Contacts of the helix formed by residues 61 - 79 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20G ALA* 3.4 30.4 - - - +
23G GLY* 4.5 0.2 - - - -
24G ALA* 3.4 13.9 + - + -
57G MET 3.4 10.8 + - - +
58G GLY* 3.1 15.3 + - - +
60G VAL* 1.3 75.9 - - - +
62G ALA* 1.3 57.4 + - - +
64G PRO* 3.0 18.6 - - - +
65G MET 4.1 4.0 + - - -
21H ALA* 5.3 6.5 - - - +
25H ALA* 3.8 20.8 - - - +
28H ILE* 6.6 0.2 - - - -
59H LEU* 5.3 9.0 - - + +
62H ALA* 5.5 6.1 - - - +
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Residues in contact with ALA 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F ASP* 5.4 6.3 - - - +
20G ALA 4.4 0.2 - - - -
21G ALA* 3.3 38.8 - - + +
24G ALA* 3.3 14.2 - - + +
58G GLY 4.0 0.8 + - - +
59G LEU* 5.0 5.4 - - + +
60G VAL* 4.3 0.4 - - - +
61G ASP* 1.3 75.8 - - - +
63G ILE* 1.3 64.3 + - + +
64G PRO* 2.8 6.6 - - - +
65G MET* 3.2 2.3 + - - +
66G ILE* 2.9 35.6 + - + +
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Residues in contact with ILE 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59G LEU* 3.7 17.7 + - + +
60G VAL* 3.9 18.4 - - + +
62G ALA* 1.3 77.1 - - + +
64G PRO* 1.3 66.2 - - + +
66G ILE* 3.8 13.1 - - + +
67G ALA* 3.1 27.4 + - + +
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Residues in contact with PRO 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G VAL* 2.7 27.8 - - + +
61G ASP* 3.0 15.7 - - - +
62G ALA 2.8 7.9 - - - +
63G ILE* 1.3 92.5 - - + +
65G MET* 1.3 53.0 + - - +
66G ILE 3.0 1.1 - - - -
67G ALA* 3.0 7.5 + - + +
68G VAL* 2.7 45.1 + - + +
66H ILE* 6.2 3.8 - - + -
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Residues in contact with MET 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G MET* 2.7 68.6 - - + +
17G MET* 3.3 6.4 - - - +
20G ALA* 3.0 27.6 - - + -
21G ALA 4.7 0.2 - - - +
61G ASP 4.1 2.0 + - - +
62G ALA 3.2 6.8 + - - +
64G PRO* 1.3 80.1 - - - +
66G ILE* 1.3 52.8 + - - +
68G VAL* 3.2 23.3 + - + +
69G GLY* 2.5 32.4 + - - -
17H MET* 4.2 18.2 - - + -
18H GLY* 5.4 4.5 - - - -
21H ALA* 5.9 1.8 - - - -
66H ILE* 6.1 7.0 - - + -
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Residues in contact with ILE 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F PRO* 6.2 3.6 - - + -
65F MET* 6.1 7.6 - - + -
68F VAL* 5.9 10.1 - - + -
17G MET* 3.5 31.9 - - + +
21G ALA* 4.7 7.9 - - + -
62G ALA* 2.9 35.7 + - + +
63G ILE* 3.8 15.3 - - + +
65G MET* 1.3 72.7 - - - +
67G ALA* 1.3 56.4 + - - +
68G VAL 3.0 1.1 - - - -
69G GLY* 2.9 1.0 + - - -
70G LEU* 2.5 51.0 + - + +
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Residues in contact with ALA 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63G ILE* 3.1 17.0 + - + +
64G PRO* 3.0 8.1 + - + +
66G ILE* 1.3 79.2 - - - +
68G VAL* 1.3 57.4 + - + +
70G LEU* 3.6 10.3 - - - +
71G GLY* 2.9 23.7 + - - -
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Residues in contact with VAL 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G MET* 4.4 9.0 - - - -
64G PRO* 2.7 35.6 + - + +
65G MET* 3.3 26.2 - - + +
67G ALA* 1.3 74.5 - - + +
69G GLY* 1.3 59.9 + - - +
70G LEU 3.2 0.2 - - - -
71G GLY* 3.1 1.0 + - - -
72G LEU* 2.9 46.2 + - + +
17H MET* 4.8 7.9 - - + -
66H ILE* 5.9 9.0 - - + -
70H LEU* 6.3 3.4 - - + -
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Residues in contact with GLY 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G ALA* 3.1 33.8 - - - +
16G MET* 3.8 8.5 - - - +
17G MET* 3.9 5.2 - - - -
65G MET 2.5 20.0 + - - -
66G ILE 3.4 2.0 - - - -
68G VAL* 1.3 73.4 - - - +
70G LEU* 1.3 58.0 + - - +
72G LEU* 3.9 0.5 - - - +
73G TYR* 2.9 31.0 + - - +
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Residues in contact with LEU 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F VAL* 6.3 3.4 - - + -
