Contacts of the helix formed by residues 75 - 86 (chain C) in PDB entry 4U7D
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 TRP 75 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73C PHE* 2.8 40.3 + + + +
74C PRO* 1.3 95.2 - - + +
76C SER* 1.3 59.5 + - - +
77C GLY 3.1 2.9 - - - -
78C LYS* 2.9 18.0 + - + +
79C VAL* 2.7 52.3 + - + +
100C ILE* 5.4 0.2 - - + -
101C ASN* 3.5 36.4 + - - +
104C MET* 3.6 48.6 - - + +
105C ALA* 3.9 21.5 - - + -
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Residues in contact with SER 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C LYS 4.5 0.2 + - - -
71C GLU* 2.9 45.1 - - - +
73C PHE* 2.8 39.1 + - - +
75C TRP* 1.3 84.8 + - - +
77C GLY* 1.3 62.2 + - - +
79C VAL* 3.6 5.5 - - - +
80C LYS* 3.0 25.8 + - - +
101C ASN* 5.0 0.9 + - - -
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Residues in contact with GLY 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 PHE 4.5 0.8 + - - -
74C PRO 5.0 2.0 + - - -
75C TRP 3.1 0.8 - - - +
76C SER* 1.3 81.3 - - - +
78C LYS* 1.3 60.4 + - - +
80C LYS* 3.7 3.6 + - - +
81C ASP* 3.4 22.7 + - - +
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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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74C PRO 5.3 1.9 + - - +
75C TRP* 2.9 18.8 + - + +
77C GLY* 1.3 74.4 - - - +
79C VAL* 1.3 61.4 + - - +
81C ASP* 3.4 6.5 + - - +
82C ILE* 3.2 34.3 + - + +
128C LEU 5.1 1.5 + - - +
129C CYS* 3.7 43.9 + - + +
130C SER 6.1 0.2 - - - -
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Residues in contact with VAL 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C GLU* 5.0 3.8 - - - +
75C TRP* 2.7 44.1 + - + +
76C SER* 3.6 7.2 - - - +
77C GLY 3.3 0.2 - - - -
78C LYS* 1.3 70.9 - - - +
80C LYS* 1.3 67.3 + - - +
81C ASP 3.2 0.2 + - - -
82C ILE* 3.3 3.9 + - - +
83C LEU* 3.0 21.8 + - - +
92C PHE* 3.7 28.9 - - + -
97C LEU* 5.2 5.4 - - + -
100C ILE* 4.4 12.8 - - + -
101C ASN* 5.8 0.7 - - - +
104C MET* 4.9 2.0 - - + -
125C LEU* 3.9 22.6 - - + +
129C CYS* 4.0 17.0 - - + -
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Residues in contact with LYS 80 (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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411A LYS* 6.1 4.0 - - + -
71C GLU* 3.9 15.3 - - - +
76C SER 3.0 13.3 + - - +
77C GLY* 4.1 4.7 - - - +
79C VAL* 1.3 82.6 - - - +
81C ASP* 1.3 61.6 + - - +
83C LEU* 3.5 9.6 + - + +
84C GLN* 3.1 35.3 + - + +
92C PHE* 5.2 1.8 - - + -
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Residues in contact with ASP 81 (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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411A LYS* 5.3 5.5 - - - +
77C GLY 3.4 16.0 + - - +
78C LYS* 3.7 7.0 - - - +
79C VAL 3.1 0.8 - - - -
80C LYS* 1.3 80.2 - - - +
82C ILE* 1.3 61.7 + - - +
84C GLN* 4.9 1.1 - - - -
85C ASN* 2.5 65.1 + - - +
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Residues in contact with ILE 82 (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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78C LYS* 3.2 23.6 + - + +
79C VAL 3.3 3.6 + - - +
81C ASP* 1.3 79.7 - - - +
83C LEU* 1.3 65.6 + - - +
86C VAL* 3.0 21.0 + - + -
87C PHE* 2.9 49.4 + - + -
125C LEU* 4.0 10.1 - - + -
128C LEU* 3.9 29.2 - - + +
129C CYS* 3.2 31.6 - - - -
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Residues in contact with LEU 83 (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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79C VAL 3.0 13.8 + - - +
80C LYS* 3.5 10.1 - - + +
82C ILE* 1.3 78.6 - - - +
84C GLN* 1.3 60.7 + - + +
87C PHE* 3.1 6.5 - - - +
88C LYS 2.9 23.6 + - - -
89C LEU* 3.0 34.8 + - + +
90C GLU 3.9 21.5 - - - +
91C LYS* 4.0 10.5 - - - +
92C PHE* 3.7 47.6 - - + -
121C LEU* 3.8 19.3 - - + -
125C LEU* 3.9 11.2 - - + +
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Residues in contact with GLN 84 (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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285A ASN* 6.0 0.2 - - - +
384A ARG* 5.5 0.3 + - - -
409A ASP 4.4 2.6 + - - -
410A MET* 3.1 47.8 - - + +
411A LYS* 2.7 45.1 + - - +
80C LYS* 3.1 22.0 + - + +
81C ASP 4.2 1.3 - - - +
83C LEU* 1.3 84.3 - - + +
85C ASN* 1.3 69.3 + - - +
88C LYS* 3.3 12.0 - - - +
89C LEU 3.1 15.9 - - - +
90C GLU* 3.3 27.1 + - - +
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Residues in contact with ASN 85 (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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315A GLN* 3.7 22.1 + - - +
384A ARG* 3.1 32.9 + - - +
411A LYS* 3.9 11.1 - - - +
81C ASP* 2.5 59.0 + - - +
84C GLN* 1.3 82.9 - - - +
86C VAL* 1.3 61.0 + - + +
88C LYS* 2.6 28.7 + - - +
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Residues in contact with VAL 86 (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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82C ILE* 3.0 32.6 + - + +
85C ASN* 1.3 83.0 - - + +
87C PHE* 1.3 64.3 + - + +
88C LYS* 3.3 10.3 + - - +
128C LEU* 3.9 24.0 - - + -
154C LEU* 3.4 29.0 - - - +
156C ILE* 4.0 20.6 - - + -
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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