Contacts of the helix formed by residues 53 - 67 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A THR 3.3 22.2 + - - -
50A LEU* 3.2 15.6 + - - +
51A THR 4.1 0.2 - - - +
52A SER* 1.3 79.0 - - - +
54A ALA* 1.3 63.5 + - - +
55A SER* 3.8 11.9 - - - +
56A TRP* 3.2 14.5 + - + +
57A THR* 3.2 14.3 + - - -
119A LEU* 4.9 2.0 - - + -
122A GLU* 3.3 25.6 - - - +
123A ARG* 3.8 27.4 - - - -
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Residues in contact with ALA 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A SER 3.6 3.9 + - - -
53A CYS* 1.3 71.0 - - - +
55A SER* 1.3 56.3 + - - +
57A THR* 3.4 8.5 + - - -
58A GLN* 3.0 28.6 + - - +
118A ARG* 5.7 0.4 - - - -
122A GLU* 3.1 13.6 + - - +
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Residues in contact with SER 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A CYS* 3.8 2.8 - - - +
54A ALA* 1.3 74.8 - - - +
56A TRP* 1.3 59.4 + - - +
58A GLN* 3.5 7.4 + - - +
59A LEU* 3.0 34.0 + - - +
115A ALA 4.4 4.7 - - - +
118A ARG* 4.1 14.9 + - - +
119A LEU* 3.5 41.7 - - - +
122A GLU* 2.7 30.0 + - - +
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Residues in contact with TRP 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 3.4 52.5 - - + +
51A THR* 3.7 32.8 - - + +
53A CYS* 3.2 9.7 + - + +
55A SER* 1.3 76.5 + - - +
57A THR* 1.3 62.2 + - - +
59A LEU* 3.2 6.6 + - - +
60A GLN* 3.0 31.7 + - + +
119A LEU* 3.8 27.1 - - + +
378A VAL* 4.2 6.1 - - + -
382A ASN* 3.6 40.2 - - + -
383A PHE* 3.7 25.1 - + - -
426A THR* 3.6 22.0 - - + +
556A ILE* 4.4 2.5 - - + -
557A TRP* 4.9 0.9 - - - -
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Residues in contact with THR 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A THR 4.0 10.6 + - - -
52A SER 5.2 1.4 - - - -
53A CYS 3.2 11.0 + - - -
54A ALA* 3.6 11.3 - - - +
55A SER 3.4 0.2 - - - -
56A TRP* 1.3 79.1 - - - +
58A GLN* 1.3 62.6 + - - +
60A GLN* 3.4 8.4 + - - +
61A LYS* 3.1 23.7 + - + +
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Residues in contact with GLN 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ALA 3.0 16.6 + - - +
55A SER 3.7 3.4 - - - +
56A TRP 3.2 0.2 - - - -
57A THR* 1.3 76.3 - - - +
59A LEU* 1.3 59.3 + - - +
61A LYS* 3.2 32.7 + - - +
62A LEU* 2.9 66.0 + - + +
65A GLN* 5.6 0.4 + - - -
115A ALA* 4.7 0.7 - - + -
118A ARG* 3.2 30.5 - - - +
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Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A SER 3.0 21.7 + - - +
56A TRP* 3.2 2.6 + - - +
58A GLN* 1.3 75.6 - - - +
60A GLN* 1.3 57.8 + - - +
62A LEU* 3.4 4.6 + - + -
63A TYR* 3.0 24.8 + - - +
112A ILE* 4.2 4.5 - - + +
115A ALA* 3.7 32.1 - - + +
116A LEU* 3.9 27.1 - - + -
119A LEU* 3.8 31.0 - - + -
379A TRP* 3.5 30.0 - - + -
383A PHE* 3.6 25.6 - - + -
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Residues in contact with GLN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A TRP* 3.0 19.2 + - + +
57A THR* 3.6 11.2 - - - +
58A GLN 3.2 0.2 - - - -
59A LEU* 1.3 75.5 - - - +
61A LYS* 1.3 62.4 + - - +
63A TYR* 3.4 19.1 + - - +
64A GLU* 3.2 45.1 + - - +
382A ASN 4.7 5.5 + - - -
383A PHE* 3.5 27.2 - - + +
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Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A THR* 3.1 15.1 + - + +
58A GLN* 3.2 35.6 + - - +
60A GLN* 1.3 77.4 - - - +
62A LEU* 1.3 59.7 + - - +
64A GLU* 3.4 13.9 + - - +
65A GLN* 3.2 50.5 + - - +
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A GLN* 2.9 41.4 + - + +
59A LEU* 3.8 7.4 - - + +
61A LYS* 1.3 73.0 - - - +
63A TYR* 1.3 59.3 + - - +
65A GLN* 3.8 11.7 - - - +
66A TYR* 2.9 57.7 + - + +
67A GLY 4.0 0.3 + - - -
111A GLU* 3.6 28.3 - - + +
112A ILE* 4.1 15.5 - - + -
115A ALA* 3.5 31.4 - - + -
118A ARG* 5.9 0.2 - - - +
379A TRP* 4.1 4.5 - - + -
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Residues in contact with TYR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU 3.0 17.0 + - - +
60A GLN* 3.5 22.7 - - - +
61A LYS 3.3 0.2 - - - -
62A LEU* 1.3 73.7 - - - +
64A GLU* 1.3 65.8 + - + +
67A GLY* 2.8 32.8 + - - +
68A ASP 4.7 0.2 + - - -
379A TRP* 3.6 16.1 - + + -
383A PHE* 3.2 37.2 + - + -
384A PHE* 3.6 54.8 + + - -
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Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A GLN* 3.2 36.5 + - - +
61A LYS* 3.4 13.3 + - - +
63A TYR* 1.3 83.1 - - + +
65A GLN* 1.3 62.2 + - + +
67A GLY 4.8 0.5 + - - -
68A ASP* 5.2 6.1 + - - +
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Residues in contact with GLN 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A GLN* 5.6 0.4 + - - +
61A LYS* 3.2 49.5 + - - +
62A LEU* 3.8 12.9 - - - +
64A GLU* 1.3 82.0 - - + +
66A TYR* 1.3 96.4 + - + +
68A ASP* 5.2 2.3 + - - +
69A GLU* 4.5 6.6 - - - +
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Residues in contact with TYR 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU* 2.9 45.2 + - + +
65A GLN* 1.3 93.7 + - + +
67A GLY* 1.3 65.1 + - - +
68A ASP 3.3 3.1 - - - -
69A GLU* 3.2 50.7 + - - +
74A HIS* 5.0 4.3 + - + -
107A HIS* 5.2 4.4 - - - +
109A ASN* 3.5 24.0 - - - +
111A GLU* 2.7 36.5 + - + -
112A ILE* 4.0 21.6 - - + +
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Residues in contact with GLY 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU 4.0 0.4 + - - -
63A TYR* 2.8 36.8 + - - +
64A GLU 4.8 0.2 - - - -
65A GLN 3.8 0.6 - - - -
66A TYR* 1.3 72.1 - - - +
68A ASP* 1.3 61.6 + - - +
69A GLU 3.6 0.5 + - - -
107A HIS* 4.0 9.7 - - - -
379A TRP* 5.4 2.2 - - - -
384A PHE* 3.6 36.6 - - - -
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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