Contacts of the helix formed by residues 54 - 61 (chain E) in PDB entry 4L2O
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 ASN 54 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44E VAL* 4.2 4.7 - - - -
48E ALA* 5.4 0.2 - - - -
53E LYS* 1.3 73.7 - - - +
55E GLU* 1.3 65.8 + - - +
56E TRP* 2.8 20.9 + - - +
57E ASN* 2.7 27.5 + - - +
58E ALA* 2.9 26.7 + - - +
279E ARG* 2.9 39.5 + - + +
280E ASP* 2.8 28.3 + - - -
445G SER* 4.0 2.5 + - - -
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Residues in contact with GLU 55 (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 GLU* 5.3 1.9 - - + +
41E GLN* 3.5 26.9 + - - +
44E VAL* 3.7 30.8 - - + +
54E ASN* 1.3 74.1 - - - +
56E TRP* 1.3 63.1 + - - +
58E ALA* 4.2 1.6 - - - +
59E TYR* 3.7 18.0 + - - +
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Residues in contact with TRP 56 (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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54E ASN* 2.8 15.7 + - - +
55E GLU* 1.3 75.2 - - - +
57E ASN* 1.3 84.2 + - + +
59E TYR 3.2 2.8 + - - -
60E TYR* 2.9 77.9 + + + -
61E GLU* 4.0 20.4 - - + -
279E ARG* 6.1 0.2 - - - +
280E ASP* 5.5 0.9 - - - -
440G VAL* 3.2 27.8 - - + +
441G ARG* 3.5 30.3 - - + -
442G TYR 5.2 2.9 - - - -
443G PRO* 5.8 3.6 - - + -
445G SER* 3.6 26.7 - - - +
446G PRO* 3.5 33.2 - - + +
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Residues in contact with ASN 57 (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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52E HIS 5.4 0.2 + - - -
53E LYS* 3.4 25.8 + - - +
54E ASN* 2.7 49.4 + - - +
56E TRP* 1.3 84.1 - - + +
58E ALA* 1.3 70.3 + - - +
59E TYR 3.1 2.0 - - - -
61E GLU* 3.1 55.1 + - - +
62E GLU 3.8 0.2 + - - -
279E ARG 4.7 0.4 + - - -
280E ASP* 3.8 23.8 + - - +
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Residues in contact with ALA 58 (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 VAL* 4.0 26.9 - - + -
47E LEU* 3.6 29.6 - - + +
53E LYS* 4.5 7.0 - - + +
54E ASN 2.9 20.7 + - - +
55E GLU 4.2 0.2 - - - +
57E ASN* 1.3 78.9 + - - +
59E TYR* 1.3 58.2 + - - +
62E GLU* 3.5 7.0 - - - +
63E VAL* 3.1 31.0 + - + +
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Residues in contact with TYR 59 (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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36E ILE* 5.7 0.2 - - + -
40E GLU* 3.6 31.2 - - + -
44E VAL* 5.9 2.5 - - + -
55E GLU 3.7 11.1 + - - +
56E TRP 3.2 7.7 + - - +
57E ASN 3.1 0.2 - - - -
58E ALA* 1.3 79.2 - - - +
60E TYR* 1.3 98.9 + + + +
61E GLU 3.3 0.2 - - - -
63E VAL* 3.2 22.5 + - + -
64E VAL* 2.8 52.9 + - + +
67E LEU* 3.6 30.0 - - + +
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Residues in contact with TYR 60 (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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56E TRP* 2.9 78.6 + + + +
59E TYR* 1.3 105.7 - + + +
61E GLU* 1.3 62.1 + - - +
64E VAL* 3.9 14.4 - - + +
65E TYR* 3.5 19.8 + - - -
504E 1DD 5.0 0.7 - - - -
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Residues in contact with GLU 61 (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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53E LYS* 4.1 13.2 + - - +
56E TRP* 4.0 17.1 - - + -
57E ASN* 3.1 38.6 + - + +
60E TYR* 1.3 82.5 - - - +
62E GLU* 1.3 62.2 + - - +
65E TYR* 4.6 0.2 - - - -
115E TYR* 3.6 6.5 + - + -
233E TRP* 4.2 19.4 + - + +
237E MET* 4.3 26.1 - - + +
238E ASN 4.8 3.1 + - - -
504E 1DD 3.2 46.4 + - + -
441G ARG 4.4 1.4 - - - +
443G PRO* 5.4 6.1 - - - +
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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