Contacts of the helix formed by residues 53 - 67 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B THR 3.4 21.6 + - - -
50B LEU 3.2 14.6 + - - +
52B SER* 1.3 78.1 - - - +
54B ALA* 1.3 65.6 + - - +
55B SER* 4.0 7.6 - - - +
56B TRP* 3.1 15.8 + - + +
57B THR* 3.3 13.4 + - - +
119B LEU* 4.7 3.4 - - + -
122B GLU* 3.5 31.2 - - - +
123B ARG* 3.8 26.0 - - - -
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B SER 3.5 3.9 + - - -
53B CYS* 1.3 71.3 - - - +
55B SER* 1.3 57.1 + - - +
57B THR* 2.9 21.7 + - - -
58B GLN* 3.2 15.8 + - - +
122B GLU* 3.0 15.0 + - - +
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Residues in contact with SER 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B CYS* 4.0 0.9 - - - +
54B ALA* 1.3 76.9 - - - +
56B TRP* 1.3 59.8 + - - +
58B GLN* 3.7 8.2 - - - +
59B LEU* 3.0 34.7 + - - +
115B ALA* 4.1 8.6 - - - +
118B ARG* 4.1 14.3 - - - +
119B LEU* 3.3 42.7 - - - +
122B GLU* 2.5 26.5 + - - -
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Residues in contact with TRP 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 3.4 49.6 - - + +
51B THR* 3.8 31.3 - - + +
53B CYS* 3.1 10.5 + - + +
55B SER* 1.3 77.3 + - - +
57B THR* 1.3 67.0 + - + +
59B LEU* 3.3 6.6 + - - +
60B GLN* 3.1 23.3 + - + +
119B LEU* 3.9 23.6 - - + -
378B VAL* 4.4 7.0 - - + -
382B ASN* 3.5 38.8 - - + -
383B PHE* 3.8 26.5 - + - -
426B THR* 3.6 26.5 - - + -
556B ILE* 4.7 1.8 - - + -
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Residues in contact with THR 57 (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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51B THR 3.9 19.3 - - - +
52B SER* 5.3 2.9 - - - +
53B CYS 3.3 5.7 + - - +
54B ALA* 2.9 23.7 + - - -
56B TRP* 1.3 77.2 - - + +
58B GLN* 1.3 60.7 + - - +
60B GLN* 3.4 8.8 + - - +
61B LYS* 3.2 21.0 + - - +
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Residues in contact with GLN 58 (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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54B ALA 3.2 18.2 + - - +
55B SER* 3.7 9.0 - - - +
56B TRP 3.2 0.2 - - - -
57B THR* 1.3 75.1 + - - +
59B LEU* 1.3 59.2 + - - +
61B LYS* 3.2 30.2 + - - +
62B LEU* 2.9 65.5 + - + +
111B GLU* 4.9 4.6 + - - -
115B ALA* 4.6 8.3 - - + -
118B ARG* 5.9 4.3 - - - +
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B SER 3.0 25.0 + - - +
56B TRP* 3.3 1.8 + - - +
58B GLN* 1.3 77.5 - - - +
60B GLN* 1.3 56.6 + - - +
62B LEU* 3.4 5.8 + - + +
63B TYR* 2.9 27.7 + - - +
112B ILE* 4.0 6.1 - - + +
115B ALA* 3.7 32.1 - - + +
116B LEU* 3.9 28.0 - - + -
119B LEU* 3.8 29.6 - - + -
379B TRP* 3.5 25.8 - - + -
383B PHE* 3.6 26.0 - - + -
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Residues in contact with GLN 60 (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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56B TRP* 3.1 15.2 + - + +
57B THR* 3.6 11.9 - - - +
58B GLN 3.3 0.2 - - - -
59B LEU* 1.3 72.5 - - - +
61B LYS* 1.3 61.8 + - - +
63B TYR* 3.3 15.9 + - - +
64B GLU* 3.0 63.4 + - - +
382B ASN 5.4 0.7 - - - +
383B PHE* 3.5 25.1 - - + +
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Residues in contact with LYS 61 (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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57B THR 3.2 13.3 + - - +
58B GLN* 3.2 35.8 + - - +
60B GLN* 1.3 75.9 - - - +
62B LEU* 1.3 57.0 + - + +
64B GLU* 3.4 13.4 + - - +
65B GLN* 2.5 68.3 + - + +
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Residues in contact with LEU 62 (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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58B GLN* 2.9 38.1 + - - +
59B LEU* 3.4 7.4 + - + +
60B GLN 3.3 0.2 - - - -
61B LYS* 1.3 75.5 - - + +
63B TYR* 1.3 58.8 + - - +
65B GLN* 4.1 10.3 - - - +
66B TYR* 2.8 52.2 + - + +
67B GLY 3.8 0.3 + - - -
111B GLU* 3.7 41.3 - - + +
112B ILE* 3.9 17.4 - - + +
115B ALA* 3.6 31.0 - - + -
379B TRP* 4.2 2.7 - - + -
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Residues in contact with TYR 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 2.9 13.9 + - - +
60B GLN* 3.5 29.8 - - - +
61B LYS 3.3 0.2 - - - -
62B LEU* 1.3 74.7 - - - +
64B GLU* 1.3 66.0 + - + +
67B GLY* 2.9 32.9 + - - +
68B ASP 4.4 0.7 + - - -
379B TRP* 3.6 15.0 - + + -
383B PHE* 3.2 35.8 + - + -
384B PHE* 3.5 56.4 + + - -
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Residues in contact with GLU 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 GLN* 3.0 47.1 + - - +
61B LYS* 3.6 10.7 - - - +
63B TYR* 1.3 81.6 - - + +
65B GLN* 1.3 63.1 + - + +
67B GLY 4.9 0.3 + - - -
68B ASP* 5.5 5.7 + - - +
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Residues in contact with GLN 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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61B LYS* 2.5 55.8 + - + +
62B LEU* 3.9 10.4 - - - +
64B GLU* 1.3 81.8 - - + +
66B TYR* 1.3 98.9 + - + +
67B GLY 3.8 0.2 - - - -
68B ASP* 5.2 3.6 + - - +
69B GLU* 5.5 1.0 + - - +
111B GLU* 5.3 1.0 + - - -
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Residues in contact with TYR 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 2.8 36.9 + - + +
65B GLN* 1.3 106.5 + - + +
67B GLY* 1.3 61.2 + - - +
68B ASP 3.2 3.4 - - - -
69B GLU* 3.2 40.6 + - + +
74B HIS* 4.9 6.0 + - + -
107B HIS* 5.2 2.9 - - - +
109B ASN* 3.3 33.2 - - - +
111B GLU* 2.7 29.8 + - + -
112B ILE* 4.0 13.1 - - + +
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Residues in contact with GLY 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU 3.8 2.4 + - - -
63B TYR* 2.9 33.7 + - - -
65B GLN 3.8 0.2 - - - -
66B TYR* 1.3 71.4 - - - +
68B ASP* 1.3 58.0 + - - +
69B GLU 3.3 0.6 + - - -
107B HIS* 3.8 13.0 - - - -
112B ILE* 5.2 0.4 - - - +
379B TRP* 5.0 4.3 - - - -
384B PHE* 3.6 36.1 - - - -
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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