Contacts of the helix formed by residues 61 - 79 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B ALA* 3.4 30.6 - - - +
23B GLY* 3.8 0.3 - - - -
24B ALA* 3.4 13.7 + - + -
57B MET 3.4 11.5 + - - +
58B GLY* 3.1 14.4 + - - +
60B VAL* 1.3 75.2 - - - +
62B ALA* 1.3 56.0 + - - +
64B PRO* 3.0 18.8 - - - +
65B MET* 4.1 4.5 + - - +
21C ALA* 5.1 7.1 - - - +
25C ALA* 3.7 23.1 + - - +
28C ILE* 6.0 1.3 - - - +
59C LEU* 5.4 8.5 - - + +
62C ALA* 5.4 7.3 - - - +
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Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASP* 5.4 6.3 - - - +
20B ALA 4.4 0.2 - - - -
21B ALA* 3.3 39.0 - - + +
24B ALA* 3.3 13.7 - - + +
58B GLY 4.0 1.1 + - - +
59B LEU* 5.0 5.4 - - + +
60B VAL* 3.3 0.6 - - - +
61B ASP* 1.3 76.2 - - - +
63B ILE* 1.3 63.9 + - + +
64B PRO* 2.8 7.0 - - - +
65B MET* 3.2 2.5 + - - +
66B ILE* 2.9 35.8 + - + +
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Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LEU* 3.7 17.6 + - + +
60B VAL* 3.9 19.7 - - + +
62B ALA* 1.3 77.3 - - + +
64B PRO* 1.3 66.4 - - + +
66B ILE* 3.8 13.7 - - + +
67B ALA* 3.1 26.4 + - + +
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Residues in contact with PRO 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B VAL* 2.7 28.0 - - + +
61B ASP* 3.0 15.5 - - - +
62B ALA 2.8 8.1 - - - +
63B ILE* 1.3 92.7 - - + +
65B MET* 1.3 53.7 + - - +
66B ILE 3.0 1.1 - - - -
67B ALA* 3.0 7.1 + - + +
68B VAL* 2.7 45.5 + - + +
66C ILE* 6.1 6.1 - - + -
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Residues in contact with MET 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B MET* 2.7 69.1 - - + +
17B MET* 3.3 6.3 - - - +
20B ALA* 3.0 28.0 - - + -
21B ALA 4.7 0.7 - - - +
61B ASP 4.1 2.6 + - - +
62B ALA 3.2 6.2 + - - +
64B PRO* 1.3 81.1 - - - +
66B ILE* 1.3 51.6 + - - +
68B VAL* 3.2 23.4 + - + +
69B GLY* 2.5 32.9 + - - -
17C MET* 4.1 17.5 - - + -
18C GLY* 5.3 4.7 - - - -
21C ALA* 5.9 2.0 - - - -
66C ILE* 6.0 7.2 - - + -
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Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A PRO* 6.1 5.2 - - + -
65A MET* 6.1 7.2 - - + -
68A VAL* 5.8 11.0 - - + -
17B MET* 3.5 31.8 - - + +
21B ALA* 4.7 7.9 - - + -
62B ALA* 2.9 36.2 + - + +
63B ILE* 3.8 15.3 - - + +
65B MET* 1.3 72.9 - - - +
67B ALA* 1.3 56.8 + - - +
68B VAL 3.0 1.1 - - - -
69B GLY* 2.9 0.9 + - - -
70B LEU* 2.5 50.8 + - + +
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Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ILE* 3.1 16.5 + - + +
64B PRO* 3.0 7.9 + - + +
66B ILE* 1.3 79.2 - - - +
68B VAL* 1.3 58.1 + - + +
70B LEU* 3.6 10.8 - - - +
71B GLY* 2.9 22.9 + - - -
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Residues in contact with VAL 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B MET* 4.4 9.2 - - - -
64B PRO* 2.7 35.7 + - + +
65B MET* 3.3 26.9 - - + +
67B ALA* 1.3 73.8 - - + +
69B GLY* 1.3 59.9 + - - +
71B GLY* 3.1 1.5 + - - -
72B LEU* 2.9 45.1 + - + +
17C MET* 4.8 7.6 - - + -
66C ILE* 5.7 10.1 - - + -
70C LEU* 6.2 4.7 - - + -
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Residues in contact with GLY 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ALA* 3.1 34.3 - - - +
16B MET* 3.8 8.5 - - - -
17B MET* 3.9 4.7 - - - -
65B MET 2.5 19.8 + - - -
66B ILE 3.4 2.0 - - - -
68B VAL* 1.3 73.1 - - - +
70B LEU* 1.3 57.5 + - - +
72B LEU* 3.7 0.9 + - - +
73B TYR* 2.9 30.5 + - - +
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A VAL* 6.2 4.5 - - + -
72A LEU* 6.4 1.6 - - + -
17B MET* 4.3 3.0 - - - -
66B ILE* 2.5 32.1 + - + +
67B ALA* 3.6 9.6 - - - +
69B GLY* 1.3 71.4 - - - +
71B GLY* 1.3 52.7 + - - +
73B TYR* 3.4 9.6 - - + +
74B VAL* 2.6 60.4 + - + +
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Residues in contact with GLY 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B ALA 2.9 16.1 + - - -
68B VAL* 3.1 4.0 + - - -
70B LEU* 1.3 72.0 - - - +
72B LEU* 1.3 53.5 + - - +
73B TYR 3.0 0.9 - - - -
74B VAL* 2.8 9.8 + - - +
75B MET* 2.7 42.7 + - - +
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Residues in contact with LEU 72 (chain B).
