Contacts of the strand formed by residues 21 - 28 (chain O) in PDB entry 2I2X
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 VAL 21 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11O TYR* 3.9 5.9 + - + +
16O GLU 5.8 2.9 - - - +
18O THR* 3.3 28.9 + - + +
19O PHE 3.1 11.3 - - - +
20O GLY* 1.3 80.7 - - - +
22O SER* 1.3 70.1 + - - +
35O GLY 3.4 6.3 - - - +
36O ALA 5.3 0.2 - - - -
37O GLY* 4.4 11.4 - - - +
277O LYS* 2.9 22.3 + - - -
308O ASP* 3.5 2.7 - - - -
344O LEU* 3.8 14.6 - - + -
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Residues in contact with SER 22 (chain O).
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 4.9 0.3 - - - +
11O TYR* 3.6 5.2 - - - -
21O VAL* 1.3 82.4 - - - +
23O LYS* 1.3 68.3 + - - +
24O TYR* 3.2 2.6 + - - -
25O PRO* 3.5 7.8 - - - +
35O GLY* 2.9 18.5 + - - +
277O LYS* 3.8 10.5 - - - -
281O GLY 3.3 14.6 - - - -
282O MET 3.8 2.7 - - - -
283O PRO* 3.1 30.5 - - - +
308O ASP* 3.1 15.2 + - - -
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Residues in contact with LYS 23 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LYS* 5.5 3.8 - - - +
22C SER 5.0 0.5 - - - +
23C LYS 3.8 2.9 - - - +
25C PRO* 3.3 20.4 - - + +
36C ALA* 3.2 35.0 + - - +
37C GLY* 5.4 0.4 - - - -
10O ALA* 3.1 34.2 + - + +
11O TYR* 3.5 15.4 + - + +
22O SER* 1.3 71.9 - - - +
24O TYR* 1.3 93.4 + - + +
25O PRO* 3.2 9.4 - - - +
281O GLY* 3.1 16.7 + - - +
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Residues in contact with TYR 24 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C PRO* 3.9 35.7 - - + -
27C LYS* 3.8 32.8 - - + +
33C GLU* 2.6 30.5 + - + -
36C ALA* 4.0 1.6 - - + +
6O TYR* 6.4 0.2 - + - -
10O ALA* 4.7 3.0 - - + +
22O SER 4.2 0.7 - - - -
23O LYS* 1.3 107.9 + - + +
25O PRO* 1.3 71.0 - - - +
26O VAL* 4.1 2.8 - - - +
263O VAL 4.7 0.7 - - - +
280O THR 3.3 27.1 - - - -
281O GLY* 3.0 13.1 + - - +
282O MET* 4.4 9.6 - - + -
283O PRO* 3.3 20.2 - - - +
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Residues in contact with PRO 25 (chain O).
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* 3.3 24.0 - - + +
24C TYR* 3.7 32.4 - - + -
25C PRO* 4.2 4.0 - - + -
22O SER* 3.7 3.5 - - - +
23O LYS 3.2 13.5 - - - +
24O TYR* 1.3 89.5 - - - +
26O VAL* 1.3 61.8 + - - +
27O LYS* 4.3 1.3 + - - +
33O GLU* 5.8 0.2 - - + -
34O ILE 3.2 15.5 - - - +
35O GLY* 3.6 22.2 - - - +
36O ALA* 4.2 5.8 - - + -
283O PRO* 4.8 0.9 - - + -
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Residues in contact with VAL 26 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24O TYR 4.1 1.8 - - - +
25O PRO* 1.3 77.2 - - - +
27O LYS* 1.3 62.2 + - - +
28O ALA* 4.6 0.9 - - + -
33O GLU* 3.4 2.8 - - - +
34O ILE* 2.7 60.3 + - + +
213O ILE* 3.4 35.2 - - + -
263O VAL* 3.4 36.1 - - + +
264O GLY 3.5 18.6 - - - +
283O PRO* 3.8 9.4 - - + -
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Residues in contact with LYS 27 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C TYR* 5.2 2.3 + - - -
24C TYR* 3.6 45.0 - - + +
263C VAL* 6.1 4.1 - - + +
280C THR 5.2 0.2 + - - -
282C MET* 4.0 22.7 - - - +
25O PRO 4.3 1.3 + - - +
26O VAL* 1.3 74.3 - - - +
28O ALA* 1.3 61.3 + - - +
32O LEU 3.6 5.4 - - - +
33O GLU* 3.1 32.5 - - + +
213O ILE* 3.0 21.2 - - - +
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Residues in contact with ALA 28 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26O VAL* 4.1 3.1 + - + -
27O LYS* 1.3 75.5 - - - +
29O GLY* 1.3 69.8 + - - +
31O ASP 4.1 0.2 + - - -
32O LEU* 3.0 36.0 + - + +
34O ILE* 5.0 5.1 - - + +
121O ALA* 4.6 3.1 - - + -
159O ASP* 4.4 5.4 - - + +
160O LEU* 3.9 22.4 - - + -
213O ILE* 3.6 17.0 - - + -
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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