Contacts of the helix formed by residues 38 - 43 (chain F) in PDB entry 1GLE
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 ASP 38 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36F VAL* 2.6 15.3 + - + +
37F PRO* 1.3 75.1 - - - +
39F VAL* 1.3 61.2 + - - +
40F VAL* 2.5 46.0 + - - +
41F PHE* 2.9 27.3 + - + +
42F ALA* 2.8 28.6 + - - -
93F ILE* 4.8 12.4 - - + +
94F ASP* 5.5 2.6 - - - +
477G THR* 4.6 10.2 - - - +
479G ARG* 3.2 25.6 + - - -
480G ASN* 4.7 6.2 + - - -
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Residues in contact with VAL 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F ASP* 1.3 76.0 + - - +
40F VAL* 1.3 63.0 + - + +
41F PHE 2.8 6.5 - - - -
42F ALA* 3.7 7.2 - - + +
43F GLU* 2.8 50.4 + - + +
45F ILE* 2.8 17.7 - - + +
402G ARG* 4.2 10.3 - - - +
479G ARG* 4.5 14.4 - - - +
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Residues in contact with VAL 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F ASP* 2.5 36.8 + - - +
39F VAL* 1.3 72.1 - - + +
41F PHE* 1.4 57.4 - - + +
44F LYS* 3.3 0.7 + - - -
45F ILE* 2.7 47.4 + - + -
46F VAL* 2.8 32.2 + - + +
427G GLY* 4.5 8.7 - - - +
476G THR* 3.6 20.4 - - + +
477G THR* 4.2 19.1 - - + -
479G ARG* 3.1 29.4 - - - +
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Residues in contact with PHE 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F ILE* 3.2 26.3 - - + +
36F VAL* 3.8 23.8 - - + -
38F ASP* 2.9 20.0 - - + +
39F VAL 2.8 0.2 - - - -
40F VAL* 1.4 79.2 - - + +
42F ALA* 1.3 62.0 - - - +
43F GLU 3.2 1.1 - - - -
44F LYS* 2.9 16.3 + - - +
46F VAL* 4.2 14.1 - - + -
47F GLY 5.5 0.4 - - - -
88F PHE* 4.0 21.5 - + - -
90F HIS* 4.1 12.1 - - + -
93F ILE* 4.4 6.5 - - + -
137F PRO* 3.8 40.4 - - + -
139F VAL* 4.3 17.9 - - + -
477G THR* 3.2 34.3 - - + -
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Residues in contact with ALA 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F ILE 3.8 12.0 + - - +
34F GLU* 4.0 24.9 - - - +
36F VAL 3.3 23.3 - - - +
38F ASP 2.8 10.8 + - - +
39F VAL* 4.2 4.5 - - - -
41F PHE* 1.3 79.7 - - - +
43F GLU* 1.3 62.6 + - + +
44F LYS* 3.6 12.1 + - - +
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Residues in contact with GLU 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F VAL* 2.8 37.1 + - + +
42F ALA* 1.3 76.1 - - + +
44F LYS* 1.3 79.5 + - - +
45F ILE* 3.0 13.0 + - + +
402G ARG* 2.6 36.3 + - - -
404G HIS* 4.6 5.5 + - - -
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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