Contacts of the helix formed by residues 73 - 89 (chain C) in PDB entry 2V32
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 73 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C ASP* 1.3 77.6 - - - +
74C VAL* 1.3 63.7 + - - +
75C ALA* 3.4 10.8 + - - +
76C ASP* 2.7 47.7 + - - +
77C HIS* 3.2 18.7 + - - -
100C ALA* 3.9 3.6 - - - -
102C GLU* 3.6 29.4 + - - +
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Residues in contact with VAL 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ASP* 4.1 13.9 - - - +
16C SER* 3.5 41.3 - - - +
17C THR* 3.9 5.6 - - - +
73C ASN* 1.3 75.7 - - - +
75C ALA* 1.3 63.5 + - - +
77C HIS* 3.1 10.0 + - - +
78C LYS* 2.9 54.1 + - + +
100C ALA* 3.9 13.8 - - + +
102C GLU* 4.9 1.0 + - - -
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Residues in contact with ALA 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ASN* 3.3 10.9 + - - +
74C VAL* 1.3 79.6 - - - +
76C ASP* 1.3 65.1 + - - +
78C LYS* 3.3 8.7 + - - +
79C GLU* 3.1 23.3 + - - +
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Residues in contact with ASP 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ASP* 3.3 11.4 - - - +
41C PHE* 3.8 25.7 - - + -
72C ASP* 4.4 15.4 - - + +
73C ASN* 2.7 34.4 + - - +
75C ALA* 1.3 72.4 - - - +
77C HIS* 1.3 57.8 + - - +
79C GLU* 3.2 8.6 + - - +
80C TRP* 2.8 37.6 + - - +
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Residues in contact with HIS 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C THR* 3.6 15.9 - - + -
40C ASP* 2.4 42.5 + - - -
70C SER* 3.1 21.5 + - - -
72C ASP* 3.6 10.8 - - + +
73C ASN 3.2 9.6 + - - -
74C VAL* 3.1 10.8 + - - +
76C ASP* 1.3 75.5 - - - +
78C LYS* 1.3 52.5 + - - +
80C TRP* 3.8 1.3 - - - +
81C SER* 2.6 39.5 + - - -
98C ILE* 3.4 36.9 + - + +
99C ILE 3.0 32.5 - - - -
100C ALA* 3.5 14.3 + - - +
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Residues in contact with LYS 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C SER 5.3 0.2 + - - -
17C THR* 3.5 37.4 + - + +
74C VAL* 2.9 38.2 + - + +
75C ALA* 3.9 7.0 - - - +
77C HIS* 1.3 72.6 - - - +
79C GLU* 1.3 68.1 + - - +
81C SER* 3.5 16.5 + - - -
82C GLU* 3.9 13.0 + - - +
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Residues in contact with GLU 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C PHE* 3.6 19.7 - - + -
75C ALA 3.1 15.8 + - - +
76C ASP* 3.8 10.4 - - - +
78C LYS* 1.3 77.6 - - - +
80C TRP* 1.3 63.4 + - - +
82C GLU* 3.3 21.1 + - - +
83C ASP* 4.1 4.7 + - - +
208D SER* 3.9 18.0 - - - +
210D LYS* 3.7 21.4 + - - -
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Residues in contact with TRP 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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37C HIS* 3.2 37.9 - + - -
40C ASP* 3.5 18.2 - - + -
41C PHE* 3.3 47.1 - + + +
45C SER* 3.8 6.5 - - - -
46C THR* 2.9 41.2 + - - +
49C LEU* 3.6 33.4 - - + -
76C ASP 2.8 17.6 + - - +
77C HIS 4.0 0.9 - - - +
79C GLU* 1.3 73.9 - - - +
81C SER* 1.3 56.6 + - - +
82C GLU 3.0 2.2 - - - -
83C ASP* 2.7 26.8 + - + +
84C VAL* 3.1 24.9 + - + +
98C ILE* 4.5 11.2 - - + -
212D TYR* 3.4 18.4 + - - -
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Residues in contact with SER 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C THR* 5.1 2.3 - - - +
77C HIS 2.6 24.6 + - - -
78C LYS* 3.7 10.5 - - - -
79C GLU 3.4 0.2 - - - -
80C TRP* 1.3 77.0 - - - +
82C GLU* 1.3 53.0 + - - +
84C VAL* 3.1 11.9 + - - +
85C LYS* 2.7 45.3 + - - +
94C MET* 3.5 27.2 - - - +
98C ILE* 3.6 19.2 - - - +
