Contacts of the helix formed by residues 22 - 33 (chain C) in PDB entry 1S89
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 CYS 22 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18C ALA* 4.1 1.7 - - - +
19C HIS 2.8 7.1 + - - +
21C HIS* 1.3 83.6 - - - +
23C LYS* 1.3 63.1 + - - +
24C GLN 3.4 2.2 - - - -
25C MET* 3.3 34.0 + - + +
26C LEU* 3.2 20.8 + - - +
89C PHE* 3.5 34.5 - - + +
90C TRP 3.9 15.0 - - - -
91C ASP* 3.9 19.1 - - - -
92C PRO* 4.6 6.1 - - - -
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Residues in contact with LYS 23 (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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18C ALA* 2.8 33.7 + - + +
19C HIS* 3.1 9.0 + - - +
20C ASP* 2.8 39.8 + - - +
22C CYS* 1.3 74.5 - - - +
24C GLN* 1.3 66.8 + - - +
26C LEU* 3.1 3.7 + - - +
27C MET* 2.8 31.5 + - + +
47C THR* 3.6 21.1 - - + -
48C THR* 3.7 15.5 - - + +
51C LEU* 3.6 23.8 - - + -
203C PGA 2.7 29.6 + - - -
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Residues in contact with GLN 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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20C ASP 4.7 1.4 + - - -
21C HIS 5.2 3.1 + - - +
22C CYS 3.4 0.4 - - - -
23C LYS* 1.3 76.8 - - - +
25C MET* 1.3 63.8 + - + +
27C MET* 3.2 10.6 + - - +
28C SER* 3.0 28.4 + - - +
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Residues in contact with MET 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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21C HIS 4.5 5.4 + - - +
22C CYS* 3.3 44.7 + - + +
23C LYS 3.2 0.4 - - - -
24C GLN* 1.3 80.2 - - - +
26C LEU* 1.3 62.4 + - - +
28C SER* 3.4 5.1 + - - -
29C TRP* 3.0 23.9 + - - +
32C ARG* 5.1 1.2 + - - -
89C PHE* 4.6 12.6 - - + -
120C VAL* 4.5 20.9 - - + +
3F LEU* 5.3 14.6 - - + -
139F LEU* 6.6 0.2 - - + -
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Residues in contact with LEU 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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16C LEU* 4.4 8.3 - - + -
17C VAL 3.8 17.0 - - - +
18C ALA* 3.4 26.0 - - + -
22C CYS 3.2 6.5 + - - +
23C LYS* 3.1 8.1 + - - +
25C MET* 1.3 76.7 - - - +
27C MET* 1.3 56.8 + - + +
29C TRP* 3.2 8.3 + - + +
30C VAL* 2.8 56.4 + - + +
48C THR* 3.8 21.1 - - + -
52C ILE* 4.8 3.8 - - + -
87C ILE* 4.0 19.1 - - + -
89C PHE* 3.8 30.0 - - + -
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Residues in contact with MET 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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23C LYS* 2.8 31.2 + - + +
24C GLN* 3.3 10.8 - - - +
26C LEU* 1.3 77.9 - - - +
28C SER* 1.3 63.8 + - - +
30C VAL* 3.1 8.6 + - - +
31C GLU* 3.0 33.2 + - - +
48C THR* 5.0 2.5 - - - +
51C LEU* 3.4 49.8 - - + +
52C ILE* 3.9 25.4 - - - +
55C ALA* 4.1 15.0 - - + -
56C THR* 5.5 0.6 - - + +
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Residues in contact with SER 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 GLN* 3.0 15.7 + - - +
25C MET* 3.8 4.9 - - - -
27C MET* 1.3 78.1 - - - +
29C TRP* 1.3 63.8 + - - +
31C GLU* 3.3 15.4 + - - +
32C ARG* 3.0 47.2 + - - +
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Residues in contact with TRP 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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16C LEU* 4.7 4.7 - - + -
25C MET 3.0 15.2 + - - +
26C LEU* 3.2 18.6 + - + +
28C SER* 1.3 76.4 - - - +
30C VAL* 1.3 77.6 + - + +
32C ARG* 3.4 21.6 + - - +
33C HIS* 2.7 45.0 + + - +
37C LEU* 4.3 17.9 - - + -
87C ILE* 4.3 27.4 - - + -
89C PHE* 4.7 7.0 - + + -
120C VAL* 4.1 14.6 - - + -
123C ALA* 3.5 40.1 - - + +
124C ASP* 2.6 28.0 + - - -
127C ILE* 3.7 30.7 - - + -
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Residues in contact with VAL 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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16C LEU* 4.1 24.2 - - + -
26C LEU* 2.8 29.3 + - + +
27C MET* 3.4 9.4 - - - +
29C TRP* 1.3 83.1 - - + +
31C GLU* 1.3 51.3 + - - +
33C HIS 3.0 3.6 + - - -
34C GLN* 2.7 33.4 + - - -
37C LEU* 3.7 12.2 - - + +
52C ILE* 4.1 19.3 - - + -
56C THR* 4.2 11.4 - - + -
58C MET* 3.4 30.3 - - + -
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Residues in contact with GLU 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 MET* 3.0 20.9 + - - +
28C SER* 3.3 22.4 + - - +
30C VAL* 1.3 76.7 - - - +
32C ARG* 1.3 61.8 + - + +
33C HIS 3.1 0.9 + - - -
34C GLN* 3.2 25.7 + - - +
35C PRO* 4.5 2.1 - - - +
55C ALA* 4.5 18.9 - - - +
56C THR* 4.1 17.7 - - + -
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Residues in contact with ARG 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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25C MET 5.1 1.2 + - - -
28C SER* 3.0 51.9 + - - +
29C TRP* 3.7 32.2 - - - +
30C VAL 3.3 0.2 - - - -
31C GLU* 1.3 77.7 - - + +
33C HIS* 1.3 69.9 + - + +
34C GLN 3.5 0.4 - - - -
35C PRO* 4.4 6.2 - - - +
120C VAL* 4.7 10.7 - - - +
124C ASP* 5.4 1.2 + - - -
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Residues in contact with HIS 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 TRP* 2.7 55.7 + + + +
30C VAL 3.0 5.3 + - - +
32C ARG* 1.3 90.9 + - + +
34C GLN* 1.3 66.5 + - - +
35C PRO* 3.2 6.3 - - - -
36C LEU* 3.2 7.7 + - + +
37C LEU* 3.0 26.5 + - + +
124C ASP* 3.3 16.3 + - - -
127C ILE* 3.8 42.7 - - + +
128C GLN* 5.6 5.6 - - + -
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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