Contacts of the helix formed by residues 61 - 71 (chain C) in PDB entry 2Q8T
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21C THR 4.4 9.9 - - - +
22C THR* 6.0 0.3 - - - -
58C ASN* 3.1 40.8 + - - +
60C SER* 1.4 77.0 + - - +
62C LYS* 1.3 65.1 + - - +
63C TRP* 3.5 25.9 + - + +
64C VAL* 3.1 22.1 + - + +
65C GLN* 3.2 15.2 + - - +
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Residues in contact with LYS 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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60C SER 3.7 2.8 + - - -
61C ASP* 1.3 69.3 - - - +
63C TRP* 1.3 63.1 + - - +
64C VAL 3.1 0.5 + - - -
65C GLN* 3.1 17.5 + - - +
66C ASP* 2.8 65.3 + - - +
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Residues in contact with TRP 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 THR* 4.0 6.9 + - + -
22C THR 5.7 2.0 + - - -
23C TYR 3.8 15.4 - - - -
24C LYS* 3.7 47.5 - - + +
25C ILE* 3.7 23.1 - - + -
47C PHE* 3.8 17.9 - + - -
57C THR* 3.4 30.5 - - + -
61C ASP* 3.5 27.1 + - + -
62C LYS* 1.3 78.5 - - - +
64C VAL* 1.3 70.1 + - + +
66C ASP* 3.4 7.7 + - - -
67C TYR* 3.0 66.1 + + + -
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Residues in contact with VAL 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ILE* 3.8 27.4 - - + -
47C PHE* 4.0 8.9 - - + -
57C THR* 3.6 27.6 - - - +
58C ASN 3.4 22.2 - - - +
59C PRO* 4.2 4.5 - - + +
61C ASP* 3.1 16.6 + - + +
63C TRP* 1.3 105.4 - - + +
65C GLN* 1.3 63.9 + - - +
67C TYR* 3.4 2.6 + - - +
68C ILE* 3.0 31.3 + - + +
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Residues in contact with GLN 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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59C PRO 3.4 21.9 + - - +
60C SER* 3.8 17.4 + - - +
61C ASP 3.4 11.7 - - - +
62C LYS* 3.4 17.5 - - - +
64C VAL* 1.3 76.1 - - - +
66C ASP* 1.3 63.8 + - - +
68C ILE* 3.3 12.0 + - + +
69C LYS* 3.1 42.8 + - - +
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Residues in contact with ASP 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 LYS* 2.8 61.1 + - - +
63C TRP* 3.9 6.7 + - - +
65C GLN* 1.3 68.7 - - - +
67C TYR* 1.3 73.3 + - + +
69C LYS* 3.2 26.4 + - - +
70C ASP* 2.9 23.7 + - - +
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Residues in contact with TYR 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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24C LYS* 3.0 34.3 - - - -
25C ILE 2.7 29.6 + - - -
26C PRO* 4.2 0.3 - - - +
27C ARG* 3.3 37.3 + - + +
30C ILE* 3.5 27.1 - - + -
47C PHE* 3.8 7.6 - + + -
63C TRP* 3.0 43.1 + + + +
64C VAL 3.7 4.5 - - - +
66C ASP* 1.3 79.3 - - + +
68C ILE* 1.3 62.1 + - - +
70C ASP* 3.3 8.5 + - + +
71C MET* 3.1 44.9 + - + +
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Residues in contact with ILE 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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33C TYR* 3.7 47.2 + - + +
45C ILE* 3.7 37.2 - - + -
47C PHE* 4.5 7.2 - - + -
59C PRO 6.1 0.7 - - - +
64C VAL* 3.0 25.0 + - + +
65C GLN* 3.6 10.1 - - + +
66C ASP 3.2 0.2 - - - -
67C TYR* 1.3 73.9 - - - +
69C LYS* 1.3 63.0 - - + +
71C MET* 3.2 14.2 + - - +
72C LYS* 3.5 10.2 + - - +
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Residues in contact with LYS 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 GLN* 3.1 30.8 + - - +
66C ASP* 3.4 32.5 + - - +
68C ILE* 1.3 73.2 - - + +
70C ASP* 1.3 62.1 + - - +
71C MET 3.0 5.9 + - - -
72C LYS* 3.4 18.6 + - - +
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Residues in contact with ASP 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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27C ARG* 4.0 36.5 + - + +
66C ASP 2.9 15.9 + - - +
67C TYR* 3.3 9.4 + - + +
69C LYS* 1.3 75.7 - - - +
71C MET* 1.3 62.8 + - + +
72C LYS 3.5 3.4 + - - +
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Residues in contact with MET 71 (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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27C ARG* 5.6 5.8 - - + -
30C ILE* 2.9 38.4 - - + -
31C MET 4.7 6.5 - - - +
32C ASP* 4.6 7.0 - - - -
33C TYR* 3.9 32.1 - - + -
47C PHE* 3.8 8.1 - - + -
67C TYR* 3.1 39.9 + - + +
68C ILE 3.6 7.2 - - - +
69C LYS 3.0 1.8 - - - -
70C ASP* 1.3 81.2 - - + +
72C LYS* 1.3 66.0 + - - +
73C GLU* 3.3 19.1 + - - +
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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