Contacts of the strand formed by residues 21 - 28 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A TYR* 3.7 6.4 + - + +
16A GLU 6.0 1.6 - - - +
18A THR* 3.5 33.0 + - + +
19A PHE 2.9 4.9 + - - +
20A GLY* 1.3 86.2 - - - +
22A SER* 1.3 72.3 + - - +
35A GLY 3.4 5.4 - - - +
37A GLY* 4.2 10.8 - - - +
277A LYS* 3.1 20.1 + - - -
308A ASP* 3.5 2.5 - - - -
344A LEU* 3.9 13.9 - - + -
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Residues in contact with SER 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A TYR* 3.5 5.2 - - - -
21A VAL* 1.3 84.3 - - - +
23A LYS* 1.3 67.3 + - - +
24A TYR 3.3 3.2 + - - -
25A PRO* 3.5 8.3 - - - +
34A ILE 4.3 0.9 + - - -
35A GLY* 2.9 31.4 + - - +
277A LYS* 3.8 14.1 - - - -
281A GLY 3.4 13.9 - - - -
282A MET 3.8 0.2 - - - -
283A PRO* 3.3 28.6 - - - +
308A ASP* 3.9 1.1 - - - -
23I LYS 5.0 0.5 - - - +
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Residues in contact with LYS 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ALA* 3.7 30.3 + - + +
11A TYR* 3.5 16.7 + - + +
21A VAL* 5.0 0.4 - - - +
22A SER* 1.3 71.8 - - - +
24A TYR* 1.3 95.6 + - + +
25A PRO* 3.3 9.0 - - - +
281A GLY* 3.1 16.8 + - - +
22I SER 5.2 0.2 - - - +
23I LYS 3.8 3.3 - - - +
25I PRO* 3.3 18.7 - - + +
33I GLU* 4.3 1.6 + - - -
36I ALA* 3.2 37.1 + - - +
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Residues in contact with TYR 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ALA* 4.5 4.1 - - + +
22A SER* 4.3 2.7 - - - -
23A LYS* 1.3 109.1 + - + +
25A PRO* 1.3 69.5 - - - +
26A VAL* 4.2 3.3 - - - +
263A VAL 4.7 1.2 - - - +
280A THR 3.3 27.4 - - - -
281A GLY* 3.0 12.9 + - - +
282A MET* 4.6 9.0 - - + -
283A PRO* 3.6 16.3 - - - +
25I PRO* 3.9 36.8 - - + -
27I LYS* 4.0 31.4 - - + +
33I GLU* 2.5 37.5 + - - -
36I ALA* 4.7 0.9 - - + -
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Residues in contact with PRO 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A SER* 3.5 17.7 - - - +
23A LYS 3.3 10.5 - - - +
24A TYR* 1.3 89.9 - - - +
26A VAL* 1.3 60.8 + - - +
27A LYS* 4.2 1.7 + - - +
34A ILE 3.3 14.6 - - - +
35A GLY 3.6 13.5 - - - +
36A ALA* 4.3 5.4 - - + +
23I LYS* 3.4 22.9 - - + +
24I TYR* 3.6 33.0 - - + -
25I PRO* 4.1 4.5 - - + -
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Residues in contact with VAL 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A TYR 4.2 1.1 - - - +
25A PRO* 1.3 77.9 - - - +
27A LYS* 1.3 64.5 + - - +
28A ALA* 4.6 0.9 - - + -
33A GLU* 3.5 2.1 - - - -
34A ILE* 2.8 59.1 + - + +
160A LEU* 4.9 0.2 - - + -
213A ILE* 3.7 31.0 - - + -
263A VAL* 3.4 34.1 - - + +
264A GLY 3.5 19.5 - - - +
265A PRO* 4.6 0.4 - - + -
283A PRO* 3.7 13.2 - - + -
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Residues in contact with LYS 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A PRO 4.3 1.7 + - - +
26A VAL* 1.3 73.8 - - - +
28A ALA* 1.3 62.1 + - - +
32A LEU 3.7 6.7 - - - +
33A GLU* 3.4 28.4 + - + -
213A ILE* 3.0 21.3 - - - +
6I TYR* 5.0 4.8 + - - -
24I TYR* 3.5 48.2 - - + +
263I VAL* 6.2 3.8 - - + -
282I MET* 3.9 23.5 - - + +
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL* 4.1 3.5 + - + -
27A LYS* 1.3 76.4 - - - +
29A GLY* 1.3 69.5 + - - +
31A ASP 4.2 0.2 + - - -
32A LEU* 3.1 34.7 + - + +
34A ILE* 5.0 5.4 - - + -
121A ALA* 4.6 5.2 - - + -
159A ASP* 4.8 6.3 - - + +
160A LEU* 4.0 19.5 - - + -
213A ILE* 3.5 19.3 - - + -
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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