Contacts of the helix formed by residues 75 - 90 (chain C) in PDB entry 5B6N
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 SER 75 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C ASP* 1.3 77.3 - - - +
76C VAL* 1.3 66.1 + - - +
77C GLU* 3.1 11.2 - - - +
78C ASP* 3.0 31.9 + - - +
79C HIS* 3.1 15.3 + - - -
104C ASP* 3.2 7.6 - - - -
106C ARG* 3.5 22.9 - - - +
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Residues in contact with VAL 76 (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 ASN* 4.2 10.8 - - + -
18C THR 3.7 28.5 - - - +
19C THR* 4.3 4.5 - - + +
75C SER* 1.3 71.3 - - - +
77C GLU* 1.3 65.7 + - - +
79C HIS* 3.2 10.2 + - + +
80C LEU* 3.0 46.3 + - + +
104C ASP* 3.6 28.3 + - + -
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Residues in contact with GLU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C SER* 4.1 11.4 - - - +
76C VAL* 1.3 79.3 - - - +
78C ASP* 1.3 66.0 + - - +
80C LEU* 3.7 8.9 + - - +
81C ALA* 3.2 23.6 + - - +
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Residues in contact with ASP 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ASP* 3.9 3.8 - - - +
43C PHE* 3.9 19.2 - - + -
74C ASP* 4.0 26.4 - - + +
75C SER* 3.0 23.5 + - - +
77C GLU* 1.3 82.3 - - - +
79C HIS* 1.3 60.7 + - - +
81C ALA* 3.7 6.0 - - - +
82C TRP* 2.8 31.9 + - - +
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Residues in contact with HIS 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C THR* 3.5 15.5 - - + -
42C ASP* 2.6 31.1 + - - -
72C SER* 3.8 21.3 - - - -
74C ASP 3.7 23.8 + - - -
75C SER 3.1 9.1 + - - -
76C VAL* 3.2 21.7 + - + +
78C ASP* 1.3 75.1 - - - +
80C LEU* 1.3 53.2 + - - +
82C TRP* 2.9 6.2 + - - +
83C SER* 2.8 38.6 + - - -
102C ILE* 3.3 39.7 - - + +
103C ILE 3.2 22.9 + - - -
104C ASP* 3.9 2.4 + - - -
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Residues in contact with LEU 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C THR* 3.6 38.8 - - + +
76C VAL* 3.0 29.3 + - + +
77C GLU* 3.8 7.0 - - - +
79C HIS* 1.3 80.3 - - - +
81C ALA* 1.3 60.6 + - - +
83C SER* 3.4 11.8 + - - -
84C LYS* 3.6 3.1 - - - +
96C GLU* 3.4 62.7 - - + +
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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
----------------------------------------------------------
43C PHE* 4.1 14.4 - - + -
77C GLU 3.2 15.5 + - - +
78C ASP* 3.7 6.5 - - - +
79C HIS 3.2 0.4 - - - -
80C LEU* 1.3 77.4 - - - +
82C TRP* 1.3 63.6 + - - +
84C LYS* 3.4 33.0 - - - +
85C ASP* 3.2 15.4 - - - +
96C GLU* 5.1 0.4 + - - -
213D SER* 5.2 2.0 - - - -
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Residues in contact with TRP 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C HIS* 3.4 28.9 - + - -
42C ASP* 3.3 22.9 - - + +
43C PHE* 3.3 40.0 - + + +
44C THR 4.4 0.2 - - - -
47C CSD 3.4 43.3 - - + -
48C THR* 3.5 17.5 + - - +
51C LEU* 3.7 17.9 - - + -
78C ASP 2.8 17.6 + - - +
79C HIS 3.2 5.4 - - - +
81C ALA* 1.3 75.6 - - - +
83C SER* 1.3 53.7 + - - +
84C LYS 2.9 4.9 - - - -
85C ASP* 2.4 30.9 + - + +
86C ILE* 2.9 28.6 + - + +
102C ILE* 4.7 8.3 - - + -
217D TYR* 3.5 22.9 + - - -
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Residues in contact with SER 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C THR* 5.0 2.8 - - - +
79C HIS 2.8 16.7 + - - -
80C LEU* 3.6 5.3 - - - -
81C ALA 3.3 0.2 - - - -
82C TRP* 1.3 75.9 - - - +
84C LYS* 1.3 56.6 + - - +
85C ASP 3.2 0.2 - - - -
86C ILE* 3.8 13.4 - - - +
87C ASN* 3.2 27.2 + - - +
