Contacts of the strand formed by residues 21 - 28 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11G TYR* 3.9 6.3 + - + +
16G GLU 6.0 1.1 - - - +
18G THR* 3.2 38.1 + - + +
19G PHE 3.0 5.6 + - - +
20G GLY* 1.3 79.7 - - - +
22G SER* 1.3 71.0 + - - +
35G GLY 3.3 5.4 - - - +
36G ALA 5.4 0.2 - - - -
37G GLY* 4.5 9.2 - - - +
277G LYS* 2.8 24.6 + - - -
308G ASP* 3.6 2.2 - - - -
344G LEU* 3.9 15.3 - - + -
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Residues in contact with SER 22 (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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11G TYR* 3.5 7.2 - - - -
21G VAL* 1.3 85.3 - - - +
23G LYS* 1.3 68.6 + - - +
24G TYR 3.5 4.3 + - - -
25G PRO* 3.9 6.8 - - - +
35G GLY* 2.9 18.2 + - - +
277G LYS* 3.7 17.9 - - - -
281G GLY 3.3 12.0 + - - -
283G PRO* 3.3 34.7 - - - +
308G ASP* 3.7 2.2 + - - -
23M LYS 5.0 0.5 - - - +
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Residues in contact with LYS 23 (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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10G ALA* 3.6 35.0 + - + +
11G TYR* 3.8 12.2 + - + +
22G SER* 1.3 72.6 - - - +
24G TYR* 1.3 93.2 + - + +
25G PRO* 3.3 8.4 - - - +
281G GLY* 2.9 18.0 + - - +
22M SER 4.9 0.7 - - - +
23M LYS 3.8 2.8 - - - +
25M PRO* 3.5 22.6 - - + +
36M ALA* 2.8 36.5 + - - +
37M GLY* 4.9 2.0 - - - -
11P LYS* 5.0 7.7 - - - +
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Residues in contact with TYR 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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10G ALA* 4.9 1.8 - - + +
22G SER* 4.3 3.4 - - - -
23G LYS* 1.3 110.5 + - + +
25G PRO* 1.3 69.5 - - - +
26G VAL* 4.0 3.1 - - - +
263G VAL 4.6 1.6 - - - +
280G THR 3.2 28.3 - - - -
281G GLY 3.0 12.2 + - - +
282G MET* 4.4 12.8 - - + -
283G PRO* 3.5 17.0 - - - +
25M PRO* 3.9 32.8 - - + -
27M LYS* 3.7 27.1 - - + +
33M GLU* 2.8 30.4 + - - -
36M ALA* 4.4 0.9 - - + -
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Residues in contact with PRO 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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22G SER* 3.9 8.3 - - - +
23G LYS 3.3 6.1 - - - +
24G TYR* 1.3 91.4 - - - +
26G VAL* 1.3 62.8 + - - +
27G LYS* 4.4 1.1 + - - +
33G GLU* 5.8 0.2 - - + -
34G ILE 3.1 15.5 - - - +
35G GLY 3.6 21.3 - - - +
36G ALA* 4.2 6.3 - - + +
23M LYS* 3.3 29.4 - - + +
24M TYR* 4.0 29.3 - - + -
25M PRO* 4.3 4.3 - - + -
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Residues in contact with VAL 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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24G TYR 4.0 1.8 - - - +
25G PRO* 1.3 79.2 - - - +
27G LYS* 1.3 64.6 + - - +
28G ALA* 4.5 5.2 - - + -
33G GLU* 3.4 2.6 - - - +
34G ILE* 2.6 55.2 + - + +
213G ILE* 3.5 40.4 - - + -
263G VAL* 3.7 27.4 - - + +
264G GLY 3.7 18.2 - - - +
265G PRO* 4.8 0.2 - - + -
283G PRO* 3.8 11.2 - - + -
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Residues in contact with LYS 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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25G PRO* 4.4 1.5 + - + +
26G VAL* 1.3 71.9 - - - +
28G ALA* 1.3 61.1 + - - +
32G LEU 3.6 6.5 - - - +
33G GLU* 3.3 31.6 + - + +
213G ILE* 3.1 21.2 - - - +
6M TYR* 5.5 1.3 + - - -
24M TYR* 3.4 47.8 - - + +
263M VAL* 6.4 2.7 - - + -
282M MET* 4.3 17.8 - - - +
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Residues in contact with ALA 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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26G VAL* 4.1 3.7 + - + -
27G LYS* 1.3 77.7 - - - +
29G GLY* 1.3 69.1 + - - +
32G LEU* 3.2 33.8 + - + +
34G ILE* 5.0 5.2 - - + -
121G ALA* 4.5 5.2 - - + -
159G ASP* 4.4 7.6 - - + +
160G LEU* 4.0 21.5 - - + -
213G ILE* 3.9 16.2 - - + -
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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