Contacts of the helix formed by residues 61 - 79 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20D ALA* 3.4 30.6 - - - +
23D GLY* 4.5 0.2 - - - -
24D ALA* 3.4 13.2 + - + -
57D MET 3.4 11.0 + - - +
58D GLY* 3.1 15.1 + - - +
60D VAL* 1.3 76.3 - - - +
62D ALA* 1.3 55.9 + - - +
64D PRO* 3.0 19.7 - - - +
65D MET* 4.1 4.0 + - - +
21E ALA* 5.0 8.4 - - - +
22E ILE* 5.8 0.2 - - - -
25E ALA* 3.5 23.6 - - + +
28E ILE* 6.0 1.6 - - - +
59E LEU* 5.5 6.6 - - + +
62E ALA* 5.3 7.3 - - - +
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Residues in contact with ALA 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C ASP* 5.3 7.0 - - - +
20D ALA 4.4 0.2 - - - -
21D ALA* 3.3 38.1 - - + +
24D ALA* 3.3 13.6 - - + +
58D GLY 4.0 0.9 + - - +
59D LEU* 5.0 5.6 - - + +
60D VAL 3.3 0.2 - - - -
61D ASP* 1.3 76.4 - - - +
63D ILE* 1.3 63.9 + - - +
64D PRO* 2.8 6.1 - - - +
65D MET* 3.2 2.1 + - - +
66D ILE* 2.9 35.6 + - + +
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Residues in contact with ILE 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D LEU* 3.7 17.5 + - + +
60D VAL* 3.9 19.7 - - + +
62D ALA* 1.3 76.7 - - + +
64D PRO* 1.3 64.9 - - + +
66D ILE* 3.8 13.6 - - + +
67D ALA* 3.1 27.1 + - + +
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Residues in contact with PRO 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D VAL* 2.7 27.6 - - + +
61D ASP* 3.0 16.4 - - - +
62D ALA 2.8 7.4 - - - +
63D ILE* 1.3 91.8 - - + +
65D MET* 1.3 51.2 + - - +
66D ILE 3.0 1.3 - - - -
67D ALA* 3.0 6.7 + - + +
68D VAL* 2.7 46.3 + - + +
66E ILE* 6.1 4.9 - - + -
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Residues in contact with MET 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D MET* 2.7 67.8 - - + +
17D MET* 3.3 6.0 - - - +
20D ALA* 3.0 28.0 - - + -
21D ALA 4.7 0.2 - - - +
61D ASP 4.1 2.6 + - - +
62D ALA 3.2 6.9 + - - +
64D PRO* 1.3 79.7 - - - +
66D ILE* 1.3 52.1 + - - +
68D VAL* 3.2 22.8 + - + +
69D GLY* 2.5 32.7 + - - -
17E MET* 4.1 14.8 - - + -
18E GLY 5.1 9.4 - - - -
21E ALA* 5.8 1.8 - - - -
66E ILE* 6.1 5.8 - - + -
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Residues in contact with ILE 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C PRO* 6.1 5.6 - - + -
65C MET* 6.1 7.0 - - + -
68C VAL* 5.8 10.8 - - + -
17D MET* 3.5 31.9 - - + +
21D ALA* 4.7 7.9 - - + -
62D ALA* 2.9 36.1 + - + +
63D ILE* 3.8 15.0 - - + +
65D MET* 1.3 73.1 - - - +
67D ALA* 1.3 57.6 + - - +
68D VAL 3.0 1.1 - - - -
69D GLY* 2.9 0.5 + - - -
70D LEU* 2.5 50.8 + - + +
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Residues in contact with ALA 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D ILE* 3.1 17.2 + - + +
64D PRO* 3.0 7.4 + - + +
66D ILE* 1.3 80.2 - - - +
68D VAL* 1.3 58.2 + - + +
70D LEU* 3.6 10.6 - - - +
71D GLY* 2.9 23.4 + - - -
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Residues in contact with VAL 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D MET* 4.4 9.6 - - - -
64D PRO* 2.7 35.5 + - + +
65D MET* 3.3 26.0 - - + +
67D ALA* 1.3 73.8 - - + +
69D GLY* 1.3 59.3 + - - +
71D GLY* 3.1 1.5 + - - -
72D LEU* 2.9 45.5 + - + +
17E MET* 4.7 7.6 - - + -
66E ILE* 5.8 9.9 - - + -
70E LEU* 6.4 2.2 - - + -
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Residues in contact with GLY 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ALA* 3.1 34.2 - - - +
16D MET* 3.8 8.3 - - - +
17D MET* 3.9 4.7 - - - -
65D MET 2.5 18.7 + - - -
66D ILE 3.4 2.7 - - - -
68D VAL* 1.3 73.5 - - - +
70D LEU* 1.3 58.1 + - - +
72D LEU* 3.9 0.3 - - - +
73D TYR* 2.9 30.5 + - - +
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Residues in contact with LEU 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C VAL* 6.3 3.1 - - + -
