Contacts of the helix formed by residues 81 - 97 (chain C) in PDB entry 4B94
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 ASP 81 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80C SER* 1.3 71.7 - - - +
82C ALA* 1.3 57.3 + - - +
84C LEU* 3.3 14.2 + - - +
85C ASN* 3.0 31.1 + - - +
123C GLN* 5.7 0.5 + - - -
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Residues in contact with ALA 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C SER* 3.3 7.7 + - - +
81C ASP* 1.3 78.3 - - - +
83C LEU* 1.3 64.0 + - + +
85C ASN* 3.4 7.2 + - - +
86C LYS* 3.1 27.4 + - - +
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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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75C ASN 5.3 1.3 - - - +
76C SER* 3.9 29.1 + - - +
77C VAL 5.5 0.7 - - - -
78C PRO* 3.5 25.6 - - + +
79C LEU* 4.4 9.1 - - + +
80C SER* 3.2 24.9 + - - +
82C ALA* 1.3 81.3 - - + +
84C LEU* 1.4 60.2 + - - +
86C LYS* 3.4 11.4 + - + +
87C LEU* 3.0 28.8 + - - +
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Residues in contact with LEU 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 LEU* 4.0 27.5 - - + +
80C SER 2.9 17.3 + - - +
81C ASP* 3.6 14.4 - - - +
83C LEU* 1.4 76.1 - - - +
85C ASN* 1.3 56.7 + - - +
87C LEU* 3.3 5.5 + - + +
88C ILE* 2.9 49.3 + - + +
119C LEU* 3.8 32.1 - - + +
122C ILE* 4.0 25.8 - - + -
123C GLN* 4.1 22.4 - - + +
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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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81C ASP 3.0 17.0 + - - +
82C ALA* 3.7 7.6 - - - +
84C LEU* 1.3 74.7 - - - +
86C LYS* 1.3 58.1 + - - +
88C ILE* 3.9 6.6 - - - +
89C GLY* 3.0 24.9 + - - -
123C GLN* 2.8 32.4 - - - +
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Residues in contact with LYS 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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72C LEU* 5.3 15.9 - - + -
82C ALA 3.1 17.2 + - - +
83C LEU* 3.7 11.7 - - + +
85C ASN* 1.3 75.5 - - - +
87C LEU* 1.3 57.3 + - - +
89C GLY* 3.3 3.5 + - - -
90C ARG* 3.1 27.3 + - - +
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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
----------------------------------------------------------
69C LEU* 4.1 4.9 - - + +
72C LEU* 3.8 30.7 - - + +
73C GLU* 3.7 39.9 - - + +
76C SER* 4.8 11.0 - - - +
79C LEU* 4.9 9.9 - - + -
83C LEU 3.0 17.9 + - - +
84C LEU* 3.3 5.8 + - + +
86C LYS* 1.3 73.2 - - - +
88C ILE* 1.4 65.1 + - - +
90C ARG* 3.1 4.7 + - - +
91C TYR* 3.1 43.3 + - + -
119C LEU* 4.0 28.7 - - + -
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Residues in contact with ILE 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 LEU* 2.9 28.3 + - + +
85C ASN* 3.9 7.4 - - - +
86C LYS 3.4 0.2 - - - -
87C LEU* 1.4 73.5 - - - +
89C GLY* 1.3 57.2 + - - +
91C TYR* 3.2 10.9 + - - +
92C SER* 3.0 28.6 + - - +
116C PHE* 3.9 9.2 - - + +
119C LEU* 3.7 43.7 - - + +
120C LYS* 3.8 34.3 - - + +
123C GLN* 3.6 35.9 - - + +
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Residues in contact with GLY 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 ASN 3.0 15.3 + - - -
86C LYS* 3.6 5.2 - - - -
87C LEU 3.3 0.2 - - - -
88C ILE* 1.3 75.5 - - - +
90C ARG* 1.3 60.2 + - - +
92C SER* 3.3 10.3 + - - -
93C GLN* 3.1 29.5 + - - +
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Residues in contact with ARG 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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65C TRP* 3.9 19.2 - - + -
