Contacts of the helix formed by residues 66 - 82 (chain D) in PDB entry 3RKR
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 66 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63D ASP* 3.2 31.1 + - + +
64D LEU 3.2 2.7 - - - -
65D SER* 1.3 90.2 + - - +
67D SER* 1.3 64.8 + - - +
68D ASP* 4.5 4.5 - - + +
69D ALA* 3.3 20.3 + - + +
70D ILE* 3.1 24.8 + - - +
121D LEU* 4.9 1.1 - - - -
243D SO4 2.7 23.6 + - - +
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Residues in contact with SER 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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66D HIS* 1.3 68.9 - - - +
68D ASP* 1.3 73.7 + - - +
70D ILE* 2.9 4.9 + - - +
71D ALA* 2.8 23.8 + - - +
117D LYS* 4.2 10.6 + - - -
121D LEU* 3.9 30.4 - - - +
243D SO4 2.3 32.8 + - - -
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Residues in contact with ASP 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D HIS* 3.4 4.2 - - + +
67D SER* 1.3 78.8 - - - +
69D ALA* 1.3 57.0 + - - +
71D ALA* 3.1 7.9 + - - +
72D ALA* 2.8 32.5 + - - +
243D SO4 5.0 8.3 + - - -
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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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62D CYS* 3.9 3.6 - - - -
63D ASP* 3.4 35.2 - - + +
66D HIS* 3.3 16.1 + - + +
68D ASP* 1.3 79.3 - - - +
70D ILE* 1.3 57.1 + - - +
72D ALA* 3.5 5.7 + - - +
73D PHE* 3.0 28.9 + - - +
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Residues in contact with ILE 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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62D CYS* 4.2 7.9 - - - -
64D LEU* 3.5 45.3 - - + +
66D HIS 3.1 6.9 + - - +
67D SER 2.9 7.7 + - - +
69D ALA* 1.3 77.8 - - - +
71D ALA* 1.3 63.3 + - - +
73D PHE* 3.4 2.5 + - - +
74D ALA* 3.0 22.9 + - - +
118D ALA* 3.9 16.8 - - + +
121D LEU* 3.9 41.5 - - + +
122D LEU* 3.8 29.4 - - + +
125D ALA* 5.0 3.8 - - + -
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Residues in contact with ALA 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 SER 2.8 12.4 + - - +
68D ASP* 3.4 12.3 - - - +
70D ILE* 1.3 75.5 - - - +
72D ALA* 1.3 65.1 + - - +
74D ALA* 3.3 4.5 + - - +
75D THR* 2.8 30.8 + - - +
125D ALA* 5.2 5.6 - - - -
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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 ASP 2.8 20.1 + - - +
69D ALA* 3.9 5.4 - - - +
71D ALA* 1.3 73.0 - - - +
73D PHE* 1.3 64.5 + - - +
75D THR* 3.5 7.5 + - - -
76D GLY* 3.1 19.6 + - - -
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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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10D VAL* 4.0 26.9 - - + -
12D THR* 5.8 1.1 - - + -
34D VAL* 4.0 8.3 - - + -
36D THR* 3.5 23.3 - - - -
60D HIS* 3.9 32.9 + + + -
61D ALA 5.5 1.6 - - - +
62D CYS* 3.8 24.7 - - + -
64D LEU* 6.2 0.7 - - + -
69D ALA 3.0 18.8 + - - +
70D ILE 3.7 5.8 - - - +
71D ALA 3.2 0.2 - - - -
72D ALA* 1.3 78.6 - - - +
74D ALA* 1.3 64.9 + - - +
76D GLY* 3.4 1.6 + - - -
77D VAL* 3.3 39.3 + - + +
122D LEU* 4.1 19.1 - - + -
126D PHE* 4.1 8.7 - + - -
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Residues in contact with ALA 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 ILE* 3.0 12.6 + - + +
71D ALA 4.0 1.8 - - - +
73D PHE* 1.3 75.1 - - + +
75D THR* 1.3 67.8 + - - +
77D VAL* 3.1 3.7 + - - +
78D LEU* 2.9 29.0 + - + +
125D ALA* 3.5 33.9 - - + +
126D PHE* 3.5 31.9 - - + -
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Residues in contact with THR 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 ALA* 2.8 20.2 + - - +
72D ALA* 3.6 9.1 - - - -
74D ALA* 1.3 76.8 - - - +
76D GLY* 1.3 57.1 + - - +
78D LEU* 3.3 6.7 + - - +
79D ALA* 2.8 33.5 + - + +
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Residues in contact with GLY 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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60D HIS* 5.8 5.6 - - - -
72D ALA 3.1 11.1 + - - -
73D PHE 3.9 3.4 - - - -
74D ALA 3.2 0.4 - - - -
75D THR* 1.3 79.4 - - - +
77D VAL* 1.3 57.0 + - - +
79D ALA* 3.3 5.9 + - - +
80D ALA* 2.8 33.1 + - - +
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Residues in contact with VAL 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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8D VAL* 4.6 13.0 - - + -
10D VAL* 4.4 6.7 - - + -
34D VAL* 3.9 31.4 - - + -
58D GLU* 4.8 2.0 - - - +
60D HIS* 4.7 8.5 - - + +
73D PHE* 3.3 40.3 + - + +
74D ALA 3.1 7.2 + - - +
76D GLY* 1.3 74.2 - - - +
78D LEU* 1.3 58.0 + - + +
80D ALA* 3.4 4.0 + - - -
81D HIS* 2.9 35.8 + - - +
82D GLY 4.0 0.2 + - - -
83D ARG 4.9 4.0 - - - +
126D PHE* 4.2 18.8 - - + -
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Residues in contact with LEU 78 (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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74D ALA* 2.9 21.3 + - + +
75D THR* 3.8 6.1 - - - +
77D VAL* 1.3 75.2 - - + +
79D ALA* 1.3 61.6 + - - +
82D GLY* 2.6 33.3 + - - +
83D ARG 4.2 24.9 - - - +
84D CYS 4.2 0.2 - - - +
125D ALA 4.0 20.9 - - - +
126D PHE* 4.1 22.4 - - + -
128D PRO* 6.5 0.4 - - + -
129D ALA* 4.1 27.4 - - + +
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Residues in contact with ALA 79 (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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75D THR* 2.8 24.8 + - + +
76D GLY* 3.8 5.2 - - - +
78D LEU* 1.3 73.1 - - - +
80D ALA* 1.3 64.0 + - - +
81D HIS* 4.6 0.3 - - - -
82D GLY 4.6 0.3 + - - -
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Residues in contact with ALA 80 (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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58D GLU* 5.0 2.5 - - - +
76D GLY 2.8 20.6 + - - +
77D VAL* 3.7 1.8 - - - +
79D ALA* 1.3 76.3 - - - +
81D HIS* 1.3 85.6 + - + +
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Residues in contact with HIS 81 (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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8D VAL* 4.0 24.7 - - + -
32D ARG* 2.9 44.3 + - - -
34D VAL* 5.2 2.4 - - + +
58D GLU* 3.0 33.9 + - - -
77D VAL* 2.9 24.1 + - - +
79D ALA 4.9 0.7 - - - -
80D ALA* 1.3 93.3 - - + +
82D GLY* 1.3 56.4 + - - +
83D ARG* 3.2 18.8 + - + +
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Residues in contact with GLY 82 (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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78D LEU* 2.6 38.2 + - - +
79D ALA 4.6 0.2 + - - -
81D HIS* 1.3 70.3 - - - +
83D ARG* 1.3 59.2 + - - +
129D ALA* 4.7 6.9 - - - +
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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