Contacts of the helix formed by residues 61 - 79 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ALA* 3.4 30.7 - - - +
23A GLY* 3.8 0.5 - - - -
24A ALA* 3.4 13.7 + - + -
57A MET 3.4 11.6 + - - +
58A GLY* 3.1 14.7 + - - +
60A VAL* 1.3 75.5 - - - +
62A ALA* 1.3 56.6 + - - +
64A PRO* 3.0 20.0 - - - +
65A MET* 4.1 4.0 + - - +
21B ALA* 5.1 7.6 - - - +
25B ALA* 3.8 23.2 - - + +
28B ILE* 6.1 0.9 - - - +
59B LEU* 5.5 7.4 - - + +
62B ALA* 5.4 7.1 - - - +
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Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ALA 4.4 0.2 - - - -
21A ALA* 3.3 39.0 - - + +
24A ALA* 3.3 14.2 - - + +
58A GLY 4.0 0.6 + - - +
59A LEU* 5.0 6.1 - - + +
60A VAL* 4.3 0.2 - - - +
61A ASP* 1.3 76.6 - - - +
63A ILE* 1.3 63.9 + - - +
64A PRO* 2.8 6.6 - - - +
65A MET* 3.2 2.4 + - - +
66A ILE* 2.9 35.5 + - + +
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Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU* 3.7 17.0 + - + +
60A VAL* 3.9 20.4 - - + +
62A ALA* 1.3 76.3 - - + +
64A PRO* 1.3 65.5 - - + +
66A ILE* 3.8 14.5 - - + +
67A ALA* 3.1 26.9 + - + +
63L ILE* 6.2 3.8 - - + -
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Residues in contact with PRO 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A VAL* 2.7 27.4 - - + +
61A ASP* 3.0 15.7 - - - +
62A ALA 2.8 8.3 - - - -
63A ILE* 1.3 92.9 - - + +
65A MET* 1.3 54.1 + - - +
66A ILE 3.0 0.9 - - - -
67A ALA* 3.0 7.1 + - + +
68A VAL* 2.7 44.2 + - + +
66B ILE* 6.1 5.6 - - + -
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Residues in contact with MET 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A MET* 2.7 68.9 - - + +
17A MET* 3.3 5.8 - - - +
20A ALA* 3.0 28.0 - - + -
21A ALA 4.7 0.4 - - - +
61A ASP 4.1 2.7 + - - +
62A ALA 3.2 6.8 + - - +
64A PRO* 1.3 78.6 - - - +
66A ILE* 1.3 52.0 + - - +
68A VAL* 3.2 23.2 + - + +
69A GLY* 2.5 32.9 + - - -
17B MET* 4.1 17.7 - - + -
18B GLY* 5.4 4.9 - - - -
21B ALA* 6.0 2.0 - - - -
66B ILE* 6.1 6.7 - - + -
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Residues in contact with ILE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A MET* 3.5 31.1 - - + +
21A ALA* 4.7 7.4 - - + -
62A ALA* 2.9 36.8 + - + +
63A ILE* 3.8 15.0 - - + +
65A MET* 1.3 72.9 - - - +
67A ALA* 1.3 57.1 + - - +
68A VAL 3.0 1.3 - - - -
69A GLY* 2.9 1.2 + - - -
70A LEU* 2.5 50.2 + - + +
16L MET* 6.1 3.1 - - + -
19L LEU* 6.4 1.3 - - + -
20L ALA* 6.1 5.2 - - + -
63L ILE* 6.1 7.0 - - + -
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Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ILE* 3.1 18.3 + - + +
64A PRO* 3.0 6.8 + - + +
66A ILE* 1.3 80.3 - - - +
68A VAL* 1.3 57.6 + - + +
70A LEU* 3.6 10.6 - - - +
71A GLY* 2.9 23.9 + - - -
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Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A MET* 4.4 9.0 - - - -
64A PRO* 2.7 35.6 + - + +
65A MET* 3.3 26.7 - - + +
67A ALA* 1.3 73.0 - - + +
69A GLY* 1.3 59.6 - - - +
70A LEU 3.2 0.2 - - - -
71A GLY* 3.1 1.5 + - - -
72A LEU* 2.9 45.0 + - + +
17B MET* 4.8 8.1 - - + -
66B ILE* 5.8 10.5 - - + -
70B LEU* 6.2 4.3 - - + -
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Residues in contact with GLY 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ALA* 3.1 33.5 - - - +
16A MET* 3.8 8.7 - - - -
17A MET* 3.9 5.8 - - - -
65A MET 2.5 18.9 + - - -
66A ILE 3.4 2.0 - - - -
68A VAL* 1.3 73.3 - - - +
70A LEU* 1.3 57.3 + - - +