68C LEU* 3.8 24.0 - - + +
69C LEU* 3.7 20.3 - - + +
72C LEU* 3.7 30.5 - - + -
86C LYS* 3.1 10.2 + - - +
87C LEU 3.1 8.0 + - - +
89C GLY* 1.3 71.5 - - - +
91C TYR* 1.4 62.6 + - - +
93C GLN* 2.7 46.7 + - - +
94C ALA* 3.1 17.7 + - - +
1196C PGE 3.3 32.7 + - - -
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Residues in contact with TYR 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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66C LEU* 4.7 3.8 - - + +
69C LEU* 3.7 41.8 - - + +
70C LEU* 4.4 10.6 - - - +
73C GLU* 3.3 16.7 + - - -
87C LEU* 3.1 39.6 + - + -
88C ILE* 3.2 9.2 + - - +
90C ARG* 1.4 72.4 - - - +
92C SER* 1.4 60.1 + - - +
94C ALA* 3.2 5.9 + - - +
95C ILE* 3.0 31.2 + - - +
112C ILE* 3.6 36.3 - - + -
115C ARG* 3.5 21.4 - - + +
116C PHE* 3.7 21.5 - - + -
119C LEU* 3.7 24.9 - - + -
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Residues in contact with SER 92 (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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96A GLU 5.1 1.3 + - - -
97A ALA* 6.0 3.3 - - - -
88C ILE* 3.0 15.1 + - - +
89C GLY* 3.3 12.1 + - - -
91C TYR* 1.4 74.2 - - - +
93C GLN* 1.3 59.4 + - - +
95C ILE* 3.4 7.6 + - - +
96C GLU* 3.0 29.7 + - - +
116C PHE* 3.3 28.3 - - - -
120C LYS* 5.2 1.9 + - - -
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Residues in contact with GLN 93 (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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65C TRP* 4.1 8.2 - - + -
89C GLY 3.1 14.3 + - - +
90C ARG* 2.7 55.9 + - - +
92C SER* 1.3 74.4 - - - +
94C ALA* 1.4 63.4 + - - +
96C GLU* 3.4 7.0 + - - +
97C ALA* 3.1 23.9 + - - +
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Residues in contact with ALA 94 (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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65C TRP* 3.5 39.4 - - + -
69C LEU* 3.8 21.1 - - + -
90C ARG 3.1 6.7 + - - +
91C TYR 3.2 8.7 + - - +
93C GLN* 1.4 74.7 - - - +
95C ILE* 1.4 61.3 + - - +
97C ALA* 3.0 11.4 + - - -
98C LEU* 3.1 24.6 + - + +
112C ILE* 4.1 9.6 - - + -
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Residues in contact with ILE 95 (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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93A GLN* 2.9 31.5 + - + +
96A GLU* 3.8 36.8 - - + +
91C TYR 3.0 18.3 + - - +
92C SER* 3.4 5.8 + - - +
94C ALA* 1.4 72.4 - - - +
96C GLU* 1.3 58.3 + - - +
97C ALA 3.4 0.5 + - - -
98C LEU* 3.5 12.5 + - - +
109C PHE* 5.5 2.0 - - + -
112C ILE* 4.0 18.8 - - + +
113C GLN* 3.9 22.0 - - - +
116C PHE* 3.5 48.7 - - + -
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Residues in contact with GLU 96 (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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65A TRP* 3.2 21.4 - - + -
90A ARG* 3.1 32.3 + - - -
93A GLN* 3.4 16.1 + - - +
97A ALA* 5.7 0.7 - - - +
1200A PG4 3.3 32.1 - - - +
92C SER 3.0 18.2 + - - +
93C GLN* 3.8 8.1 - - - +
94C ALA 3.3 0.2 - - - -
95C ILE* 1.3 77.4 - - - +
97C ALA* 1.3 57.4 + - - +
98C LEU 3.5 0.2 - - - -
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Residues in contact with ALA 97 (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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-2C GLY 5.8 2.3 + - - -
-1C PRO 5.1 1.7 - - - +
65C TRP* 3.9 24.5 - - + +
93C GLN 3.1 15.0 + - - +
94C ALA 3.0 6.0 + - - +
96C GLU* 1.3 77.7 - - - +
98C LEU* 1.3 63.0 + - - +
99C PRO* 3.5 10.6 - - - +
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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