Contacts of the helix formed by residues 53 - 67 (chain C) in PDB entry 2O2C
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 CYS 53 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49C THR 3.3 23.5 + - - -
50C LEU 3.2 14.5 + - - +
52C SER* 1.3 79.1 - - - +
54C ALA* 1.3 65.3 + - - +
55C SER* 4.1 9.6 - - - +
56C TRP* 3.1 17.0 + - + +
57C THR* 3.4 13.2 + - - -
119C LEU* 4.5 3.1 - - + -
122C GLU* 3.5 23.3 - - - +
123C ARG* 3.8 27.8 - - - -
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Residues in contact with ALA 54 (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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52C SER 3.6 3.9 + - - -
53C CYS* 1.3 70.5 - - - +
55C SER* 1.3 59.8 + - - +
56C TRP 3.5 0.2 + - - -
57C THR* 3.5 7.7 + - - -
58C GLN* 3.0 42.0 + - - +
122C GLU* 3.1 18.2 + - - +
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Residues in contact with SER 55 (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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53C CYS* 4.1 0.9 - - - +
54C ALA* 1.3 73.4 - - - +
56C TRP* 1.3 59.8 + - - +
58C GLN* 3.5 14.4 + - - +
59C LEU* 3.0 34.0 + - - +
115C ALA* 3.9 8.8 - - - +
118C ARG* 4.1 7.9 - - - -
119C LEU* 3.3 43.4 - - - +
122C GLU* 3.0 24.2 + - - -
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Residues in contact with TRP 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU* 3.5 46.2 - - + +
51C THR* 3.8 31.5 - - + +
53C CYS* 3.1 12.6 + - + +
55C SER* 1.3 77.8 + - - +
57C THR* 1.3 66.2 + - - +
59C LEU* 3.4 5.2 + - - +
60C GLN* 3.1 25.0 + - + +
119C LEU* 3.8 26.4 - - + +
378C VAL* 4.3 5.8 - - + -
382C ASN* 3.6 37.7 - - + -
383C PHE* 3.8 27.8 - + - -
426C THR* 3.7 26.0 - - + -
556C ILE* 4.7 1.6 - - + -
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Residues in contact with THR 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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51C THR 4.2 9.5 + - - -
52C SER 5.2 1.6 + - - -
53C CYS 3.4 9.7 + - - -
54C ALA* 3.8 9.9 - - - -
55C SER 3.4 0.2 - - - -
56C TRP* 1.3 79.8 - - - +
58C GLN* 1.3 60.9 + - - +
60C GLN* 3.4 7.7 + - + +
61C LYS* 3.1 52.5 + - + +
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Residues in contact with GLN 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 ALA* 3.0 36.7 + - - +
55C SER* 3.6 10.6 - - - +
57C THR* 1.3 77.9 - - - +
59C LEU* 1.3 55.8 + - - +
61C LYS* 3.3 16.3 + - + +
62C LEU* 3.0 36.2 + - + +
115C ALA* 4.8 3.8 - - + +
118C ARG* 2.9 41.4 + - - +
122C GLU* 4.9 1.2 + - - -
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Residues in contact with LEU 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C SER 3.0 22.5 + - - +
56C TRP* 3.7 2.2 - - - +
57C THR 3.3 0.4 - - - -
58C GLN* 1.3 73.8 - - - +
60C GLN* 1.3 59.2 + - - +
62C LEU* 3.4 4.1 + - + -
63C TYR* 3.0 23.7 + - - +
112C ILE* 4.0 6.5 - - + +
115C ALA* 3.7 31.6 - - + +
116C LEU* 3.9 28.0 - - + -
119C LEU* 3.9 28.5 - - + -
379C TRP* 3.5 32.2 - - + -
383C PHE* 3.6 25.6 - - + -
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Residues in contact with GLN 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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56C TRP* 3.1 18.3 + - + +
57C THR* 3.7 11.4 - - + +
59C LEU* 1.3 75.1 - - - +
61C LYS* 1.3 63.3 - - + +
63C TYR* 3.3 24.4 + - - -
64C GLU* 3.3 31.2 + - + +
382C ASN 5.0 3.3 - - - +
383C PHE* 3.7 21.9 - - + +
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Residues in contact with LYS 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 THR* 3.1 35.8 + - + +
58C GLN* 3.5 14.9 - - + +
59C LEU 3.3 0.2 - - - -
60C GLN* 1.3 77.4 - - + +
62C LEU* 1.3 57.9 + - + +
64C GLU* 3.5 6.7 + - - +
65C GLN* 3.2 31.1 + - - +
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Residues in contact with LEU 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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58C GLN* 3.0 23.6 + - + +
59C LEU* 3.8 7.4 - - + +
60C GLN 3.3 0.2 - - - -
61C LYS* 1.3 77.9 - - + +
63C TYR* 1.3 58.6 + - - +
65C GLN* 3.4 21.5 - - - +
66C TYR* 2.9 44.4 + - + +
67C GLY 4.0 0.2 + - - -
111C GLU* 3.6 52.0 - - + +
112C ILE* 4.0 15.6 - - + +
115C ALA* 3.9 16.2 - - + -
118C ARG* 5.3 2.5 - - - +
379C TRP* 4.1 5.1 - - + -
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Residues in contact with TYR 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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59C LEU 3.0 13.5 + - - +
60C GLN* 3.6 29.6 - - - +
61C LYS 3.3 0.4 - - - -
62C LEU* 1.3 76.0 - - - +
64C GLU* 1.3 71.8 + - - +
65C GLN 3.1 0.2 - - - -
67C GLY* 2.8 36.9 + - - +
68C ASP 4.6 0.3 + - - -
379C TRP* 3.8 13.0 - + + -
383C PHE* 3.2 36.2 + - + -
384C PHE* 3.7 53.2 + + - -
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Residues in contact with GLU 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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60C GLN* 3.3 27.1 + - + +
61C LYS* 3.5 8.5 + - - +
63C TYR* 1.3 89.3 - - - +
65C GLN* 1.3 59.4 + - - +
67C GLY 4.7 0.4 + - - -
68C ASP* 5.7 1.4 + - - +
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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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61C LYS* 3.2 19.5 + - - +
62C LEU* 3.4 26.9 - - - +
63C TYR 3.1 0.2 - - - -
64C GLU* 1.3 80.7 - - - +
66C TYR* 1.3 89.8 + - + +
67C GLY 3.8 0.4 - - - -
68C ASP 5.5 0.4 + - - -
69C GLU* 5.3 0.9 - - - +
111C GLU* 4.9 1.5 + - - +
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Residues in contact with TYR 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 LEU* 2.9 32.0 + - + +
65C GLN* 1.3 111.6 + - + +
67C GLY* 1.3 63.6 + - - +
68C ASP 3.4 3.1 - - - -
69C GLU* 3.3 47.6 + - - +
74C HIS* 5.0 5.8 + - + -
107C HIS* 5.1 6.3 - - - +
109C ASN* 3.3 32.1 - - - +
111C GLU* 2.8 27.3 + - - -
112C ILE* 4.1 13.0 - - + -
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Residues in contact with GLY 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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62C LEU 4.0 0.2 + - - -
63C TYR* 2.8 38.0 + - - +
64C GLU 4.7 0.2 - - - -
65C GLN 3.8 0.6 - - - -
66C TYR* 1.3 72.9 - - - +
68C ASP* 1.3 62.0 + - - +
69C GLU 3.3 0.7 + - - -
107C HIS* 4.0 8.4 + - - -
379C TRP* 5.4 2.0 - - - -
384C PHE* 3.6 35.9 - - - -
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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