Contacts of the strand formed by residues 32 - 36 (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 LEU 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A LYS* 3.7 0.7 - - - +
28A ALA 3.1 37.3 + - - +
30A LEU 3.1 2.1 + - - +
31A ASP* 1.3 77.9 - - - +
33A GLU* 1.3 70.2 + - - +
34A ILE* 4.1 9.6 - - + -
38A TYR* 3.8 10.3 - - - +
40A ILE* 3.9 15.7 - - + -
80A ALA* 3.8 19.5 - - + -
82A ILE* 3.5 37.5 - - + -
119A LYS* 3.7 25.1 - - + +
120A CYS* 4.1 11.4 - - - +
121A ALA* 3.6 17.5 - - + +
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Residues in contact with GLU 33 (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* 5.9 0.2 - - + -
26A VAL 3.5 4.9 - - - +
27A LYS* 3.4 35.1 + - + -
31A ASP 4.9 4.7 - - - +
32A LEU* 1.3 81.1 - - - +
34A ILE* 1.3 64.3 + - - +
35A GLY 4.2 0.7 + - - -
36A ALA* 3.5 17.3 + - + +
38A TYR* 3.0 35.5 + - + +
40A ILE* 3.3 9.4 - - - +
6I TYR* 6.0 1.9 - - - -
24I TYR* 2.6 32.5 + - + -
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Residues in contact with ILE 34 (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* 3.3 6.8 - - - +
26A VAL* 2.8 52.0 + - + +
28A ALA* 5.0 4.3 - - + -
32A LEU* 4.1 16.8 - - + -
33A GLU* 1.3 78.0 - - - +
35A GLY* 1.3 63.8 + - - +
40A ILE* 3.9 14.6 - - + -
82A ILE* 4.4 7.4 - - + -
121A ALA* 5.6 0.2 - - + -
160A LEU* 4.4 15.5 - - + -
265A PRO* 3.9 29.8 - - + -
283A PRO* 3.9 20.0 - - + +
308A ASP* 4.2 2.7 - - + -
309A CYS* 3.5 26.5 - - - -
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Residues in contact with GLY 35 (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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20A GLY 3.3 12.4 + - - -
21A VAL* 3.4 4.2 - - - +
22A SER* 2.9 46.5 + - - +
25A PRO* 3.6 5.8 - - - +
33A GLU 4.2 0.2 + - - -
34A ILE* 1.3 77.9 - - - +
36A ALA* 1.3 55.2 + - - +
38A TYR 4.7 5.3 + - - -
308A ASP* 3.3 20.9 + - - +
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Residues in contact with ALA 36 (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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20A GLY 3.5 0.6 + - - -
21A VAL* 5.1 0.2 - - - -
25A PRO* 4.3 10.5 - - + -
33A GLU* 3.5 45.7 + - + +
34A ILE* 4.1 0.2 - - - +
35A GLY* 1.3 77.4 - - - +
37A GLY* 1.3 59.0 + - - +
38A TYR* 3.6 11.8 + - + +
11D LYS* 5.0 1.9 + - - -
23I LYS* 2.7 34.6 + - - +
24I TYR* 3.8 8.7 - - - +
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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