Contacts of the helix formed by residues 61 - 79 (chain C) in PDB entry 1C17
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 61 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ALA* 3.4 30.5 - - - +
23C GLY* 4.5 0.2 - - - -
24C ALA* 3.4 13.9 + - + -
57C MET 3.4 11.4 + - - +
58C GLY* 3.1 14.5 + - - +
60C VAL* 1.3 75.7 - - - +
62C ALA* 1.3 56.3 + - - +
64C PRO* 3.0 19.8 - - - +
65C MET* 4.1 4.2 + - - +
21D ALA* 5.0 7.9 - - - +
22D ILE* 5.9 0.2 - - - -
25D ALA* 3.6 23.5 + - - +
28D ILE* 6.0 1.4 - - - +
59D LEU* 5.4 8.5 - - + +
62D ALA* 5.3 7.4 - - - +
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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
----------------------------------------------------------
61B ASP* 5.4 7.0 - - - +
20C ALA 4.4 0.2 - - - -
21C ALA* 3.3 38.4 - - + +
24C ALA* 3.3 13.5 - - + +
58C GLY 4.0 0.9 + - - +
59C LEU* 5.0 5.6 - - + +
60C VAL* 3.3 0.4 - - - +
61C ASP* 1.3 76.2 - - - +
63C ILE* 1.3 63.9 + - + +
64C PRO* 2.8 6.2 - - - +
65C MET* 3.2 2.1 + - - +
66C ILE* 2.9 35.1 + - + +
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Residues in contact with ILE 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C LEU* 3.7 17.3 - - + +
60C VAL* 3.9 19.5 - - + +
62C ALA* 1.3 76.4 - - - +
64C PRO* 1.3 65.1 - - + +
66C ILE* 3.8 14.4 - - + +
67C ALA* 3.1 26.9 + - + +
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Residues in contact with PRO 64 (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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60C VAL* 2.7 28.0 - - + +
61C ASP* 3.0 15.3 - - - +
62C ALA 2.8 8.3 - - - -
63C ILE* 1.3 90.9 - - + +
65C MET* 1.3 52.4 + - - +
66C ILE 3.0 1.1 - - - -
67C ALA* 3.0 7.4 + - + +
68C VAL* 2.7 45.0 + - + +
66D ILE* 6.1 5.4 - - + -
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Residues in contact with MET 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C MET* 2.7 68.2 - - + +
17C MET* 3.3 5.4 - - - +
20C ALA* 3.0 28.0 - - + -
21C ALA 4.7 0.4 - - - +
61C ASP 4.1 2.4 + - - +
62C ALA 3.2 6.7 + - - +
64C PRO* 1.3 78.8 - - - +
66C ILE* 1.3 52.3 + - - +
68C VAL* 3.2 23.4 + - + +
69C GLY* 2.5 33.1 + - - -
17D MET* 4.1 18.4 - - + -
18D GLY* 5.2 4.9 - - - -
21D ALA* 5.8 1.8 - - - -
66D ILE* 6.1 6.1 - - + -
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Residues in contact with ILE 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PRO* 6.1 5.6 - - + -
65B MET* 6.0 7.2 - - + -
68B VAL* 5.7 12.8 - - + -
17C MET* 3.5 32.2 - - + +
21C ALA* 4.7 7.4 - - + -
62C ALA* 2.9 36.2 + - + +
63C ILE* 3.8 15.5 - - + +
65C MET* 1.3 72.9 - - - +
67C ALA* 1.3 57.9 + - - +
68C VAL 3.0 1.1 - - - -
69C GLY 2.9 0.5 + - - -
70C LEU* 2.5 50.2 + - + +
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Residues in contact with ALA 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ILE* 3.1 17.0 + - + +
64C PRO* 3.0 7.5 + - + +
66C ILE* 1.3 79.8 - - - +
68C VAL* 1.3 59.0 + - + +
70C LEU* 3.6 9.9 - - - +
71C GLY* 2.9 23.4 + - - -
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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
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16C MET* 4.4 9.4 - - - -
64C PRO* 2.7 35.9 + - + +
65C MET* 3.3 26.5 - - + +
67C ALA* 1.3 74.1 - - + +
69C GLY* 1.3 59.1 + - - +
71C GLY* 3.1 1.5 + - - -
72C LEU* 2.9 44.3 + - + +
17D MET* 4.7 8.5 - - + -
66D ILE* 5.8 10.5 - - + -
70D LEU* 6.3 2.9 - - + -
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Residues in contact with GLY 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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13C ALA* 3.1 33.5 - - - +
16C MET* 3.8 8.5 - - - -
17C MET* 3.9 4.9 - - - -
65C MET 2.5 20.0 + - - -
66C ILE 3.4 2.2 - - - -
68C VAL* 1.3 73.3 - - - +
70C LEU* 1.3 57.9 + - - +
72C LEU* 3.7 0.5 + - - +
73C TYR* 2.9 30.7 + - - +