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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
----------------------------------------------------------
78C LYS 3.9 9.9 - - - +
79C GLU* 3.5 15.0 - - - +
80C TRP 3.0 1.0 + - - -
81C SER* 1.3 73.8 - - - +
83C ASP* 1.3 66.2 + - - +
85C LYS* 2.9 41.9 + - - +
86C CYS* 3.1 23.9 + - - +
207D PRO* 3.6 20.5 - - + +
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Residues in contact with ASP 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C PHE* 3.9 4.5 - - - -
46C THR* 4.2 4.4 - - + +
79C GLU 4.4 1.7 - - - +
80C TRP* 2.7 22.1 + - + +
82C GLU* 1.3 73.5 - - - +
84C VAL* 1.3 55.5 + - - +
86C CYS* 3.4 4.5 - - - +
87C LEU* 3.0 29.6 + - - +
206D VAL* 3.7 15.6 - - + +
207D PRO* 3.3 12.3 - - - +
208D SER* 2.7 50.2 + - - -
212D TYR* 2.5 34.1 + - - +
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Residues in contact with VAL 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C THR* 4.0 13.0 - - + -
49C LEU* 3.7 40.2 - - + +
50C GLY* 3.8 2.3 - - - +
53C ILE* 3.8 13.0 - - + -
80C TRP* 3.1 53.4 + - + +
81C SER* 3.1 12.5 + - - +
83C ASP* 1.3 74.8 - - - +
85C LYS* 1.3 57.7 + - - +
87C LEU* 3.2 4.2 + - - +
88C SER* 2.9 27.7 + - - -
94C MET* 4.2 9.2 - - + -
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Residues in contact with LYS 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ILE* 4.1 8.1 - - + -
81C SER* 2.7 24.0 + - - +
82C GLU* 2.9 46.4 + - - +
84C VAL* 1.3 69.1 - - - +
86C CYS* 1.3 66.6 + - - +
88C SER* 2.7 25.4 + - - -
89C GLY* 3.2 3.8 + - - -
90C VAL 4.1 10.9 - - - +
92C GLY 3.5 23.1 + - - +
93C ASP* 4.5 13.5 + - - -
94C MET* 4.2 31.1 - - - +
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Residues in contact with CYS 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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200A ASN* 3.4 12.1 + - - +
82C GLU 3.1 13.9 + - - +
83C ASP 3.4 9.4 - - - +
85C LYS* 1.3 79.6 - - - +
87C LEU* 1.3 62.9 + - - +
89C GLY* 3.2 9.7 + - - -
204D LYS* 4.0 23.6 - - - -
205D ALA 4.9 1.1 - - - -
206D VAL* 5.0 2.2 - - + -
207D PRO* 3.8 24.5 - - + -
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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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200A ASN* 3.3 31.6 + - + +
217A PRO* 5.9 0.5 - - - +
46C THR* 3.9 19.3 - - + +
47C THR* 3.9 38.8 - - + +
50C GLY* 5.1 2.2 - - - -
54C GLN* 4.3 5.5 + - - -
83C ASP 3.0 16.4 + - - +
84C VAL 3.2 3.8 + - - +
86C CYS* 1.3 75.6 - - - +
88C SER* 1.3 64.6 + - - +
204D LYS* 4.3 10.5 - - + -
213D LEU* 4.0 19.1 - - + -
215D TYR* 3.8 15.9 - - - +
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Residues in contact with SER 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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200A ASN* 4.2 1.2 + - - -
217A PRO* 5.3 1.0 - - - +
50C GLY* 3.4 29.1 - - - -
53C ILE* 3.6 25.3 - - - +
54C GLN* 3.0 27.9 + - - +
84C VAL 2.9 13.2 + - - -
85C LYS* 2.7 21.6 + - - -
87C LEU* 1.3 78.3 - - - +
89C GLY* 1.3 57.8 + - - +
90C VAL* 3.0 14.7 + - - +
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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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199A PRO* 5.5 6.9 - - - +
200A ASN* 3.5 17.7 - - - -
85C LYS 3.2 1.9 + - - -
86C CYS 3.2 12.8 + - - -
87C LEU 3.2 0.6 - - - -
88C SER* 1.3 76.9 + - - +
90C VAL* 1.3 61.5 + - - +
91C LYS* 4.1 2.6 + - - +
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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