17G MET* 4.3 3.0 - - - -
66G ILE* 2.5 31.8 + - + +
67G ALA* 3.6 9.6 - - - +
69G GLY* 1.3 71.0 - - - +
71G GLY* 1.3 51.3 - - - +
73G TYR* 3.4 11.3 - - + +
74G VAL* 2.6 60.2 + - + +
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Residues in contact with GLY 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67G ALA 2.9 16.6 + - - -
68G VAL* 3.1 3.5 + - - -
70G LEU* 1.3 72.8 - - - +
72G LEU* 1.3 54.7 + - - +
73G TYR 3.0 1.1 - - - -
74G VAL* 2.8 9.8 + - - +
75G MET* 2.7 42.2 + - - +
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Residues in contact with LEU 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G LEU* 2.9 36.8 - - + +
12G ALA* 4.6 4.9 - - + -
16G MET* 3.0 40.2 - - + -
68G VAL* 2.9 25.1 + - + +
69G GLY 4.1 3.1 - - - +
71G GLY* 1.3 72.3 - - - +
73G TYR* 1.3 61.4 + - - +
75G MET* 3.2 21.1 - - - +
76G PHE 3.3 0.2 + - - -
13H ALA* 6.3 0.4 - - + -
17H MET* 5.5 2.2 - - + -
70H LEU* 6.5 0.7 - - + -
73H TYR* 3.0 54.5 - - + +
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Residues in contact with TYR 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F LEU* 4.7 1.9 - - - +
12F ALA* 6.1 0.2 - - + -
72F LEU* 2.9 54.0 + - + +
75F MET* 3.4 25.3 - - + +
9G LEU* 3.5 8.9 - - - +
10G TYR* 2.9 58.7 + + - -
13G ALA* 4.4 13.5 - - + -
69G GLY 2.9 21.0 + - - +
70G LEU* 3.4 12.6 - - + +
72G LEU* 1.3 74.4 - - - +
74G VAL* 1.3 71.0 + - + +
75G MET 3.0 1.3 - - - -
76G PHE* 3.1 16.7 + + - +
77G ALA* 3.2 11.6 + - + +
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Residues in contact with VAL 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70G LEU* 2.6 52.1 + - + +
71G GLY* 3.4 7.6 - - - +
73G TYR* 1.3 75.8 - - + +
75G MET* 1.3 63.3 + - - +
77G ALA* 3.0 27.5 - - + +
78G VAL* 3.3 11.9 + - + +
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Residues in contact with MET 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G LEU* 4.6 3.1 - - + -
71G GLY 2.7 20.8 + - - +
72G LEU* 3.2 25.1 - - - +
73G TYR 3.0 0.2 - - - -
74G VAL* 1.3 69.7 - - + +
76G PHE* 1.3 57.3 + - - +
78G VAL* 2.7 39.3 + - + +
79G ALA 3.5 2.6 + - - -
10H TYR* 4.8 5.4 - - - +
73H TYR* 3.4 35.4 - - + +
77H ALA* 6.2 3.8 - - + -
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Residues in contact with PHE 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F ASN* 3.5 19.5 - - - -
5G ASN* 5.8 0.4 - - - -
6G MET* 3.1 52.7 - - + -
9G LEU* 3.4 22.5 - - + +
10G TYR* 2.9 35.9 - + + -
72G LEU 3.3 2.4 + - - -
73G TYR* 3.1 10.9 + + - +
75G MET* 1.3 77.5 - - - +
77G ALA* 1.3 69.0 + - + +
79G ALA* 2.9 19.4 + - - +
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Residues in contact with ALA 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F MET* 6.2 3.4 - - + -
73G TYR* 3.2 7.8 + - + +
74G VAL* 3.0 27.5 + - + +
75G MET 3.0 0.4 - - - -
76G PHE* 1.3 89.3 - - + +
78G VAL* 1.3 58.8 + - + +
79G ALA* 3.5 3.5 + - - +
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Residues in contact with VAL 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74G VAL* 3.5 14.6 - - + +
75G MET* 2.7 25.9 + - - +
77G ALA* 1.3 71.0 - - + +
79G ALA* 1.3 75.0 + - - +
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Residues in contact with ALA 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75G MET 3.5 3.0 + - - -
76G PHE* 2.9 18.0 + - - +
77G ALA 4.3 3.6 - - - +
78G VAL* 1.3 95.1 - - - +
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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
------------------------------------------------------------
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