Contacts of the helix formed by residues 56 - 70 (chain C) in PDB entry 2QY7
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 GLN 56 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C GLU* 5.6 4.0 - - - +
24C ILE* 3.9 27.8 - - + +
50C ALA* 3.8 25.3 - - + +
53C MET* 2.9 44.9 + - + +
55C GLU* 1.3 78.3 - - + +
57C PHE* 1.3 66.6 + - - +
58C PRO* 3.5 0.8 - - - -
59C GLU* 3.5 9.0 + - - +
60C LEU* 3.2 23.1 + - - +
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Residues in contact with PHE 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ALA 4.3 3.5 + - - -
51C THR* 3.6 37.5 - - + +
53C MET 3.1 6.5 + - - +
56C GLN* 1.3 77.1 - - - +
58C PRO* 1.4 67.7 - - + +
60C LEU* 3.3 6.3 + - - +
61C MET* 2.9 57.9 + - + +
96C ARG* 3.3 71.3 - - + +
97C VAL* 3.6 26.7 - - + -
100C SER* 4.3 6.1 - - - -
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Residues in contact with PRO 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C TYR 3.7 12.3 - - - +
55C GLU 3.8 9.2 - - - +
56C GLN 3.6 3.4 - - - -
57C PHE* 1.4 98.8 - - + +
59C GLU* 1.3 52.1 + - + +
61C MET* 3.2 3.8 + - + +
62C ASN* 2.7 50.8 + - - +
96C ARG* 4.2 15.3 - - - +
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Residues in contact with GLU 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C SER* 3.2 26.6 + - - -
24C ILE* 4.0 7.8 - - + +
25C GLU* 3.8 25.4 - - + +
55C GLU 4.1 15.3 - - - +
56C GLN* 3.5 7.2 + - - +
57C PHE 3.4 0.6 - - - -
58C PRO* 1.3 75.7 - - + +
60C LEU* 1.3 66.9 + - - +
62C ASN* 3.9 8.5 - - - +
63C MET* 2.9 26.5 + - - +
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Residues in contact with LEU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ILE* 3.6 34.4 - - + +
28C VAL* 3.9 16.7 - - + +
47C ILE* 3.5 39.9 - - + +
50C ALA* 3.7 11.2 - - + +
51C THR* 3.6 22.0 - - + +
56C GLN 3.2 11.3 + - - +
57C PHE* 3.4 8.3 - - - +
59C GLU* 1.3 79.5 - - - +
61C MET* 1.3 76.4 + - + +
63C MET* 3.7 3.2 - - - +
64C LEU* 2.9 27.1 + - + +
89C LEU* 4.1 6.3 - - + -
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Residues in contact with MET 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C PHE* 2.9 52.2 + - + +
58C PRO* 3.8 4.7 - - + +
60C LEU* 1.3 90.2 - - + +
62C ASN* 1.3 67.6 + - - +
64C LEU* 3.1 14.2 + - + +
65C TRP* 3.0 57.1 + - + +
86C LEU* 4.3 16.8 - - + -
89C LEU* 4.7 1.3 - - - -
97C VAL* 4.5 15.0 - - + -
100C SER* 3.4 27.6 - - - +
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Residues in contact with ASN 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C GLU* 6.1 0.4 - - - +
58C PRO* 2.7 38.0 + - - +
59C GLU* 3.9 7.6 + - - +
61C MET* 1.3 75.2 - - - +
63C MET* 1.3 57.5 + - - +
65C TRP* 3.6 8.7 + - - +
66C SER* 3.0 29.7 + - - -
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Residues in contact with MET 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C TYR* 3.8 33.0 - - + -
25C GLU* 3.8 39.7 - - + +
28C VAL* 3.8 13.5 - - + -
29C ARG* 3.6 22.7 - - + -
59C GLU 2.9 18.3 + - - +
60C LEU 3.7 3.4 - - - +
62C ASN* 1.3 76.2 - - - +
64C LEU* 1.3 59.6 + - - +
66C SER* 3.3 11.7 + - - +
67C ARG* 2.9 39.0 + - + +
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Residues in contact with LEU 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C VAL* 3.8 13.2 - - + +
60C LEU* 2.9 16.5 + - + +
61C MET* 3.1 15.9 + - + +
63C MET* 1.3 76.2 - - - +
65C TRP* 1.3 72.3 + - + +
67C ARG* 3.3 3.5 + - - +
68C MET* 3.0 54.9 + - + +
82C SER* 4.2 10.0 - - - +
85C LEU* 4.1 19.5 - - + -
86C LEU* 4.2 24.7 - - + +
89C LEU* 3.7 29.8 - - + -
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Residues in contact with TRP 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C MET* 3.0 45.3 + - + +
62C ASN* 4.0 9.2 - - - +
64C LEU* 1.3 76.2 - - + +
66C SER* 1.3 57.1 + - - +
68C MET* 3.4 33.4 + - + -
69C LEU* 2.8 55.5 + - + +
86C LEU* 3.7 20.0 - - + -
100C SER* 3.0 23.9 + - - -
101C ALA* 3.8 20.6 - - - -
104C HIS* 3.6 47.2 - + + +
108C LEU* 3.8 19.3 - - + -
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Residues in contact with SER 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C ASN 3.0 18.8 + - - -
63C MET* 3.6 16.2 - - - +
64C LEU 3.3 0.2 - - - -
65C TRP* 1.3 74.3 - - - +
67C ARG* 1.3 65.4 + - - +
70C LYS* 3.0 61.6 + - - +
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Residues in contact with ARG 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C VAL* 4.7 2.5 - - + -
29C ARG* 3.0 63.4 + - + +
32C THR* 2.8 44.8 + - + +
33C ASN* 4.0 5.3 - - - +
34C ASP* 5.7 1.6 + - - -
63C MET* 2.9 40.8 + - + +
64C LEU* 3.3 5.1 + - - +
66C SER* 1.3 75.4 - - - +
68C MET* 1.3 60.2 + - - +
70C LYS 4.8 1.0 - - - +
72C ASN* 4.5 4.0 - - - +
78C ARG* 3.2 61.8 - - + +
79C VAL* 4.4 5.2 - - - +
82C SER* 4.5 2.0 - - - -
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Residues in contact with MET 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C LEU* 3.0 36.4 + - + +
65C TRP* 3.6 23.6 - - + +
67C ARG* 1.3 78.9 - - - +
69C LEU* 1.3 58.1 + - + +
70C LYS 3.9 0.2 - - - -
72C ASN* 2.7 29.4 + - - +
79C VAL* 3.6 14.2 - - + +
82C SER* 3.2 30.9 + - - +
83C LEU* 3.6 22.7 - - + -
86C LEU* 3.9 9.6 - - + -
108C LEU* 3.6 22.2 - - - -
111C LEU* 3.7 19.2 - - + +
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Residues in contact with LEU 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C TRP* 2.8 38.2 + - + +
68C MET* 1.3 85.3 - - + +
70C LYS* 1.3 65.8 + - + +
71C ASP 3.8 1.9 + - - -
72C ASN* 3.6 14.0 + - - +
104C HIS* 5.8 0.4 - - - +
107C ASP* 3.6 50.7 - - + +
110C SER* 4.1 5.8 - - - +
111C LEU* 4.0 28.9 - - + -
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Residues in contact with LYS 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C SER* 3.0 46.3 + - - +
67C ARG 4.8 0.7 - - - +
69C LEU* 1.3 78.2 - - + +
71C ASP* 1.3 80.2 + - - +
72C ASN* 3.2 5.1 + - - +
78C ARG* 4.6 6.1 + - - -
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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
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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