72C LEU* 6.5 0.9 - - + -
17D MET* 4.3 3.4 - - - -
66D ILE* 2.5 33.0 + - + +
67D ALA* 3.6 9.9 - - - +
69D GLY* 1.3 70.6 - - - +
71D GLY* 1.3 52.3 + - - +
73D TYR* 3.4 10.3 - - + +
74D VAL* 2.6 60.8 + - + +
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Residues in contact with GLY 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D ALA 2.9 16.3 + - - -
68D VAL* 3.1 4.0 + - - -
70D LEU* 1.3 72.5 - - - +
72D LEU* 1.3 54.0 + - - +
73D TYR 3.0 1.1 - - - -
74D VAL* 2.8 10.1 + - - +
75D MET* 2.7 42.9 + - - +
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Residues in contact with LEU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LEU* 2.9 37.1 - - + +
12D ALA* 4.6 5.2 - - + -
13D ALA* 5.6 0.2 - - + -
16D MET* 3.0 39.5 - - + -
68D VAL* 2.9 26.2 + - + +
69D GLY 4.1 2.7 - - - +
71D GLY* 1.3 72.9 - - - +
73D TYR* 1.3 60.0 + - - +
75D MET* 3.2 19.7 - - - +
13E ALA* 6.2 0.4 - - + -
17E MET* 5.4 1.8 - - + -
70E LEU* 6.6 0.2 - - + -
73E TYR* 2.9 56.5 - - + +
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Residues in contact with TYR 73 (chain D).
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 1.9 - - - +
72C LEU* 3.0 55.0 + - + +
75C MET* 3.3 28.0 - - + +
9D LEU* 3.5 8.9 - - - +
10D TYR* 2.9 55.9 + + - -
13D ALA* 4.4 13.7 - - + -
69D GLY 2.9 21.0 + - - +
70D LEU* 3.4 13.5 - - + +
72D LEU* 1.3 74.2 - - - +
74D VAL* 1.3 70.7 + - + +
75D MET 3.0 1.3 - - - -
76D PHE* 3.1 16.8 + + - +
77D ALA* 3.2 10.8 + - + +
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Residues in contact with VAL 74 (chain D).
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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70D LEU* 2.6 52.4 + - + +
71D GLY* 3.4 7.4 - - - +
73D TYR* 1.3 75.6 - - + +
75D MET* 1.3 64.0 + - - +
77D ALA* 3.0 26.6 - - + +
78D VAL* 3.3 11.6 + - + +
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Residues in contact with MET 75 (chain D).
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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9D LEU* 4.6 4.0 - - + -
71D GLY 2.7 21.4 + - - +
72D LEU* 3.2 24.7 - - - +
74D VAL* 1.3 69.8 - - - +
76D PHE* 1.3 57.6 + - - +
78D VAL* 2.7 38.9 + - - +
79D ALA 3.5 2.8 + - - -
10E TYR* 4.8 4.9 - - - +
73E TYR* 3.3 37.2 - - + +
77E ALA* 6.3 2.9 - - + -
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Residues in contact with PHE 76 (chain D).
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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5C ASN* 3.6 20.2 - - - -
5D ASN* 5.8 1.1 - - - -
6D MET* 3.1 51.8 - - + -
9D LEU* 3.4 21.6 - - + +
10D TYR* 2.9 38.4 - + + -
72D LEU 3.3 2.4 + - - -
73D TYR* 3.1 10.2 + + - +
75D MET* 1.3 79.1 - - - +
77D ALA* 1.3 71.1 + - + +
79D ALA* 2.9 19.0 + - - +
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Residues in contact with ALA 77 (chain D).
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* 6.2 3.1 - - + -
73D TYR* 3.2 7.8 + - + +
74D VAL* 3.0 27.1 + - + +
75D MET 3.0 0.4 - - - -
76D PHE* 1.3 87.5 - - + +
78D VAL* 1.3 60.4 + - + +
79D ALA* 3.5 3.6 + - - +
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Residues in contact with VAL 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D VAL* 3.5 15.0 - - + +
75D MET* 2.7 26.7 + - - +
77D ALA* 1.3 70.6 - - + +
79D ALA* 1.3 75.2 + - - +
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Residues in contact with ALA 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D MET 3.5 3.2 + - - -
76D PHE* 2.9 17.4 + - - +
77D ALA 4.3 3.6 - - - +
78D VAL* 1.3 95.2 - - - +
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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