95C THR 2.9 9.9 - - - +
96C GLU 3.4 29.0 + - - -
97C LYS 4.4 0.2 - - - -
98C LEU* 3.8 26.2 - - - +
102C ILE* 4.2 6.1 - - - +
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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
----------------------------------------------------------
80C LEU 3.6 9.9 - - - +
81C ALA* 3.4 31.5 - - - +
82C TRP 2.8 0.4 + - - -
83C SER* 1.3 80.1 - - - +
85C ASP* 1.3 63.3 + - - +
87C ASN 4.1 0.2 - - - -
88C ALA* 3.5 11.8 + - - +
94C PRO* 3.6 16.4 - - + +
95C THR* 3.2 24.9 - - - +
96C GLU* 4.0 21.5 + - + -
212D PRO* 3.1 31.6 - - + +
213D SER* 6.0 1.6 - - - +
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Residues in contact with ASP 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C PHE* 4.1 5.4 - - - -
48C THR* 4.4 3.0 - - - +
81C ALA 3.2 15.2 - - - +
82C TRP* 2.4 24.7 + - + +
84C LYS* 1.3 75.6 - - - +
86C ILE* 1.3 61.1 + - - -
87C ASN 3.4 0.4 - - - -
88C ALA 3.5 0.6 + - - -
89C TYR* 3.2 21.5 + - - +
211D LEU* 3.1 21.9 - - + +
212D PRO* 3.9 6.5 - - - +
213D SER* 2.3 45.1 + - - -
217D TYR* 3.1 28.7 + - - +
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Residues in contact with ILE 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C THR* 3.9 19.3 - - + +
51C LEU* 3.7 25.6 - - + +
52C GLY* 3.7 25.1 - - - -
55C ALA* 5.0 0.7 - - + -
82C TRP* 2.9 55.9 + - + +
83C SER* 3.9 13.7 - - - +
85C ASP* 1.3 76.8 - - - +
87C ASN* 1.3 58.7 + - - +
88C ALA 3.0 5.1 + - - -
89C TYR* 3.1 14.4 + - - +
90C ASN* 3.3 14.6 + - - +
98C LEU* 4.1 20.2 - - + -
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Residues in contact with ASN 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ALA* 5.1 3.5 - - - +
83C SER 3.2 19.1 + - - +
84C LYS 4.4 0.2 - - - -
85C ASP 3.4 0.4 - - - -
86C ILE* 1.3 79.8 - - - +
88C ALA* 1.3 56.5 + - - +
90C ASN* 4.1 10.3 + - - -
92C GLU* 2.8 49.9 + - + +
93C GLU 4.0 14.4 - - - +
94C PRO* 4.1 5.8 - - + -
95C THR* 3.4 14.3 + - - -
97C LYS 2.6 30.7 + - - +
98C LEU* 3.6 15.8 - - - +
99C PRO* 5.6 1.4 - - - +
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Residues in contact with ALA 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 LYS 3.5 17.6 + - - +
85C ASP 3.5 2.4 + - - +
86C ILE 3.0 0.6 - - - -
87C ASN* 1.3 77.5 - - - +
89C TYR* 1.3 61.6 - - - +
90C ASN 3.0 1.6 - - - -
91C CYS* 3.1 20.8 + - - +
92C GLU 4.0 6.5 - - - +
94C PRO* 4.6 7.4 - - + -
209D LYS* 4.6 12.8 + - - -
210D GLU 5.8 1.3 - - - +
211D LEU* 4.9 3.8 - - + -
212D PRO* 3.9 21.8 - - + -
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Residues in contact with TYR 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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48C THR* 4.1 20.4 - - + -
49C THR* 3.8 43.4 + - + +
52C GLY* 4.5 4.9 - - - -
53C ARG 5.2 0.2 - - - -
85C ASP 3.2 13.6 + - - +
86C ILE 3.1 9.8 + - - +
88C ALA* 1.3 76.0 - - - +
90C ASN* 1.3 77.9 + - - +
91C CYS* 3.2 9.7 + - - -
179D VAL* 5.1 2.9 - - - +
209D LYS* 5.5 7.0 - - + +
211D LEU* 4.9 4.0 - - + +
218D LEU* 4.2 24.9 - - + -
220D TYR* 3.8 22.3 + + - -
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Residues in contact with ASN 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C GLY* 2.7 40.2 + - - +
55C ALA* 4.1 9.9 - - - +
56C LYS* 3.5 37.4 + - - +
86C ILE* 3.3 12.5 + - - +
87C ASN* 4.5 6.3 + - - +
88C ALA 3.0 0.6 - - - -
89C TYR* 1.3 93.2 - - - +
91C CYS* 1.3 71.0 + - - +
92C GLU* 3.2 18.3 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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