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Residues in contact with LEU 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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68B VAL* 6.2 5.2 - - + -
72B LEU* 6.3 1.8 - - + -
17C MET* 4.3 3.7 - - - -
66C ILE* 2.5 33.2 + - + +
67C ALA* 3.6 10.1 - - - +
69C GLY* 1.3 72.2 - - - +
71C GLY* 1.3 52.5 + - - +
73C TYR* 3.4 10.9 - - + +
74C VAL* 2.6 60.5 + - + +
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Residues in contact with GLY 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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67C ALA 2.9 16.9 + - - -
68C VAL* 3.1 3.7 + - - -
70C LEU* 1.3 72.0 - - - +
72C LEU* 1.3 54.4 + - - +
73C TYR 3.0 0.9 - - - -
74C VAL* 2.8 9.4 + - - +
75C MET* 2.7 43.2 + - - +
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Residues in contact with LEU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU* 2.9 36.7 - - + +
12C ALA* 4.6 4.9 - - + -
16C MET* 3.0 38.8 - - + -
68C VAL* 2.9 25.6 + - + +
69C GLY 4.1 2.7 - - - +
71C GLY* 1.3 75.0 - - - +
73C TYR* 1.3 59.6 + - - +
75C MET* 3.2 20.4 - - - +
10D TYR* 5.5 0.2 - - + -
13D ALA* 6.2 0.4 - - + -
17D MET* 5.4 2.2 - - + -
70D LEU* 6.5 1.1 - - + -
73D TYR* 3.0 55.4 - - + +
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Residues in contact with TYR 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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9B LEU* 4.5 3.3 - - - +
12B ALA* 6.0 0.2 - - + -
72B LEU* 3.0 57.0 + - + +
75B MET* 3.5 26.1 - - + +
9C LEU* 3.5 9.1 - - + +
10C TYR* 2.9 56.5 + + - -
13C ALA* 4.4 13.9 - - + -
17C MET* 6.4 0.2 - - + -
69C GLY 2.9 21.4 + - - +
70C LEU* 3.4 12.3 - - + +
72C LEU* 1.3 74.2 - - - +
74C VAL* 1.3 70.3 + - + +
75C MET 3.0 1.1 - - - -
76C PHE* 3.1 16.6 + + - +
77C ALA* 3.2 10.8 + - + +
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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
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70C LEU* 2.6 52.3 + - + +
71C GLY* 3.4 7.6 - - - +
73C TYR* 1.3 75.4 - - + +
75C MET* 1.3 62.8 + - - +
77C ALA* 3.0 26.6 - - + +
78C VAL* 3.3 12.0 + - + +
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Residues in contact with MET 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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9C LEU* 4.6 3.8 - - + -
71C GLY 2.7 20.6 + - - +
72C LEU* 3.2 24.7 - - - +
73C TYR 3.0 0.2 - - - -
74C VAL* 1.3 70.7 - - - +
76C PHE* 1.3 57.6 + - - +
78C VAL* 2.7 39.6 + - - +
79C ALA* 3.5 2.3 + - - -
10D TYR* 4.8 5.4 - - - +
73D TYR* 3.3 37.2 - - + +
77D ALA* 6.2 3.4 - - + -
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Residues in contact with PHE 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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5B ASN* 3.4 22.0 - - - -
5C ASN* 5.8 0.4 - - - -
6C MET* 3.1 52.0 - - + -
9C LEU* 3.4 21.2 - - + +
10C TYR* 2.9 37.2 - + + -
72C LEU 3.3 2.2 + - - -
73C TYR* 3.1 11.0 + + - +
75C MET* 1.3 78.1 - - - +
77C ALA* 1.3 70.9 + - + +
79C ALA* 2.9 18.9 + - - +
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Residues in contact with ALA 77 (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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75B MET* 6.1 4.5 - - + -
73C TYR* 3.2 7.8 + - + +
74C VAL* 3.0 27.7 + - + +
76C PHE* 1.3 88.6 - - + +
78C VAL* 1.3 59.5 + - + +
79C ALA* 3.5 3.8 + - - +
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Residues in contact with VAL 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* 3.5 14.4 - - + +
75C MET* 2.7 26.5 + - + +
77C ALA* 1.3 71.1 - - + +
79C ALA* 1.3 74.9 + - - +
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Residues in contact with ALA 79 (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 MET 3.5 3.4 + - - -
76C PHE* 2.9 17.8 + - - +
77C ALA 4.3 4.0 - - - +
78C VAL* 1.3 94.3 - - - +
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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