Contacts of the helix formed by residues 68 - 78 (chain E) in PDB entry 1GUL
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 THR 68 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15E ARG* 3.7 25.8 - - + +
18E SER* 5.0 3.8 - - - +
19E VAL* 4.6 7.9 - - + -
56E PRO* 3.4 15.1 - - + +
67E GLN* 1.3 72.3 + - - +
69E ARG* 1.3 70.4 + - + +
71E ILE* 3.2 13.5 + - - +
72E LEU* 3.0 42.2 + - + +
100E LEU* 5.6 5.8 - - + -
301E IBG 2.9 30.2 + - - -
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Residues in contact with ARG 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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15E ARG* 6.0 1.6 - - - +
67E GLN* 3.2 1.6 + - - +
68E THR* 1.3 80.9 - - - +
70E SER* 1.3 58.8 + - - +
72E LEU* 3.4 8.0 + - - +
73E HIS* 2.9 49.9 + - + +
97E GLU* 2.7 31.5 + - - +
100E LEU* 3.8 39.4 - - + +
101E ASP* 4.6 10.1 + - - -
301E IBG 4.6 17.2 + - - -
69F ARG* 3.4 23.1 - - - +
97F GLU* 3.4 30.0 + - + -
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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
----------------------------------------------------------
65E LEU* 5.5 2.0 - - - -
66E VAL 3.7 10.8 - - - -
67E GLN* 2.9 11.5 + - - +
69E ARG* 1.3 75.0 - - - +
71E ILE* 1.3 66.8 + - - +
73E HIS* 3.4 2.4 + - - +
74E TYR* 3.0 23.4 + - - +
90F THR* 5.1 4.0 - - - +
93F ASP* 2.9 38.6 + - - +
94F MET* 3.8 15.3 - - - -
97F GLU* 3.2 18.5 - - - +
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Residues in contact with ILE 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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19E VAL* 4.4 17.9 - - + -
56E PRO* 3.9 37.2 - - + +
58E VAL* 4.1 20.4 - - + -
60E ILE* 6.3 0.2 - - + -
65E LEU* 3.8 36.1 - - + +
66E VAL 3.9 3.1 - - - +
67E GLN 2.9 20.6 + - - +
68E THR* 3.4 7.9 - - - +
70E SER* 1.3 78.8 - - - +
72E LEU* 1.3 62.4 + - - +
74E TYR* 3.0 15.5 + - - +
75E ILE* 3.1 32.3 + - + +
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Residues in contact with LEU 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E SER* 4.0 17.0 - - - -
19E VAL* 3.9 31.0 - - + +
22E VAL* 3.8 28.1 - - + +
68E THR* 3.0 29.7 + - + +
69E ARG* 3.7 9.6 - - - +
71E ILE* 1.3 76.0 - - - +
73E HIS* 1.3 66.0 + - + +
74E TYR 3.3 0.2 + - - -
75E ILE* 3.3 5.9 + - + +
76E ALA* 3.0 24.1 + - - +
96E VAL* 5.4 3.6 - - + -
100E LEU* 4.8 13.2 - - + -
155E LEU* 4.2 18.7 - - + +
159E ILE* 4.3 13.2 - - + -
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Residues in contact with HIS 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E ARG* 2.9 27.2 + - + +
70E SER 3.6 4.9 - - - +
72E LEU* 1.3 78.8 - - + +
74E TYR* 1.3 64.8 + - - +
76E ALA* 3.7 1.4 - - - +
77E ASP* 2.9 30.1 + - - +
82E PHE* 3.6 36.3 - + + -
89E ARG* 5.3 2.0 - - - +
93E ASP* 4.6 4.2 + - - -
96E VAL* 5.8 4.2 - - + +
97E GLU* 4.2 12.3 + - - -
155E LEU* 4.5 9.2 - - + -
73F HIS* 3.9 26.3 - + - -
82F PHE* 6.2 0.2 - - - -
93F ASP* 2.7 30.2 + - - +
97F GLU* 5.0 1.3 - - - -
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Residues in contact with TYR 74 (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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60E ILE* 3.8 29.2 - - + -
61E ASP* 2.5 36.2 + - + +
63E MET* 4.5 8.1 - - - -
65E LEU* 3.7 23.6 - - + -
70E SER 3.0 14.3 + - - +
71E ILE 3.0 6.9 + - - +
73E HIS* 1.3 79.0 - - - +
75E ILE* 1.3 68.2 + - + +
77E ASP* 3.1 4.8 + - - +
78E LYS* 2.8 44.0 + - + +
86F LEU* 3.8 21.5 - - + -
87F LYS* 3.0 32.0 + - - -
90F THR* 3.7 26.2 - - + +
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Residues in contact with ILE 75 (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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19E VAL* 4.1 11.2 - - + +
22E VAL* 3.8 25.6 - - + +
23E LEU* 4.0 36.8 - - + +
26E ALA* 5.0 2.0 - - + -
58E VAL* 5.6 2.5 - - + -
60E ILE* 4.4 20.0 - - + -
71E ILE* 3.1 32.3 + - + +
72E LEU* 3.8 8.1 - - + +
74E TYR* 1.3 80.8 - - + +
76E ALA* 1.3 65.6 + - - +
78E LYS* 3.0 4.1 + - - +
79E HIS* 2.9 44.9 + - + +
81E LEU* 5.2 0.2 - - + -
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Residues in contact with ALA 76 (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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22E VAL* 5.0 0.6 - - - +
72E LEU 3.0 17.3 + - - +
73E HIS 3.7 3.8 - - - +
75E ILE* 1.3 76.5 - - - +
77E ASP* 1.3 60.2 + - - +
79E HIS 2.9 14.7 + - - -
80E ASN* 3.2 1.4 + - - -
81E LEU* 3.0 49.0 + - + -
82E PHE* 3.7 21.2 + - + -
155E LEU* 4.0 15.5 - - + -
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Residues in contact with ASP 77 (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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73E HIS* 2.9 17.8 + - - +
74E TYR 3.6 3.8 - - - +
76E ALA* 1.3 80.5 - - - +
78E LYS* 1.3 62.4 + - - +
79E HIS 3.4 0.2 + - - -
80E ASN* 4.3 3.9 + - - +
82E PHE* 3.4 10.9 - - - +
89E ARG* 2.7 46.3 + - - -
86F LEU* 4.1 28.5 - - + +
89F ARG* 4.5 4.5 + - - -
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Residues in contact with LYS 78 (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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60E ILE* 5.9 0.7 - - + -
61E ASP* 4.1 7.9 - - - +
74E TYR* 2.8 52.7 + - + +
75E ILE* 3.0 3.3 + - - +
77E ASP* 1.3 77.7 - - - +
79E HIS* 1.3 85.5 + - + +
80E ASN 3.8 1.1 - - - -
86F LEU* 3.6 29.2 - - + +
87F LYS* 4.8 5.6 - - - +
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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