Contacts of the helix formed by residues 61 - 79 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20H ALA* 3.4 31.0 - - - +
23H GLY* 3.8 4.0 - - - -
24H ALA* 3.4 13.5 + - + -
57H MET 3.4 11.4 + - - +
58H GLY* 3.1 15.5 + - - +
60H VAL* 1.3 75.3 - - - +
62H ALA* 1.3 57.2 + - - +
64H PRO* 3.0 19.4 - - - +
65H MET* 4.1 4.0 + - - +
21I ALA* 5.5 3.8 - - - +
25I ALA* 4.0 15.5 - - - +
59I LEU* 5.2 10.9 - - + +
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Residues in contact with ALA 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G ASP* 5.5 6.5 - - - +
20H ALA 4.4 0.2 - - - -
21H ALA* 3.3 39.3 - - + +
24H ALA* 3.3 13.7 - - + +
58H GLY 4.0 0.6 + - - +
59H LEU* 5.0 6.3 - - + +
60H VAL* 4.3 0.2 - - - +
61H ASP* 1.3 75.7 - - - +
63H ILE* 1.3 63.6 + - + +
64H PRO* 2.8 6.0 - - - +
65H MET* 3.2 2.6 + - - +
66H ILE* 2.9 35.2 + - + +
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Residues in contact with ILE 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59H LEU* 3.7 17.5 + - + +
60H VAL* 3.9 19.7 - - + +
62H ALA* 1.3 76.7 - - + +
64H PRO* 1.3 65.7 - - + +
66H ILE* 3.8 14.6 - - + +
67H ALA* 3.1 27.3 + - + +
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Residues in contact with PRO 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60H VAL* 2.7 28.0 - - + +
61H ASP* 3.0 15.3 - - - +
62H ALA 2.8 8.7 - - - +
63H ILE* 1.3 91.9 - - + +
65H MET* 1.3 53.6 + - - +
66H ILE 3.0 1.1 - - - -
67H ALA* 3.0 6.5 + - + +
68H VAL* 2.7 46.3 + - + +
66I ILE* 6.2 4.5 - - + -
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Residues in contact with MET 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H MET* 2.7 68.0 - - + +
17H MET* 3.3 6.5 - - - +
20H ALA* 3.0 28.0 - - + -
21H ALA 4.7 0.2 - - - +
61H ASP 4.1 2.2 + - - +
62H ALA 3.2 6.7 + - - +
64H PRO* 1.3 78.5 - - - +
66H ILE* 1.3 53.4 + - - +
68H VAL* 3.3 23.0 - - + +
69H GLY* 2.5 32.7 + - - -
17I MET* 4.2 17.0 - - + -
18I GLY* 5.6 4.7 - - - -
21I ALA* 6.0 2.2 - - - -
66I ILE* 6.0 7.2 - - + -
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Residues in contact with ILE 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G PRO* 6.2 4.3 - - + -
65G MET* 6.1 6.7 - - + -
68G VAL* 5.9 10.5 - - + -
17H MET* 3.5 32.2 - - + +
21H ALA* 4.7 7.4 - - + -
62H ALA* 2.9 36.6 + - + +
63H ILE* 3.8 15.7 - - + +
65H MET* 1.3 73.3 - - - +
67H ALA* 1.3 56.4 + - - +
68H VAL 3.0 1.1 - - - -
69H GLY* 2.9 1.4 + - - -
70H LEU* 2.5 50.6 + - + +
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Residues in contact with ALA 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H ILE* 3.1 17.8 + - + +
64H PRO* 3.0 7.5 + - + +
66H ILE* 1.3 79.4 - - - +
68H VAL* 1.3 58.5 + - + +
70H LEU* 3.6 10.3 - - - +
71H GLY* 2.9 24.1 + - - -
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Residues in contact with VAL 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H MET* 4.4 9.4 - - - -
64H PRO* 2.7 35.9 + - + +
65H MET* 3.3 26.7 - - + +
67H ALA* 1.3 73.8 - - + +
69H GLY* 1.3 60.1 + - - +
71H GLY* 3.1 1.4 + - - -
72H LEU* 2.9 44.8 + - + +
17I MET* 4.9 7.6 - - + -
66I ILE* 5.7 10.8 - - + -
70I LEU* 6.0 6.7 - - + -
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Residues in contact with GLY 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H ALA* 3.1 33.8 - - - +
16H MET* 3.8 8.0 - - - +
17H MET* 3.9 5.6 - - - -
65H MET 2.5 19.1 + - - -
66H ILE 3.4 2.5 - - - -
68H VAL* 1.3 73.4 - - - +
70H LEU* 1.3 56.7 + - - +
72H LEU* 3.7 0.7 + - - +
73H TYR* 2.9 31.4 + - - +
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Residues in contact with LEU 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68G VAL* 6.3 3.8 - - + -
