Contacts of the helix formed by residues 68 - 78 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C ARG* 3.7 25.4 - - + +
18C SER* 5.0 3.8 - - - +
19C VAL* 4.6 7.2 - - + -
56C PRO* 3.4 15.1 - - + +
67C GLN* 1.3 72.2 + - - +
69C ARG* 1.3 70.3 + - + +
71C ILE* 3.2 13.5 + - - +
72C LEU* 3.0 42.9 + - + +
100C LEU* 5.6 6.3 - - + -
301C IBG 2.9 29.7 + - - -
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Residues in contact with ARG 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ARG* 6.0 1.6 - - - +
67C GLN* 3.2 1.6 - - - +
68C THR* 1.3 80.0 - - - +
70C SER* 1.3 58.4 + - - +
72C LEU* 3.4 8.3 + - - +
73C HIS* 2.9 49.6 + - + +
97C GLU* 2.7 32.3 + - - +
100C LEU* 3.8 38.1 - - + +
101C ASP* 4.6 10.1 + - - -
301C IBG 4.6 17.4 + - - -
69D ARG* 3.4 23.3 - - - +
97D GLU* 3.4 29.1 + - + -
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Residues in contact with SER 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C LEU* 5.1 2.2 - - - +
66C VAL 3.7 11.2 - - - -
67C GLN* 2.9 12.5 + - - +
69C ARG* 1.3 73.9 - - - +
71C ILE* 1.3 66.4 + - - +
73C HIS* 3.4 2.8 + - - +
74C TYR* 3.0 23.4 + - - +
90D THR* 5.5 3.0 - - - +
93D ASP* 3.1 28.6 + - - +
94D MET* 3.8 15.3 - - - -
97D GLU* 3.0 28.6 - - - +
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Residues in contact with ILE 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C VAL* 4.4 17.9 - - + -
56C PRO* 3.9 37.2 - - + +
58C VAL* 4.1 20.2 - - + -
60C ILE* 6.3 0.2 - - + -
65C LEU* 3.8 35.9 - - + +
66C VAL 3.9 3.4 - - - +
67C GLN 2.9 20.7 + - - +
68C THR* 3.4 8.3 - - - +
70C SER* 1.3 77.9 - - - +
72C LEU* 1.3 62.9 + - - +
74C TYR* 3.0 15.3 + - - +
75C ILE* 3.1 32.4 + - + +
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Residues in contact with LEU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C SER* 4.0 17.0 - - - -
19C VAL* 3.9 31.0 - - + +
22C VAL* 3.8 28.7 - - + +
68C THR* 3.0 29.3 + - + +
69C ARG* 3.7 10.3 - - - +
71C ILE* 1.3 76.6 - - - +
73C HIS* 1.3 65.4 + - + +
74C TYR 3.3 0.2 + - - -
75C ILE* 3.3 5.5 + - + +
76C ALA* 3.0 22.9 + - - +
96C VAL* 5.4 3.1 - - + -
100C LEU* 4.8 13.9 - - + -
155C LEU* 4.2 18.5 - - + +
159C ILE* 4.3 13.5 - - + -
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Residues in contact with HIS 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C ARG* 2.9 30.0 + - + +
70C SER 3.6 4.9 - - - +
72C LEU* 1.3 80.3 - - + +
74C TYR* 1.3 64.7 + - - +
76C ALA* 3.7 1.6 - - - +
77C ASP* 2.9 30.5 + - - +
82C PHE* 3.6 35.9 - + + -
89C ARG* 5.3 2.0 - - - +
93C ASP* 4.6 5.1 + - - -
96C VAL* 5.8 4.2 - - + +
97C GLU* 4.2 12.9 + - - -
155C LEU* 4.5 8.7 - - + -
73D HIS* 3.9 26.2 - + - -
93D ASP* 2.8 29.5 + - - +
97D GLU* 4.9 1.3 - - - -
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Residues in contact with TYR 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ILE* 3.8 28.9 - - + -
61C ASP* 2.5 40.1 + - + +
63C MET* 4.5 9.4 - - - -
65C LEU* 3.7 24.0 - - + -
70C SER 3.0 14.7 + - - +
71C ILE 3.0 7.8 + - - +
73C HIS* 1.3 78.4 - - - +
75C ILE* 1.3 66.3 + - + +
77C ASP* 3.1 4.4 + - - +
78C LYS* 2.8 51.5 + - + +
86D LEU* 4.1 11.0 - - + -
87D LYS* 3.3 27.2 + - - -
90D THR* 3.8 27.1 - - + -
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Residues in contact with ILE 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C VAL* 4.1 12.1 - - + +
22C VAL* 3.8 25.8 - - + +
23C LEU* 4.0 37.2 - - + +
26C ALA* 5.0 2.2 - - + -
58C VAL* 5.6 2.2 - - + -
60C ILE* 4.4 19.7 - - + -
71C ILE* 3.1 31.7 + - + +
72C LEU* 3.8 7.2 - - + +
74C TYR* 1.3 81.4 - - + +
76C ALA* 1.3 64.4 + - - +
78C LYS* 3.0 4.0 + - - -
79C HIS* 2.9 44.8 + - + +
81C LEU* 5.2 0.2 - - + -
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Residues in contact with ALA 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C VAL* 5.0 0.4 - - - +
72C LEU 3.0 17.5 + - - +
73C HIS 3.7 3.4 - - - +
75C ILE* 1.3 77.1 - - - +
77C ASP* 1.3 59.7 + - - +
79C HIS 2.9 14.7 + - - -
80C ASN* 3.2 1.4 + - - -
81C LEU* 3.0 48.7 + - + -
82C PHE* 3.7 20.8 + - + -
155C LEU* 4.0 15.9 - - + -
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Residues in contact with ASP 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C HIS* 2.9 19.9 + - - +
74C TYR 3.6 4.0 - - - +
76C ALA* 1.3 79.7 - - - +
78C LYS* 1.3 62.0 + - - +
79C HIS 3.4 0.5 + - - -
80C ASN 4.3 3.7 + - - +
82C PHE* 3.4 10.3 - - - +
89C ARG* 2.7 46.8 + - - -
86D LEU* 4.1 28.5 - - + +
89D ARG* 4.5 4.0 + - - -
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Residues in contact with LYS 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ILE* 5.9 0.7 - - + -
61C ASP* 4.1 8.3 - - - +
74C TYR* 2.8 53.5 + - + +
75C ILE* 3.0 2.9 + - - +
77C ASP* 1.3 77.3 - - - +
79C HIS* 1.3 87.9 + - + +
80C ASN 3.8 0.7 - - - -
86D LEU* 3.7 29.3 - - + +
87D LYS* 4.7 6.4 - - - +
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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