Contacts of the helix formed by residues 63 - 77 (chain D) in PDB entry 2ODE
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 HIS 63 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59D VAL* 3.5 31.4 + - + +
60D LEU* 3.2 6.9 + - - +
62D SER* 1.3 94.5 + - - +
64D LYS* 1.3 65.6 + - - +
65D TYR* 3.5 47.3 + + + -
66D GLY* 3.0 8.2 + - - +
67D VAL* 2.9 25.5 + - - +
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Residues in contact with LYS 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D SER 4.3 1.0 + - - -
63D HIS* 1.3 71.9 - - - +
65D TYR* 1.3 61.3 + - + +
67D VAL* 3.6 8.6 + - - +
68D ALA* 3.1 26.7 + - - +
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Residues in contact with TYR 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D HIS* 3.5 44.3 + + + -
64D LYS* 1.3 79.4 - - + +
66D GLY* 1.3 68.2 + - - +
68D ALA* 3.8 7.1 - - - +
69D ALA* 3.2 23.9 + - - +
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Residues in contact with GLY 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D LEU* 3.4 40.2 - - - +
63D HIS* 3.0 6.2 + - - +
65D TYR* 1.3 86.7 - - - +
67D VAL* 1.3 58.2 + - - +
69D ALA* 3.4 3.1 + - - +
70D PHE* 2.9 31.4 + - - +
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Residues in contact with VAL 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D LEU 3.7 0.4 + - - -
61D LEU* 3.3 41.3 - - + +
63D HIS 2.9 14.4 + - - +
64D LYS* 3.7 8.3 - - - +
66D GLY* 1.3 77.0 - - - +
68D ALA* 1.3 57.1 + - - +
70D PHE* 3.4 4.1 + - - -
71D ARG* 2.9 42.3 + - - +
83D LEU* 3.8 8.2 - - + +
87D LEU* 3.9 39.0 - - + -
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Residues in contact with ALA 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D LYS 3.1 18.5 + - - +
65D TYR* 3.9 7.9 - - - +
67D VAL* 1.3 75.0 - - - +
69D ALA* 1.3 63.0 + - - +
71D ARG* 3.4 19.2 + - - +
72D ALA* 3.1 23.4 + - - +
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Residues in contact with ALA 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D LEU* 5.5 0.7 - - + -
65D TYR 3.2 17.1 + - - +
66D GLY* 3.8 5.2 - - - +
68D ALA* 1.3 77.0 - - - +
70D PHE* 1.3 65.2 + - - +
72D ALA* 3.4 7.5 + - - +
73D PHE* 3.2 16.6 + - - +
162D PHE* 3.6 23.6 - - + -
167D MET* 4.2 3.4 - - - +
168D TYR* 6.2 0.9 - - + -
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Residues in contact with PHE 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D PHE* 3.4 36.3 - + - -
60D LEU* 4.0 12.6 - - + -
61D LEU* 4.4 8.5 - - + -
66D GLY 2.9 18.3 + - - +
67D VAL* 3.8 5.2 - - - +
69D ALA* 1.3 75.7 - - - +
71D ARG* 1.3 57.2 + - - +
73D PHE* 3.1 4.6 + + - +
74D LEU* 2.9 68.4 + - + +
83D LEU* 4.4 9.4 - - + -
154D MET* 4.0 10.3 - - + -
158D SER* 4.1 11.2 - - - -
159D TYR* 3.9 15.3 - + + -
162D PHE* 3.7 43.2 - + + -
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Residues in contact with ARG 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D VAL* 2.9 34.1 + - - +
68D ALA* 3.5 17.9 - - - +
69D ALA 3.3 0.2 - - - -
70D PHE* 1.3 76.9 - - - +
72D ALA* 1.3 57.9 + - - +
74D LEU* 3.3 5.5 + - - +
75D LYS* 2.9 57.9 + - + +
80D GLU* 4.4 6.0 - - + +
83D LEU* 3.7 17.6 - - + +
84D GLU* 5.5 10.6 - - + +
87D LEU* 3.5 28.0 - - - +
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Residues in contact with ALA 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D ALA 3.1 10.4 + - - +
69D ALA* 3.6 10.8 - - - +
71D ARG* 1.3 79.6 - - - +
73D PHE* 1.3 62.7 + - - +
75D LYS* 3.5 12.0 + - - +
76D THR* 3.4 23.6 + - - +
167D MET* 3.9 14.4 - - + +
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Residues in contact with PHE 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D ALA 3.2 5.1 + - - +
70D PHE* 3.1 9.3 + + - +
72D ALA* 1.3 76.2 - - - +
74D LEU* 1.3 72.4 + - + +
76D THR* 2.5 36.5 + - - -
77D GLU* 3.3 39.3 + - + +
158D SER 3.4 22.9 - - - -
161D ARG* 3.7 8.3 - - + -
162D PHE* 3.4 41.7 - + + -
165D SER* 3.7 31.6 - - - -
167D MET* 3.6 17.7 - - + -
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Residues in contact with LEU 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D PHE* 2.9 42.7 + - + +
71D ARG 3.7 4.0 - - - +
73D PHE* 1.3 80.6 - - + +
75D LYS* 1.3 62.0 + - - +
77D GLU* 2.9 5.0 + - - +
78D PHE 2.9 24.3 + - - -
79D SER* 3.0 37.9 + - - +
80D GLU* 3.7 15.3 - - + +
82D ASN* 6.3 0.2 - - - +
83D LEU* 3.7 33.2 - - + +
154D MET* 4.3 5.2 - - + -
158D SER* 3.6 27.8 - - - +
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Residues in contact with LYS 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D ARG* 2.9 43.3 + - + +
72D ALA* 3.6 11.0 - - - +
74D LEU* 1.3 76.6 - - - +
76D THR* 1.3 61.3 + - + +
78D PHE* 3.2 23.6 + - - -
80D GLU* 3.7 33.6 - - + +
84D GLU* 5.7 1.6 - - - -
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Residues in contact with THR 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C ILE 4.4 2.6 - - - +
72D ALA 3.4 14.6 - - - +
73D PHE* 2.5 30.9 + - - -
75D LYS* 1.3 75.9 - - + +
77D GLU* 1.3 61.4 + - - +
78D PHE* 3.4 14.9 - - - -
167D MET* 3.5 19.9 - - + +
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Residues in contact with GLU 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C THR 4.3 3.1 - - - +
183C GLY* 3.0 2.9 - - - -
184C ILE 2.7 40.1 + - - +
185C VAL* 4.0 14.4 - - - +
73D PHE* 3.3 38.7 - - + +
74D LEU* 2.9 8.5 + - - +
76D THR* 1.3 82.1 + - - +
78D PHE* 1.3 69.4 + - - +
79D SER* 3.2 8.1 + - - +
158D SER* 4.3 7.4 + - - -
161D ARG* 2.9 45.8 + - - -
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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