17H MET* 4.3 3.5 - - - -
66H ILE* 2.5 32.7 + - + +
67H ALA* 3.6 10.5 - - - +
69H GLY* 1.3 71.0 - - - +
71H GLY* 1.3 52.7 + - - +
73H TYR* 3.3 10.7 + - + +
74H VAL* 2.6 59.6 + - + +
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Residues in contact with GLY 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67H ALA 2.9 16.1 + - - -
68H VAL* 3.1 3.7 + - - -
70H LEU* 1.3 72.7 - - - +
72H LEU* 1.3 54.2 + - - +
73H TYR 3.0 0.9 - - - -
74H VAL* 2.8 9.8 + - - +
75H MET* 2.7 42.0 + - - +
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Residues in contact with LEU 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H LEU* 2.9 36.1 - - + +
12H ALA* 4.6 4.7 - - + -
13H ALA* 5.6 0.2 - - + -
16H MET* 3.0 40.2 - - + -
68H VAL* 2.9 25.7 + - + +
69H GLY 4.1 2.7 - - - +
71H GLY* 1.3 74.0 - - - +
73H TYR* 1.3 60.1 + - - +
75H MET* 3.2 20.4 - - - +
76H PHE 3.3 0.2 + - - -
13I ALA* 6.2 0.4 - - + -
17I MET* 5.4 1.8 - - + -
70I LEU* 6.2 2.9 - - + -
73I TYR* 3.0 54.5 - - + +
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Residues in contact with TYR 73 (chain H).
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 2.6 - - - +
12G ALA* 6.1 0.2 - - + -
72G LEU* 3.0 54.1 + - + +
75G MET* 3.4 25.4 - - + +
9H LEU* 3.5 9.4 - - - +
10H TYR* 2.9 58.6 + + - -
13H ALA* 4.4 14.1 - - + -
17H MET* 6.4 0.2 - - + -
69H GLY 2.9 21.2 + - - +
70H LEU* 3.4 13.2 - - + +
72H LEU* 1.3 73.3 - - - +
74H VAL* 1.3 69.1 + - + +
75H MET 3.0 1.6 - - - -
76H PHE* 3.1 15.9 + + - +
77H ALA* 3.2 11.2 + - + -
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Residues in contact with VAL 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70H LEU* 2.6 52.8 + - + +
71H GLY* 3.4 7.4 - - - +
73H TYR* 1.3 76.1 - - + +
75H MET* 1.3 62.6 + - - +
77H ALA* 3.0 27.6 - - + +
78H VAL* 3.3 11.6 + - + +
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Residues in contact with MET 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H LEU* 4.6 3.1 - - + -
71H GLY 2.7 20.1 + - - +
72H LEU* 3.2 25.4 - - - +
73H TYR 3.0 0.2 - - - -
74H VAL* 1.3 70.2 - - - +
76H PHE* 1.3 56.8 + - - +
78H VAL* 2.7 39.0 + - - +
79H ALA 3.5 2.6 + - - -
10I TYR* 4.8 4.9 - - - +
73I TYR* 3.5 36.1 - - + +
76I PHE* 6.4 0.9 - - + -
77I ALA* 5.8 7.2 - - + -
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Residues in contact with PHE 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G ASN* 3.5 21.1 - - - -
5H ASN* 5.8 0.9 - - - -
6H MET* 3.1 52.3 - - + -
9H LEU* 3.4 22.3 - - + +
10H TYR* 2.9 37.9 - + + -
72H LEU 3.3 2.2 + - - -
73H TYR* 3.1 10.8 + + - +
75H MET* 1.3 78.1 - - - +
77H ALA* 1.3 70.4 + - - +
79H ALA* 2.9 19.1 + - - +
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Residues in contact with ALA 77 (chain H).
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* 6.2 4.0 - - + -
73H TYR* 3.2 8.2 + - + +
74H VAL* 3.0 28.0 + - + +
75H MET 3.0 0.4 - - - -
76H PHE* 1.3 88.0 - - + +
78H VAL* 1.3 58.3 + - + +
79H ALA* 3.5 4.0 + - - +
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Residues in contact with VAL 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74H VAL* 3.5 14.6 - - + +
75H MET* 2.7 26.9 + - + +
77H ALA* 1.3 71.7 - - + +
79H ALA* 1.3 74.9 + - - +
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Residues in contact with ALA 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75H MET 3.5 3.2 + - - -
76H PHE* 2.9 16.7 + - - +
77H ALA 4.3 3.8 - - - +
78H VAL* 1.3 94.0 - - - +
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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