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* 2.9 36.2 - - + +
12B ALA* 4.6 4.3 - - + -
16B MET* 3.0 39.5 - - + -
68B VAL* 2.9 26.2 + - + +
69B GLY 4.1 3.4 - - - +
71B GLY* 1.3 73.5 - - - +
73B TYR* 1.3 59.2 + - - +
75B MET* 3.2 21.6 - - - +
17C MET* 5.4 1.8 - - + -
70C LEU* 6.3 2.2 - - + -
73C TYR* 3.0 55.4 - - + +
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Residues in contact with TYR 73 (chain B).
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* 4.6 2.8 - - - +
72A LEU* 3.0 55.7 + - + +
75A MET* 3.5 25.2 - - + +
9B LEU* 3.5 9.4 - - - +
10B TYR* 2.9 59.1 + + - -
13B ALA* 4.4 13.9 - - + -
69B GLY 2.9 21.6 + - - +
70B LEU* 3.4 12.3 - - + +
72B LEU* 1.3 73.1 - - - +
74B VAL* 1.3 69.7 + - + +
75B MET 3.0 1.3 - - - -
76B PHE* 3.1 16.4 + + - +
77B ALA* 3.2 10.6 + - + +
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Residues in contact with VAL 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B LEU* 2.6 51.9 + - + +
71B GLY* 2.8 7.4 + - - +
73B TYR* 1.3 74.5 - - + +
75B MET* 1.3 62.9 + - - +
77B ALA* 3.0 26.5 - - + +
78B VAL* 3.3 12.2 + - + +
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Residues in contact with MET 75 (chain B).
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* 4.6 3.8 - - + -
71B GLY 2.7 20.8 + - - +
72B LEU* 3.2 24.7 - - - +
73B TYR 3.0 0.2 - - - -
74B VAL* 1.3 71.1 - - + +
76B PHE* 1.3 56.4 + - - +
78B VAL* 2.7 38.6 + - - +
79B ALA 3.5 2.3 + - - -
10C TYR* 4.9 4.5 - - - +
73C TYR* 3.5 35.4 - - + +
77C ALA* 6.1 4.7 - - + -
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Residues in contact with PHE 76 (chain B).
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* 3.4 22.2 - - - -
5B ASN* 5.8 1.1 - - - -
6B MET* 3.1 52.3 - - + -
9B LEU* 3.4 21.5 - - + +
10B TYR* 2.9 37.2 - + + -
72B LEU 3.3 2.8 + - - -
73B TYR* 3.1 11.5 + + - +
75B MET* 1.3 78.7 - - - +
77B ALA* 1.3 69.4 + - - +
79B ALA* 2.9 19.1 + - - +
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Residues in contact with ALA 77 (chain B).
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* 6.1 4.7 - - + -
73B TYR* 3.2 8.0 + - + +
74B VAL* 3.0 27.1 + - + +
76B PHE* 1.3 89.4 - - + +
78B VAL* 1.3 59.2 + - + +
79B ALA* 3.5 3.6 + - - +
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Residues in contact with VAL 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B VAL* 3.5 15.0 - - + +
75B MET* 2.7 26.5 + - - +
77B ALA* 1.3 71.1 - - - +
79B ALA* 1.3 76.0 + - - +
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Residues in contact with ALA 79 (chain B).
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 3.5 3.2 + - - -
76B PHE* 2.9 18.3 + - - +
77B ALA 4.3 3.6 - - - +
78B VAL* 1.3 95.6 - - - +
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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