Contacts of the helix formed by residues 61 - 75 (chain C) in PDB entry 4DQ0
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 61 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59C ASP* 3.2 17.6 + - - +
60C LYS* 1.3 82.4 - - + +
62C ALA* 1.3 62.4 + - - +
63C MET* 2.9 24.0 + - - +
64C SER* 3.0 14.5 + - - +
65C ILE* 3.0 26.3 + - - +
84C VAL* 4.8 0.4 - - - -
137D ASP* 2.9 34.4 + - - -
142D PRO* 3.9 0.4 - - - +
143D CYS* 3.1 28.9 + - - +
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Residues in contact with ALA 62 (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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110A ALA* 3.8 30.7 - - + +
111A LYS* 3.9 14.4 - - - +
114A PRO* 5.6 0.7 - - - -
60C LYS 3.4 5.6 + - - +
61C ASN* 1.3 72.5 + - - +
63C MET* 1.3 59.5 + - + +
65C ILE* 3.5 1.9 + - - +
66C ALA* 2.8 28.8 + - - +
84C VAL* 3.9 23.2 - - + +
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Residues in contact with MET 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A PRO* 4.7 14.3 - - + +
152A LYS* 5.8 1.1 - - - +
155A GLU* 5.0 10.3 - - - +
159A TYR* 5.4 4.5 - - - +
61C ASN* 2.9 6.9 + - - +
62C ALA* 1.3 77.7 - - + +
64C SER* 1.3 64.7 + - - +
66C ALA* 3.3 8.2 + - - +
67C ASN* 3.0 22.5 + - - +
137D ASP* 3.3 28.9 - - - +
138D THR 3.5 17.7 - - - +
139D ALA* 3.9 25.6 - - - +
142D PRO* 3.8 13.6 - - + +
152D LYS* 3.6 26.7 - - - +
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Residues in contact with SER 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C GLY 3.5 21.7 + - - -
41C ASN* 4.6 4.5 - - - +
59C ASP* 4.5 2.0 - - - -
61C ASN* 3.0 21.9 + - - -
63C MET* 1.3 74.4 - - - +
65C ILE* 1.3 58.6 + - - +
67C ASN* 3.1 9.1 + - - +
68C VAL* 2.8 32.3 + - - +
142D PRO* 3.9 11.5 - - - +
143D CYS 3.6 19.2 + - - -
144D THR* 3.8 15.8 - - - +
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Residues in contact with ILE 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LYS* 4.0 20.0 - - + -
39C CYS* 3.8 29.4 - - - -
40C GLY 5.3 0.4 - - - +
57C ALA 3.8 15.7 - - - +
59C ASP* 4.0 14.4 - - + +
61C ASN 3.0 19.2 + - - +
62C ALA 3.7 3.4 - - - +
64C SER* 1.3 77.2 - - - +
66C ALA* 1.3 61.4 + - - +
68C VAL* 3.2 8.2 + - + +
69C GLU* 2.9 21.2 + - + +
82C THR* 3.6 29.2 - - + +
83C ARG 4.1 7.9 - - - +
84C VAL* 4.0 20.9 - - + -
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Residues in contact with ALA 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LYS* 3.4 26.5 - - - +
114A PRO* 3.7 26.5 - - + -
115A GLY 5.2 2.2 - - - +
62C ALA 2.8 19.7 + - - +
63C MET 3.7 5.4 - - - +
64C SER 3.3 0.4 - - - -
65C ILE* 1.3 72.7 - - - +
67C ASN* 1.3 59.0 + - - +
69C GLU* 3.1 8.8 + - - +
70C ARG* 2.8 27.8 + - - +
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Residues in contact with ASN 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C TYR 5.6 0.8 + - - -
15C LEU* 4.1 18.0 - - - +
41C ASN* 5.0 4.4 + - - +
63C MET 3.0 12.7 + - - +
64C SER* 3.4 10.5 + - - +
66C ALA* 1.3 73.6 - - - +
68C VAL* 1.3 67.0 + - - +
70C ARG* 2.9 46.8 + - - +
71C ILE* 3.0 41.3 + - - +
142D PRO* 5.8 3.6 - - + -
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Residues in contact with VAL 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C CYS* 4.9 2.2 - - - -
40C GLY 4.7 2.0 - - - +
41C ASN 3.8 23.1 - - - +
