Contacts of the helix formed by residues 70 - 88 (chain C) in PDB entry 1C3Q
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 70 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ALA* 4.2 13.2 - - - -
68C THR 4.9 1.8 - - - -
69C LEU* 1.3 74.1 - - - +
71C LYS* 1.3 64.7 + - - +
72C GLU* 3.3 17.6 + - - +
73C SER* 2.9 28.5 + - - -
74C VAL* 3.0 23.7 + - - +
103C PHE* 4.2 5.4 - - - -
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Residues in contact with LYS 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LYS* 6.0 2.3 - - - +
50A GLU* 3.7 34.4 + - + +
70C SER* 1.3 74.1 - - - +
72C GLU* 1.3 71.8 + - - +
74C VAL* 3.4 5.6 + - - +
75C GLU* 3.1 38.4 + - + +
103C PHE* 4.1 14.3 - - + -
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Residues in contact with GLU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLU* 4.3 20.0 - - - +
49C LYS* 6.1 0.2 - - - +
70C SER* 3.5 17.3 + - - +
71C LYS* 1.3 85.6 + - - +
73C SER* 1.3 61.6 + - - +
75C GLU* 3.2 16.5 + - - +
76C ALA* 3.0 21.1 + - - +
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Residues in contact with SER 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ILE* 4.7 7.8 - - - +
47C TYR* 5.7 5.6 - - - -
68C THR 4.8 1.2 + - - -
69C LEU* 3.7 9.7 - - - +
70C SER* 2.9 34.6 + - - -
72C GLU* 1.3 73.8 - - - +
74C VAL* 1.3 63.8 + - - +
76C ALA* 3.3 8.1 + - - +
77C MET* 2.9 40.4 + - - +
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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
----------------------------------------------------------
69C LEU* 4.0 12.6 - - + -
70C SER 3.0 21.5 + - - +
71C LYS* 3.7 7.0 - - - +
73C SER* 1.3 76.7 + - - +
75C GLU* 1.3 65.3 + - + +
77C MET* 3.2 28.2 + - + +
78C ILE* 3.1 37.4 + - + +
103C PHE* 4.9 1.6 - - + -
107C SER* 3.8 38.4 - - - +
110C ASP* 5.1 5.8 - - + +
111C ILE* 4.8 1.6 - - + -
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Residues in contact with GLU 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LYS* 5.3 11.8 + - + +
71C LYS* 3.1 37.1 + - + +
72C GLU* 3.3 16.8 - - - +
73C SER 3.2 0.2 - - - -
74C VAL* 1.3 78.3 - - + +
76C ALA* 1.3 56.8 + - - +
78C ILE* 3.2 9.2 + - - +
79C ILE* 3.0 40.7 + - + +
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Residues in contact with ALA 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ILE* 4.4 6.3 - - + -
47C TYR* 3.3 27.4 - - - +
49C LYS* 4.7 8.2 - - + +
52C VAL* 3.8 13.3 - - + +
72C GLU 3.0 10.3 + - - +
73C SER* 3.6 11.0 - - - +
75C GLU* 1.3 78.5 - - - +
77C MET* 1.3 58.6 + - - +
79C ILE* 3.3 10.6 + - - +
80C ALA* 2.9 32.1 + - - +
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Residues in contact with MET 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ILE* 3.9 22.7 - - + +
64C LEU* 3.7 42.8 - - + +
65C ASN 4.4 13.5 - - - +
66C ILE* 3.5 21.5 - - + -
69C LEU* 5.2 0.4 - - + -
73C SER* 2.9 25.9 + - - +
74C VAL* 3.2 41.9 + - + +
76C ALA* 1.3 77.6 - - - +
78C ILE* 1.3 58.1 + - - +
80C ALA* 3.7 1.2 - - - +
81C GLY* 2.8 25.6 + - - -
111C ILE* 3.4 28.7 - - + -
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Residues in contact with ILE 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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74C VAL* 3.1 27.1 + - + +
75C GLU* 3.7 8.5 - - - +
77C MET* 1.3 74.1 - - - +
79C ILE* 1.3 61.7 + - + +
81C GLY* 3.8 0.2 - - - -
82C LYS* 2.9 46.5 + - + +
110C ASP* 4.2 26.9 - - + +
111C ILE* 4.2 19.5 - - + +
114C GLU* 3.7 28.7 - - + -
115C VAL* 4.1 8.2 - - + +
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Residues in contact with ILE 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LYS* 4.1 32.3 - - + +
52C VAL* 4.0 15.5 - - + -
53C ALA* 4.2 16.2 - - + -
75C GLU* 3.0 31.3 + - + +
