Contacts of the strand formed by residues 40 - 46 (chain E) in PDB entry 4BEI
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E VAL* 1.3 83.4 + - + +
41E GLU* 1.3 73.3 + - - +
42E ALA 4.1 2.8 + - - +
64E ILE* 3.9 24.0 - - + -
65E ARG 3.5 6.3 - - - +
66E ASN* 4.9 3.1 - - + +
67E GLU* 4.8 1.3 - - - -
72E VAL* 3.8 28.9 - - + -
74E PHE* 4.0 22.4 - - + -
106E LEU* 5.4 0.2 - - + -
135E VAL* 4.2 15.9 - - + -
137E ALA* 4.5 8.7 - - + -
143E PHE* 3.2 51.8 - - + -
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Residues in contact with GLU 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 VAL 4.3 0.2 + - - -
40E ILE* 1.3 74.1 - - - +
42E ALA* 1.3 62.2 + - - +
43E ASN* 3.7 24.0 + - - +
63E GLY 3.7 1.6 - - - +
64E ILE* 3.5 2.6 - - - -
65E ARG* 2.8 49.3 + - + +
67E GLU* 2.1 44.3 - - + +
111E MET* 6.5 0.2 - - - -
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Residues in contact with ALA 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* 4.1 2.3 + - + -
41E GLU* 1.3 75.6 - - - +
43E ASN* 1.3 70.5 + - - +
63E GLY 3.4 7.2 - - - +
64E ILE* 4.7 0.4 - - + +
133E LEU* 4.2 14.6 - - + -
135E VAL* 4.2 20.2 - - + -
143E PHE* 4.6 10.2 - - + +
144E LYS 4.4 15.1 - - - +
145E ALA* 3.5 16.3 - - + +
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Residues in contact with ASN 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 GLU* 3.7 25.3 + - - +
42E ALA* 1.3 83.6 + - - +
44E LEU* 1.3 64.7 + - - +
61E GLN 4.4 0.4 - - - -
62E LEU* 3.7 0.5 - - - -
63E GLY* 2.9 33.1 + - - +
111E MET* 4.3 18.9 - - - +
133E LEU* 3.2 10.4 - - - +
145E ALA* 3.7 6.3 - - - -
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Residues in contact with LEU 44 (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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43E ASN* 1.3 80.0 - - - +
45E SER* 1.3 68.0 + - - +
46E LEU* 4.4 3.6 - - + -
60E SER* 3.9 16.6 - - - -
61E GLN 3.5 4.9 - - - +
62E LEU* 3.4 31.9 - - + -
78E LEU* 4.2 4.5 - - + -
131E VAL* 3.7 31.4 - - + +
133E LEU* 3.7 14.1 - - + +
145E ALA* 3.3 33.4 - - + +
147E GLN* 3.0 36.4 - - + +
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Residues in contact with SER 45 (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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44E LEU* 1.3 75.5 - - - +
46E LEU* 1.3 68.4 + - - +
60E SER* 3.4 5.5 - - - -
61E GLN* 3.0 46.7 + - - +
147E GLN* 4.1 6.1 - - - -
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Residues in contact with LEU 46 (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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44E LEU* 4.4 7.9 - - + -
45E SER* 1.3 83.8 - - - +
47E ASN* 1.3 62.3 + - - +
48E GLN* 3.4 24.5 + - - +
49E ASN* 4.5 9.1 + - - +
58E ILE* 4.3 13.0 - - + -
59E SER 3.9 1.8 - - - -
60E SER* 3.9 16.8 - - - -
118E PHE* 5.0 0.7 - - + -
131E VAL* 4.3 14.6 - - + -
147E GLN* 3.6 26.2 - - + +
148E GLU 3.6 26.2 - - - +
149E PHE* 4.1 17.7 - - + -
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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