Contacts of the helix formed by residues 80 - 90 (chain C) in PDB entry 4WYV
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 PRO 80 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ILE* 4.3 17.7 - - + -
79C PHE* 1.4 92.6 - - + +
81C ALA* 1.3 54.6 + - - +
82C GLU* 3.2 21.5 - - - +
83C GLN* 2.8 55.4 + - + +
87C PHE* 4.8 1.3 - - + -
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Residues in contact with ALA 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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76C LYS 5.3 1.5 + - - +
79C PHE* 3.4 16.1 + - - -
80C PRO* 1.3 69.8 - - - +
82C GLU* 1.3 67.6 + - - +
83C GLN 3.2 0.9 + - - -
84C TYR* 3.2 20.3 + - - +
132C GLY* 4.0 29.0 + - - +
133C PHE 5.1 2.4 + - - +
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Residues in contact with GLU 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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80C PRO* 3.1 17.5 + - - +
81C ALA* 1.3 82.3 + - - +
83C GLN* 1.3 68.7 - - + +
84C TYR* 3.3 4.5 + - - +
85C TYR 5.1 0.5 + - - -
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Residues in contact with GLN 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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20C ILE* 5.5 1.9 - - - +
79C PHE* 4.3 1.6 - - - -
80C PRO* 2.8 38.7 + - + +
82C GLU* 1.3 86.8 - - + +
84C TYR* 1.3 63.5 + - - +
85C TYR 3.3 3.1 - - - -
86C ARG* 3.0 59.6 + - + +
87C PHE* 3.7 27.2 - - + -
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Residues in contact with TYR 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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79C PHE* 3.9 12.7 - + + -
81C ALA 3.2 14.4 + - - +
82C GLU 3.3 3.4 + - - +
83C GLN* 1.3 75.8 - - - +
85C TYR* 1.3 93.0 + + + +
87C PHE 3.5 1.0 + - - -
88C HIS* 3.1 47.6 + + - +
91C TRP* 3.4 33.8 + + - -
95C LEU* 3.5 11.8 - - - +
133C PHE* 3.7 28.3 - + - +
134C HIS* 2.7 50.0 + - + -
136C ASP* 4.6 2.2 + - + -
139C ASP* 4.3 2.4 + - - -
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Residues in contact with TYR 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 5.1 0.6 + - - -
83C GLN 3.3 1.0 - - - -
84C TYR* 1.3 102.4 - + + +
86C ARG* 1.3 64.5 + - - +
87C PHE 3.2 0.6 + - - -
88C HIS* 3.7 25.0 + + + +
89C GLU* 4.0 4.5 - - - +
134C HIS* 5.8 6.7 - - + +
136C ASP* 3.2 42.7 + - - +
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Residues in contact with ARG 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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17C GLU* 3.3 39.3 + - - +
21C ARG* 3.7 15.9 + - - +
83C GLN* 3.0 48.5 + - + +
85C TYR* 1.3 78.8 - - - +
87C PHE* 1.3 72.3 + - + +
89C GLU* 3.3 18.4 - - - +
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Residues in contact with PHE 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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17C GLU* 4.4 11.2 - - + -
20C ILE* 3.7 30.5 - - + -
21C ARG* 3.5 45.3 - - + -
24C ILE* 3.6 22.2 - - + -
79C PHE* 3.9 23.6 - + + -
80C PRO* 4.8 1.8 - - + -
83C GLN* 3.7 35.9 - - + -
84C TYR 3.5 2.0 + - - -
86C ARG* 1.3 91.8 - - + +
88C HIS* 1.3 63.2 + - - +
89C GLU* 3.3 5.4 + - - -
90C HIS* 3.3 16.4 + + + +
91C TRP* 3.1 24.3 - - + -
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Residues in contact with HIS 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 TYR* 3.1 48.6 + + + +
85C TYR* 3.9 27.5 - + + +
86C ARG 3.5 0.4 - - - -
87C PHE* 1.3 77.7 - - - +
89C GLU* 1.3 62.7 + - - +
91C TRP* 3.0 32.0 + - - -
92C ARG* 3.1 49.3 + - + +
136C ASP* 4.0 8.5 + - - -
139C ASP* 2.7 28.0 + - - -
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Residues in contact with GLU 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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21C ARG* 3.8 14.6 + - - -
85C TYR 4.0 4.9 - - - +
86C ARG 3.3 24.5 - - - +
87C PHE 4.5 2.5 - - - -
88C HIS* 1.3 73.8 + - - +
90C HIS* 1.3 71.4 + - + +
91C TRP 3.2 0.6 + - - -
92C ARG* 3.3 50.4 + - - +
93C PHE* 4.9 1.4 + - - +
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Residues in contact with HIS 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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21C ARG* 3.1 42.3 + - + +
24C ILE* 3.7 25.4 - - + -
25C ARG* 3.2 53.6 + - + +
28C VAL* 3.6 19.9 - - + +
32C GLU* 5.0 1.9 - - - +
87C PHE* 3.3 28.2 + + + +
88C HIS 3.2 0.4 + - - -
89C GLU* 1.3 86.2 + - + +
91C TRP* 1.3 58.4 + - - +
93C PHE* 5.2 2.6 + - - +
94C VAL* 5.0 0.3 + - - +
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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