76C ALA* 3.3 4.9 + - - +
78C ILE* 1.3 76.9 - - + +
80C ALA* 1.3 64.0 + - - +
82C LYS* 3.4 6.3 + - - +
83C SER* 3.1 21.3 + - - -
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Residues in contact with ALA 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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21C HIS* 4.7 0.4 - - + -
23C ILE* 3.6 24.2 - - + -
52C VAL* 3.9 25.3 - - + +
56C ALA* 3.6 7.8 - - + +
62C LEU* 3.8 11.0 - - + -
76C ALA 2.9 17.5 + - - +
77C MET 3.7 2.2 - - - +
79C ILE* 1.3 79.7 - - - +
81C GLY* 1.3 56.5 + - - +
83C SER* 3.3 4.8 + - - -
84C ALA* 2.9 28.9 + - - +
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Residues in contact with GLY 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LEU* 3.7 15.2 - - - +
64C LEU* 4.9 0.2 - - - -
77C MET 2.8 18.4 + - - -
78C ILE 3.8 1.8 - - - -
79C ILE 3.3 0.2 - - - -
80C ALA* 1.3 77.9 - - - +
82C LYS* 1.3 56.1 + - - +
84C ALA* 3.3 2.8 + - - +
85C ASN* 2.8 33.4 + - - +
91C VAL* 4.6 0.7 - - - -
115C VAL* 3.8 23.5 - - - +
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Residues in contact with LYS 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ILE* 2.9 34.8 + - + +
79C ILE* 3.9 6.3 - - - +
81C GLY* 1.3 72.4 - - - +
83C SER* 1.3 67.6 + - - +
85C ASN* 3.2 9.3 + - - +
86C GLU* 2.9 24.1 + - - +
114C GLU* 2.9 51.4 + - - +
115C VAL* 4.6 0.2 - - + -
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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
----------------------------------------------------------
53C ALA* 2.8 40.0 + - - +
56C ALA* 4.6 1.8 - - - -
57C LYS* 3.7 12.8 + - - +
79C ILE 3.1 14.7 + - - -
80C ALA 3.3 8.0 + - - -
82C LYS* 1.3 75.0 - - - +
84C ALA* 1.3 63.8 + - - +
86C GLU* 3.2 4.5 + - - -
87C HIS* 2.9 37.8 + - - +
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Residues in contact with ALA 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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56C ALA* 4.5 7.1 - - + +
62C LEU* 4.1 12.8 - - + -
80C ALA 2.9 14.5 + - - +
81C GLY 3.4 8.5 - - - +
83C SER* 1.3 77.9 - - - +
85C ASN* 1.3 57.3 + - - +
87C HIS* 3.1 2.5 + - - -
88C GLY 2.9 24.8 + - - -
89C VAL* 2.9 41.1 + - + +
91C VAL* 3.6 13.0 - - + -
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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 GLY 2.8 25.9 + - - +
82C LYS* 3.2 9.3 + - - +
84C ALA* 1.3 73.6 - - - +
86C GLU* 1.3 62.3 + - - +
87C HIS 3.3 0.5 + - - -
88C GLY* 3.4 6.6 + - - +
89C VAL 4.9 1.9 - - - +
91C VAL* 3.9 6.6 - - - +
114C GLU 4.4 2.4 + - - -
115C VAL* 3.5 10.5 - - - +
116C ARG* 2.8 94.9 + - - +
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Residues in contact with GLU 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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82C LYS 2.9 16.6 + - - +
83C SER* 3.6 7.0 - - - +
85C ASN* 1.3 75.8 - - - +
87C HIS* 1.3 76.5 + - + +
88C GLY 3.9 0.3 + - - -
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Residues in contact with HIS 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C LYS* 3.7 62.0 - - + +
83C SER* 2.9 32.3 + - - +
84C ALA 3.1 2.0 + - - +
86C GLU* 1.3 95.7 - - + +
88C GLY* 1.3 61.2 + - - +
89C VAL* 3.3 7.6 + - + +
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Residues in contact with GLY 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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-10C ARG* 3.9 12.8 + - - -
84C ALA 2.9 4.1 + - - -
85C ASN* 3.4 10.6 + - - -
86C GLU 3.5 0.8 - - - -
87C HIS* 1.3 78.3 - - - +
89C VAL* 1.3 60.7 + - - +
90C PRO* 3.4 9.0 - - - +
116C ARG* 5.5 3.8 - - - -
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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