 - - - +
34E VAL* 1.3 57.0 + - - +
35E GLY 3.5 0.2 - - - -
184E GLN* 3.0 18.7 + - - -
187E LEU* 3.5 25.0 - - - +
188E TYR* 3.7 19.9 - - - +
218E CYS* 3.4 15.8 - - - -
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Residues in contact with VAL 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E TYR* 2.8 32.4 + - + +
31E ALA 3.2 10.1 + - - +
32E LEU 3.0 0.6 - - - -
33E GLY* 1.3 78.6 - - - +
35E GLY* 1.3 48.4 + - - +
57E LEU* 3.8 26.2 - - + -
59E THR* 5.5 0.2 - - - +
188E TYR* 4.2 11.2 - - + -
218E CYS* 3.6 10.3 - - - +
221E GLY* 3.3 36.1 - - - +
222E PHE* 3.3 18.9 - - - -
225E ARG* 2.4 32.9 + - - +
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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