Contacts of the strand formed by residues 44 - 49 (chain U) in PDB entry 1ZGL
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 GLN 44 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B GLU* 4.9 10.5 + - - +
35U TYR* 2.8 10.3 - - - +
36U VAL* 2.6 47.3 + - + +
38U TYR* 3.1 39.2 + - + -
41U GLU* 3.3 21.7 - - - +
42U GLY 4.3 6.5 - - - +
43U LEU* 1.3 76.4 - - - +
45U LEU* 1.3 62.8 + - - +
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Residues in contact with LEU 45 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B GLU* 4.5 12.1 - - - +
65B LYS* 5.4 10.8 + - - +
33U PHE* 4.6 10.8 - - + -
34U TRP 3.8 2.5 - - - +
35U TYR* 3.1 33.2 - - + +
36U VAL* 5.4 0.8 - - - +
43U LEU 4.3 0.6 + - - -
44U GLN* 1.3 75.5 - - - +
46U LEU* 1.3 76.2 + - - +
47U LEU 3.3 33.7 - - - +
48U LYS* 4.2 8.3 - - + +
58U ASN* 4.0 4.3 + - - +
103V GLU* 4.9 7.6 - - + +
106V ALA 4.4 7.6 - - - +
107V PHE* 4.7 23.1 - - + -
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Residues in contact with LEU 46 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B LYS* 4.8 6.2 + - - -
34U TRP* 2.9 19.3 + - + +
35U TYR* 4.6 2.0 - - - -
36U VAL* 4.4 15.7 - - + -
38U TYR* 5.2 4.3 - - - +
44U GLN 3.7 1.0 + - - -
45U LEU* 1.3 78.0 - - - +
47U LEU* 1.3 77.3 + - + +
57U SER* 3.6 4.9 + - - -
58U ASN* 2.4 60.3 + - + +
59U LYS* 5.3 1.1 - - + +
62U PHE* 4.1 27.4 - - + -
75U LEU* 4.4 2.9 - - + -
88U TYR* 3.3 40.6 - - + -
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Residues in contact with LEU 47 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B LYS* 6.0 0.7 - - - +
33U PHE* 3.0 6.6 - - - -
34U TRP* 3.0 52.0 + - + +
45U LEU* 3.3 9.6 - - - +
46U LEU* 1.3 94.0 - - + +
48U LYS* 1.3 60.9 + - - +
49U ALA 4.3 0.4 - - - -
54U ASP 5.0 1.8 - - - +
55U LYS 4.4 2.7 - - - +
56U GLY 3.7 3.6 - - - +
57U SER* 3.2 32.3 - - - +
62U PHE* 3.6 24.5 - - + +
63U GLU* 3.8 14.4 - - - +
64U ALA* 4.0 4.3 - - + +
73U PHE* 4.8 11.4 - - + -
75U LEU* 3.2 17.3 - - + -
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Residues in contact with LYS 48 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B LYS* 5.7 7.0 - - - +
32U LEU 3.5 3.8 - - - -
33U PHE* 3.8 18.6 - - + -
45U LEU* 4.5 11.0 - - + -
47U LEU* 1.3 75.3 - - - +
49U ALA* 1.3 60.6 + - - +
50U THR* 4.3 8.4 + - + +
53U ASP* 5.9 0.3 - - - +
54U ASP 5.5 0.7 - - - -
55U LYS* 4.1 22.9 - - + +
57U SER* 4.4 2.4 + - - -
73U PHE* 4.9 1.6 - - - -
103V GLU* 5.1 4.5 - - - +
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Residues in contact with ALA 49 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31U SER* 3.0 4.6 - - - -
32U LEU* 2.5 46.6 + - + +
48U LYS* 1.3 71.5 - - - +
50U THR* 1.3 62.4 + - - +
51U LYS 3.9 0.4 - - - -
53U ASP* 5.2 9.6 - - + +
54U ASP 5.3 2.0 - - - +
66U TYR* 3.8 16.8 - - + -
73U PHE* 3.1 39.1 - - + -
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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