72A LEU* 3.7 0.7 + - - +
73A TYR* 2.9 30.2 + - - +
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Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A MET* 4.3 3.2 - - - -
66A ILE* 2.5 33.4 + - + +
67A ALA* 3.6 9.6 - - - +
69A GLY* 1.3 71.4 - - - +
71A GLY* 1.3 53.8 + - - +
73A TYR* 3.4 10.7 - - + +
74A VAL* 2.6 60.0 + - + +
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Residues in contact with GLY 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ALA 2.9 16.5 + - - -
68A VAL* 3.1 3.8 + - - -
70A LEU* 1.3 72.1 - - - +
72A LEU* 1.3 54.2 + - - +
73A TYR 3.0 0.9 - - - -
74A VAL* 2.8 9.5 + - - +
75A MET* 2.7 42.1 + - - +
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 2.9 35.8 - - + +
12A ALA* 4.6 4.3 - - + -
16A MET* 3.0 39.7 - - + -
68A VAL* 2.9 26.8 + - + +
69A GLY 4.1 2.9 - - - +
71A GLY* 1.3 72.2 - - - +
73A TYR* 1.3 60.4 + - - +
75A MET* 3.2 21.8 - - - +
76A PHE 3.3 0.2 + - - -
10B TYR* 5.5 0.2 - - + -
13B ALA* 6.3 0.4 - - + -
17B MET* 5.5 1.8 - - + -
70B LEU* 6.4 2.0 - - + -
73B TYR* 3.0 56.5 - - + +
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Residues in contact with TYR 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 3.5 9.1 - - - +
10A TYR* 2.9 59.0 + + - -
13A ALA* 4.4 14.1 - - + -
17A MET* 6.4 0.2 - - + -
69A GLY 2.9 21.2 + - - +
70A LEU* 3.4 11.9 - - + +
72A LEU* 1.3 73.3 - - - +
74A VAL* 1.3 70.7 + - + +
75A MET 3.0 1.6 - - - -
76A PHE* 3.1 16.4 + + - +
77A ALA* 3.2 11.2 + - + +
9L LEU* 3.9 7.3 - - - +
12L ALA* 5.2 8.6 - - + +
75L MET* 3.4 30.3 - - + +
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Residues in contact with VAL 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LEU* 2.6 51.7 + - + +
71A GLY* 3.4 8.1 - - - +
73A TYR* 1.3 75.6 - - + +
75A MET* 1.3 63.1 + - - +
77A ALA* 3.0 26.8 - - + +
78A VAL* 3.3 11.4 + - + +
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Residues in contact with MET 75 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A LEU* 4.6 4.3 - - + -
71A GLY 2.7 20.7 + - - +
72A LEU* 3.2 25.4 - - - +
73A TYR 3.0 0.2 - - - -
74A VAL* 1.3 69.9 - - - +
76A PHE* 1.3 57.3 + - - +
78A VAL* 2.7 38.9 + - + +
79A ALA 3.5 2.8 + - - -
10B TYR* 4.9 4.3 - - - +
73B TYR* 3.5 35.4 - - + +
77B ALA* 6.1 5.2 - - + -
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Residues in contact with PHE 76 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ASN* 5.8 1.1 - - - -
6A MET* 3.1 53.8 - - + -
9A LEU* 3.4 21.7 - - + +
10A TYR* 2.9 41.5 - + + -
72A LEU 3.3 2.0 + - - -
73A TYR* 3.1 11.3 + + - +
75A MET* 1.3 78.3 - - - +
77A ALA* 1.3 69.4 + - + +
79A ALA* 2.9 19.3 + - - +
5L ASN* 4.5 13.7 - - - -
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Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A TYR* 3.2 8.1 + - + +
74A VAL* 3.0 27.8 + - + +
75A MET 3.0 0.6 - - - -
76A PHE* 1.3 89.6 - - + +
78A VAL* 1.3 59.4 + - + +
79A ALA* 3.5 3.5 + - - +
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Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A VAL* 3.5 15.3 - - + +
75A MET* 2.7 26.7 + - - +
77A ALA* 1.3 70.8 - - + +
79A ALA* 1.3 75.6 + - - +
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A MET 3.5 3.2 + - - -
76A PHE* 2.9 17.1 + - - +
77A ALA 4.3 3.4 - - - +
78A 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
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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