Contacts of the helix formed by residues 67 - 72 (chain E) in PDB entry 3GTL
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 GLU 67 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65E THR* 2.7 22.4 + - + +
66E GLU* 1.3 74.6 - - - +
68E SER* 1.3 60.4 + - - +
69E ILE 3.1 0.4 - - - -
70E SER* 3.2 24.4 + - - -
71E LYS* 4.0 6.0 + - + +
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Residues in contact with SER 68 (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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27E GLY* 2.6 33.0 + - - -
64E PRO* 4.2 10.3 - - - -
65E THR* 2.6 25.6 + - - +
67E GLU* 1.3 72.3 - - - +
69E ILE* 1.3 57.5 + - - +
70E SER 3.3 0.2 - - - -
71E LYS* 4.1 2.2 - - - +
72E PHE* 3.1 45.1 + - - +
75E MET* 4.4 11.4 - - - +
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Residues in contact with ILE 69 (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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64E PRO* 3.7 23.3 - - + -
66E GLU* 3.6 29.8 - - + +
67E GLU 3.1 1.0 - - - -
68E SER* 1.3 78.0 - - - +
70E SER* 1.3 63.2 + - - +
71E LYS 3.4 0.7 - - - -
72E PHE 4.7 0.4 - - - +
73E PRO* 3.3 42.6 - - + +
75E MET* 3.4 25.6 - - + +
76E GLY* 5.3 0.2 - - - -
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Residues in contact with SER 70 (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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66E GLU 3.8 4.6 + - - -
67E GLU* 3.2 18.1 + - - -
69E ILE* 1.3 81.9 - - - +
71E LYS* 1.3 63.2 + - - +
73E PRO* 4.8 2.9 - - - +
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Residues in contact with LYS 71 (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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67E GLU* 4.0 6.4 + - + +
68E SER* 3.8 2.1 + - - +
70E SER* 1.3 85.4 - - - +
72E PHE* 1.3 89.4 + - + +
73E PRO* 3.4 8.6 - - - +
154E ILE* 5.8 5.3 - - - +
155E ARG 5.3 5.3 + - - -
157E SER* 4.5 13.0 - - - -
160E GLU* 3.9 32.1 + - - +
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Residues in contact with PHE 72 (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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26E ARG 5.5 3.6 - - - -
27E GLY* 5.9 2.0 - - - -
68E SER* 3.1 42.1 + - - +
69E ILE* 4.2 0.3 - - - -
71E LYS* 1.3 99.8 - - + +
73E PRO* 1.4 65.0 - - - +
74E ASP* 3.1 8.2 + - + +
75E MET* 3.2 25.6 + - + +
155E ARG* 3.8 51.8 - - + +
156E LEU* 4.7 15.3 - - - -
157E SER* 4.7 14.8 - - - -
160E GLU* 5.5 0.4 - - - -
194E GLU* 5.5 2.9 - - - -
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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