Contacts of the helix formed by residues 82 - 91 (chain C) in PDB entry 4HRE
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 82 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75C TYR* 4.4 0.4 - - - -
76C GLN* 3.4 27.3 - - - +
81C LYS* 1.3 73.1 - - - +
83C LEU* 1.3 67.5 + - - +
84C PRO* 4.0 14.3 - - + +
85C SER* 3.0 28.7 + - - +
86C ALA* 3.0 12.0 + - - +
88F VAL* 6.1 1.0 - - - +
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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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42C ILE* 3.9 26.7 - - + -
46C VAL* 5.8 0.4 - - + -
60C LEU* 5.2 0.9 - - + -
71C ILE* 4.2 15.0 - - + -
72C ALA* 3.7 36.4 + - + +
75C TYR* 3.7 36.5 - - + -
81C LYS 3.3 4.8 + - - -
82C GLU* 1.3 70.7 + - - +
84C PRO* 1.3 74.2 - - + +
86C ALA* 2.8 17.1 + - + +
87C LEU* 3.0 36.6 + - + +
103C LEU* 4.4 15.3 - - + -
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Residues in contact with PRO 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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72C ALA* 4.9 9.6 - - + +
82C GLU* 3.3 15.5 - - + +
83C LEU* 1.3 98.3 - - + +
85C SER* 1.3 60.2 + - - +
87C LEU* 3.7 0.5 + - - -
88C LYS* 3.2 25.6 + - - +
100C LEU* 3.8 25.1 - - + +
103C LEU* 4.2 17.7 - - + +
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Residues in contact with SER 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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82C GLU* 3.0 23.3 + - - +
84C PRO* 1.3 77.4 - - - +
86C ALA* 1.3 67.4 + - - +
88C LYS* 3.7 12.9 + - - +
89C SER* 3.2 22.7 + - - -
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Residues in contact with ALA 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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46C VAL* 4.7 13.0 - - + +
75C TYR* 3.7 27.4 - - + +
81C LYS* 6.4 0.9 - - + -
82C GLU 3.0 10.2 + - - +
83C LEU* 2.8 19.7 + - + +
85C SER* 1.3 71.7 - - - +
87C LEU* 1.3 50.8 + - + +
89C SER* 3.1 8.8 + - - -
90C ALA* 2.7 35.6 + - - +
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Residues in contact with LEU 87 (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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42C ILE* 5.2 0.2 - - + -
46C VAL* 4.7 6.7 - - + -
56C ILE* 3.5 38.4 - - + -
60C LEU* 3.8 12.6 - - + -
83C LEU* 3.0 29.2 + - + +
84C PRO 4.2 2.9 - - - +
86C ALA* 1.3 74.3 - - + +
88C LYS* 1.3 60.3 + - - +
90C ALA* 4.1 4.9 - - + +
91C LEU* 2.8 54.4 + - + +
96C GLU* 4.3 0.2 - - - +
99C ILE* 3.7 15.5 - - + -
100C LEU* 4.3 7.4 - - + -
103C LEU* 3.5 28.5 - - + -
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Residues in contact with LYS 88 (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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84C PRO 3.2 20.1 + - - +
85C SER* 4.0 12.8 - - - +
86C ALA 3.4 0.2 - - - -
87C LEU* 1.3 76.2 - - - +
89C SER* 1.3 62.9 + - - +
91C LEU 3.5 11.8 - - - +
96C GLU* 3.5 24.4 - - - +
100C LEU* 3.8 22.7 - - + +
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Residues in contact with SER 89 (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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85C SER 3.2 11.5 + - - -
86C ALA* 3.1 11.2 + - - -
88C LYS* 1.3 79.9 - - - +
90C ALA* 1.3 63.9 + - - +
91C LEU 3.4 5.4 + - - +
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Residues in contact with ALA 90 (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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46C VAL* 3.5 32.5 - - + -
51C VAL* 3.7 36.7 - - + +
53C GLU* 5.1 2.6 - - - +
86C ALA 2.7 15.1 + - - +
87C LEU* 4.1 8.7 - - + +
89C SER* 1.3 73.4 - - - +
91C LEU* 1.3 66.9 + - + +
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Residues in contact with LEU 91 (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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51C VAL* 4.3 0.4 - - + -
53C GLU* 4.1 24.5 - - + -
56C ILE* 4.0 28.0 - - + -
57C VAL* 5.6 2.0 - - + -
87C LEU* 2.8 37.9 + - + +
88C LYS 3.5 15.8 - - - +
89C SER 3.7 4.3 - - - +
90C ALA* 1.3 81.8 - - + +
92C SER* 1.3 64.2 + - - +
95C LEU* 4.5 10.5 - - + -
96C GLU* 3.7 22.7 - - + +
99C ILE* 3.7 36.8 - - + -
100C LEU* 5.8 0.2 - - + -
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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