Contacts of the helix formed by residues 19 - 30 (chain C) in PDB entry 2O5J
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 19 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C PRO* 2.8 9.1 - - - +
18C LEU* 1.3 77.3 - - + +
20C GLU* 1.3 64.7 + - - +
21C ILE 3.2 2.9 - - - -
22C GLN* 2.9 13.6 + - - +
23C VAL* 2.9 36.9 + - - +
123C GLU 5.7 0.2 + - - -
124C ASP 3.3 27.2 + - - +
125C GLY* 5.1 1.6 - - - -
404C LEU* 3.5 24.7 - - + -
407C LYS* 4.9 5.6 - - - +
590C ASP* 3.8 20.8 + - - +
591C SER* 5.4 0.7 - - - -
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Residues in contact with GLU 20 (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 PRO* 3.3 21.4 - - - +
17C PRO* 2.4 54.8 + - + +
19C THR* 1.3 67.3 + - - +
21C ILE* 1.3 70.6 + - + +
23C VAL* 4.5 3.6 - - - -
24C GLU* 2.8 51.1 + - + +
460C ARG* 2.4 50.2 + - - +
461C VAL 4.4 4.0 + - - +
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Residues in contact with ILE 21 (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 PRO* 6.1 0.7 - - + -
17C PRO 4.9 1.3 - - - +
18C LEU* 4.5 9.2 + - - +
19C THR 3.1 1.4 + - - -
20C GLU* 1.3 96.6 - - + +
22C GLN* 1.3 58.0 + - + +
24C GLU* 5.3 0.7 - - - -
25C SER* 2.7 36.2 + - - -
138C SER* 5.3 9.6 - - - +
333C ILE* 6.5 0.2 - - + -
335C THR* 4.1 25.1 - - + -
336C VAL* 5.8 1.8 - - + +
408C ARG* 5.4 0.7 - - - +
455C LEU* 4.2 28.9 - - + -
459C ALA 4.4 2.7 - - - +
460C ARG* 4.3 4.5 - - - -
461C VAL* 3.4 36.1 - - + +
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Residues in contact with GLN 22 (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 LEU 5.5 1.8 - - - +
19C THR* 2.9 12.2 + - - +
21C ILE* 1.3 82.3 - - + +
23C VAL* 1.3 68.0 + - - +
25C SER* 2.8 17.2 + - - -
26C TYR* 3.2 7.4 + - - +
121C MET* 3.1 22.1 - - + +
125C GLY* 3.1 9.0 + - - -
127C PHE* 6.2 0.2 - - - -
135C VAL* 5.6 0.8 - - - +
136C ILE 4.4 16.9 + - - +
336C VAL* 4.7 12.7 - - + +
407C LYS* 2.6 78.8 - - - +
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Residues in contact with VAL 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C THR* 2.9 39.9 + - - +
20C GLU* 4.2 1.1 - - - +
22C GLN* 1.3 78.3 - - - +
24C GLU* 1.3 74.6 + - - +
26C TYR* 3.2 3.6 + - - +
27C ARG* 2.9 25.9 + - + +
121C MET* 3.6 15.9 - - + -
123C GLU 5.2 7.0 - - - +
124C ASP 4.5 6.7 - - - +
125C GLY* 4.8 0.7 - - - -
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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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17C PRO* 5.8 2.5 - - - +
20C GLU* 2.8 44.4 + - + +
21C ILE* 5.3 0.2 - - - -
23C VAL* 1.3 91.0 - - - +
25C SER* 1.3 66.1 + - - +
27C ARG* 2.8 27.2 + - + +
28C ARG* 2.9 35.8 + - - +
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Residues in contact with SER 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 ILE 2.7 26.0 + - - -
22C GLN* 2.8 18.9 + - - -
24C GLU* 1.3 77.1 - - - +
26C TYR* 1.3 59.3 + - - +
28C ARG* 3.5 5.4 + - - +
29C ALA* 2.8 30.2 + - - +
335C THR* 3.9 27.8 - - - -
336C VAL* 4.0 11.3 - - - +
337C GLY* 4.3 7.8 - - - -
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Residues in contact with TYR 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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22C GLN 3.5 13.5 - - - +
23C VAL 3.2 3.9 + - - +
25C SER* 1.3 79.5 + - - +
27C ARG* 1.3 64.4 + - - +
29C ALA* 3.6 11.7 - - + -
30C LEU* 2.9 61.5 + - + +
118C ILE* 4.2 0.2 - - - +
119C PRO* 2.4 36.6 + - - +
120C LEU* 4.0 3.1 - - + -
121C MET* 3.4 46.9 - - + -
127C PHE* 4.0 15.0 - + - -
336C VAL* 5.0 14.1 - - + -
337C GLY* 5.0 2.5 - - - -
340C MET* 3.9 30.2 - - + +
386C PHE* 4.7 3.9 - + - -
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Residues in contact with ARG 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 VAL* 2.9 14.2 + - + +
24C GLU* 2.8 24.0 + - + +
26C TYR* 1.3 76.8 - - - +
28C ARG* 1.3 71.2 + - + +
30C LEU* 2.8 30.8 - - - +
31C GLN* 3.4 4.1 + - - -
33C ASP* 5.2 21.1 + - - +
34C VAL* 4.9 19.8 - - - +
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Residues in contact with ARG 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* 2.9 30.4 + - + +
25C SER* 4.1 4.2 - - - +
27C ARG* 1.3 78.7 - - + +
29C ALA* 1.3 63.5 + - - +
31C GLN* 4.1 10.7 + - - +
40C GLU* 3.1 31.2 + - - +
42C VAL* 3.7 27.9 - - + +
461C VAL 5.5 0.4 + - - -
462C ASP 4.0 15.2 + - - -
463C GLU* 2.6 41.7 + - - -
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Residues in contact with ALA 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 SER 2.8 20.8 + - - +
26C TYR* 3.4 24.7 - - + +
28C ARG* 1.3 80.0 - - - +
30C LEU* 1.3 59.0 - - - +
31C GLN 3.9 0.3 + - - -
42C VAL 3.9 0.9 - - - +
43C GLY* 3.5 9.3 - - - -
44C ILE* 2.9 31.9 + - - +
337C GLY* 3.8 19.5 - - - -
340C MET* 5.9 3.6 - - + -
341C THR* 6.2 1.1 - - - -
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Residues in contact with LEU 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 TYR* 2.9 61.0 + - + +
27C ARG* 2.8 16.5 - - - +
29C ALA* 1.3 76.4 - - - +
31C GLN* 1.3 55.7 + - - +
32C ALA* 2.9 17.7 + - + +
33C ASP* 4.5 10.1 + - - +
44C ILE* 3.4 24.2 - - + -
73C LEU* 4.8 6.5 - - + -
118C ILE* 3.5 27.6 - - + -
119C PRO 4.4 3.1 - - - +
120C LEU* 5.2 12.3 - - + -
340C MET* 4.8 0.7 - - + -
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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