42C GLY* 4.0 12.8 - - - +
45C SER* 5.6 0.7 - - - -
46C LEU* 4.5 9.5 - - + +
57C ALA* 5.1 3.8 - - + -
64C SER 2.8 24.6 + - - +
65C ILE* 3.2 17.9 + - + +
67C ASN* 1.3 73.4 - - - +
69C GLU* 1.3 58.1 + - - +
71C ILE* 3.1 10.0 + - - +
72C LYS* 2.8 26.4 + - + +
80C LEU* 3.9 23.8 - - + -
82C THR* 3.8 21.3 - - + -
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Residues in contact with GLU 69 (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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111A LYS* 4.8 9.8 - - + +
65C ILE* 2.9 19.7 + - + +
66C ALA* 3.1 10.5 + - - +
68C VAL* 1.3 71.6 - - - +
70C ARG* 1.3 66.7 + - - +
72C LYS* 3.3 32.7 + - - +
73C SER* 3.1 24.1 + - - -
82C THR* 2.7 40.5 + - + +
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Residues in contact with ARG 70 (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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13C TYR* 4.1 20.4 + - - +
66C ALA 2.8 12.4 + - - +
67C ASN* 2.9 40.4 + - - +
69C GLU* 1.3 76.9 - - - +
71C ILE* 1.3 73.8 + - - +
73C SER* 3.4 4.6 + - - -
74C ILE* 3.3 47.8 + - + +
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Residues in contact with ILE 71 (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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9C PHE* 4.2 1.8 - - + -
13C TYR* 3.4 49.8 - - + -
15C LEU* 3.7 24.9 - - + -
41C ASN 5.6 0.7 - - - +
46C LEU* 3.8 24.7 - - + -
67C ASN* 3.0 28.5 + - - +
68C VAL* 3.6 6.5 - - - +
70C ARG* 1.3 86.5 - - - +
72C LYS* 1.3 66.6 + - - +
74C ILE* 3.1 7.6 + - - +
75C GLU* 2.9 29.2 + - + +
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Residues in contact with LYS 72 (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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46C LEU* 4.6 1.3 - - - +
68C VAL* 2.8 16.4 + - + +
69C GLU* 3.4 37.8 + - - +
71C ILE* 1.3 73.0 - - - +
73C SER* 1.3 59.4 + - - +
75C GLU 3.5 0.2 + - - -
76C ASN* 2.9 23.7 + - - -
77C LEU* 2.9 52.9 + - + +
78C ASP* 4.7 10.6 + - - +
80C LEU* 2.8 39.3 + - + +
81C HIS* 4.7 10.9 + - - +
82C THR* 5.6 0.2 - - + -
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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
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91A THR* 5.5 3.6 + - - +
69C GLU 3.1 13.8 + - - -
70C ARG* 3.7 6.1 - - - -
71C ILE 3.2 0.2 - - - -
72C LYS* 1.3 79.0 - - - +
74C ILE* 1.3 67.1 + - - +
76C ASN* 3.2 24.0 + - - +
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Residues in contact with ILE 74 (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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12C LYS* 5.2 5.2 - - - +
13C TYR* 3.4 29.4 - - + +
70C ARG* 3.3 40.1 + - + +
71C ILE* 3.1 7.2 + - - +
73C SER* 1.3 78.7 - - - +
75C GLU* 1.3 64.3 + - - +
76C ASN* 3.4 10.7 + - - +
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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
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4C ARG* 3.7 10.9 + - - -
8C TYR* 2.8 30.7 + - - -
9C PHE* 4.0 18.3 - - + -
12C LYS* 2.9 21.5 + - - -
13C TYR* 2.3 33.6 + - - +
71C ILE* 2.9 19.5 + - + +
74C ILE* 1.3 76.9 - - - +
76C ASN* 1.3 72.9 + - - +
77C LEU* 3.3 25.7 + - + +
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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