Contacts of the strand formed by residues 40 - 43 (chain E) 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 ILE 40 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32E LEU* 3.7 22.9 - - + -
33E GLU 3.8 13.2 - - - +
34E ILE* 3.8 30.7 - - + -
38E TYR* 3.8 17.3 - - + +
39E THR* 1.3 81.0 - - - +
41E PRO* 1.3 83.6 - - + +
80E ALA* 3.8 14.6 - - + -
81E ILE 3.8 7.0 - - - +
82E ILE* 3.7 19.1 - - + -
308E ASP 3.2 8.8 + - - +
309E CYS* 3.1 9.1 - - - +
310E TRP 3.0 21.5 + - - -
337E CYS* 3.5 4.7 - - - -
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Residues in contact with PRO 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E THR 4.6 0.4 - - - +
40E ILE* 1.3 87.8 - - + +
42E GLU* 1.3 59.4 + - - +
43E ILE 4.0 0.7 - - - -
73E MET* 4.0 14.4 - - + -
80E ALA* 3.2 30.7 - - + +
81E ILE* 3.6 6.8 - - + +
82E ILE 2.9 24.1 + - - -
310E TRP 3.6 6.3 - - - +
330E SER* 4.7 1.6 - - - +
333E LEU* 3.8 12.6 - - + -
334E ALA* 3.8 28.0 - - + +
337E CYS* 3.6 14.3 - - + -
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Residues in contact with GLU 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E ILE 3.5 0.4 + - - -
41E PRO* 1.3 71.7 - - - +
43E ILE* 1.3 59.3 + - - +
44E ASN* 4.1 2.0 - - - +
82E ILE* 3.3 32.1 - - + +
84E GLU* 3.5 25.7 - - + +
123E ARG* 2.6 45.6 + - - -
268E ASP* 4.9 0.7 - - - +
285E THR* 3.0 26.1 + - - +
309E CYS* 4.3 10.4 - - + +
310E TRP 2.8 13.3 + - - +
311E SER* 3.2 30.4 + - - -
312E ASN* 3.7 0.7 - - - +
333E LEU* 3.6 4.8 - - - +
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Residues in contact with ILE 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E PRO 4.0 1.6 + - - -
42E GLU* 1.3 71.0 - - - +
44E ASN* 1.3 67.7 + - - +
45E TYR* 3.1 13.2 - - + -
69E VAL* 3.8 22.7 - - + -
81E ILE* 3.7 15.0 - - + +
82E ILE 2.9 20.0 + - - +
83E LEU* 4.2 6.7 - - + -
84E GLU 3.1 21.0 + - - -
312E ASN* 3.3 31.0 - - - +
326E VAL* 3.8 21.8 - - + +
329E TRP* 4.0 4.3 - - + -
330E SER* 3.7 33.2 - - - +
333E LEU* 4.0 4.7 - - + +
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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