Contacts of the helix formed by residues 77 - 85 (chain C) in PDB entry 5HEN
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 ASN 77 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76C THR* 1.3 73.7 - - - +
78C GLN* 1.3 62.7 + - - +
79C LEU 3.3 0.4 - - - -
80C GLN* 3.6 17.7 - - + -
81C TYR* 2.8 30.3 + - - +
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Residues in contact with GLN 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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76C THR* 3.1 21.1 + - + +
77C ASN* 1.3 80.2 + - - +
79C LEU* 1.3 59.0 + - - +
81C TYR* 3.4 5.2 - - - +
82C LEU* 2.8 29.9 + - - +
137C ALA* 5.9 0.7 - - - +
138C ALA* 3.3 23.1 + - + +
180C MET* 3.4 43.6 - - + +
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Residues in contact with LEU 79 (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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76C THR* 4.0 19.4 + - - +
77C ASN 3.3 0.4 - - - -
78C GLN* 1.3 75.2 - - + +
80C GLN* 1.3 58.3 + - + +
82C LEU* 3.4 7.9 + - + +
83C HIS* 3.0 26.3 + - - +
130C LEU* 3.7 23.9 - - + +
135C TYR* 3.2 52.3 - - + +
136C TRP 4.0 4.5 - - - +
137C ALA* 3.9 21.5 - - - +
138C ALA 3.9 9.9 - - - +
141C CYS* 4.1 10.3 - - + -
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Residues in contact with GLN 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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76C THR 3.9 11.8 + - - +
77C ASN* 3.3 20.4 + - + +
78C GLN 3.2 0.6 - - - -
79C LEU* 1.3 76.0 - - + +
81C TYR* 1.3 54.4 + - - +
83C HIS* 3.3 6.6 + - - +
84C LYS* 2.7 75.1 + - + +
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Residues in contact with TYR 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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77C ASN* 2.8 21.8 + - - +
78C GLN* 3.4 4.7 - - - +
80C GLN* 1.3 68.7 - - - +
82C LEU* 1.3 63.5 + - - +
84C LYS* 4.9 0.9 - - - -
85C VAL* 2.9 64.8 + - + +
86C VAL* 3.0 23.1 + - + -
176C LYS* 2.5 38.4 + - - +
179C SER* 3.2 26.7 + - - -
180C MET* 3.5 35.7 - - + +
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Residues in contact with LEU 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 GLN 2.8 14.4 + - - +
79C LEU* 3.6 13.9 - - + +
80C GLN 3.3 0.2 - - - -
81C TYR* 1.3 77.2 - - - +
83C HIS* 1.3 55.9 + - - +
86C VAL* 3.4 29.6 - - + +
87C MET* 2.8 31.4 + - - +
130C LEU* 4.2 4.6 - - + +
138C ALA* 3.6 32.8 - - + +
141C CYS* 3.7 35.7 - - + -
142C MET* 4.5 12.8 - - + -
145C PHE* 5.2 1.9 - - + -
173C PHE* 4.9 3.1 - - + -
177C VAL* 4.6 6.1 - - + -
180C MET* 3.8 21.8 - - + -
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Residues in contact with HIS 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 LEU 3.0 17.3 + - - +
80C GLN* 3.7 8.2 + - - +
82C LEU* 1.3 76.3 - - - +
84C LYS* 1.3 85.1 + - + +
87C MET* 3.5 10.7 - - + +
88C LYS* 3.2 27.2 + - - +
127C LYS* 4.5 11.6 + - + +
130C LEU* 3.9 33.4 + - + +
131C GLU* 3.4 44.0 + - + +
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Residues in contact with LYS 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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80C GLN* 2.7 49.2 + - + +
81C TYR* 4.9 0.2 - - - -
83C HIS* 1.3 99.5 + - + +
85C VAL* 1.3 62.8 + - + +
88C LYS* 3.1 45.6 + - - +
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Residues in contact with VAL 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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81C TYR* 2.9 56.4 + - + +
84C LYS* 1.3 85.8 - - + +
86C VAL* 1.3 67.9 + - + +
87C MET 3.6 0.4 - - - -
88C LYS* 4.0 1.2 - - - +
89C ALA* 3.1 26.0 + - - +
176C LYS* 4.7 15.3 - - + -
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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