Contacts of the helix formed by residues 60 - 70 (chain D) in PDB entry 2BZN
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 THR 60 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56D ASP 3.8 19.1 - - - +
57D THR 4.2 0.2 - - - -
58D VAL 2.9 14.3 + - - -
59D GLY* 1.3 77.1 - - - +
61D PHE* 1.3 61.5 + - - +
62D GLU* 3.6 10.3 + - - +
63D MET* 3.0 15.1 + - - +
64D ALA* 3.0 26.7 + - - +
74D THR* 4.1 2.1 - - - +
76D VAL* 5.5 0.9 - - - -
77D HIS* 4.4 1.8 - - + +
80D TYR* 3.4 14.8 - - - +
250D GLU 2.7 21.7 + - - +
252D GLY* 3.8 27.1 - - - +
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Residues in contact with PHE 61 (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 THR* 1.3 72.5 - - - +
62D GLU* 1.3 69.4 + - - +
64D ALA* 3.1 5.7 + - + +
65D LYS* 3.1 31.0 + - - +
76D VAL* 4.0 22.0 - - + -
80D TYR* 3.0 58.8 + + - +
84D GLN* 3.9 19.5 - - + -
85D TRP* 3.8 35.4 - + - -
88D PHE* 3.4 50.9 - + + -
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Residues in contact with GLU 62 (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 THR* 3.6 16.8 - - - +
61D PHE* 1.3 84.9 + - - +
63D MET* 1.3 62.5 + - - +
65D LYS* 3.6 20.2 + - - +
66D VAL* 3.6 15.2 + - - +
80D TYR* 3.9 5.5 + - - -
249D SER 5.9 0.2 - - - +
250D GLU* 3.6 38.3 - - + +
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Residues in contact with MET 63 (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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52D ALA* 4.1 15.9 - - + -
58D VAL* 3.2 26.7 - - - +
60D THR* 3.0 24.1 + - - +
62D GLU* 1.3 76.3 - - - +
64D ALA* 1.3 64.5 + - - +
66D VAL* 3.2 3.3 + - - +
67D LEU* 3.0 52.9 + - + +
74D THR* 4.3 1.8 - - + +
245D LEU* 3.4 37.2 - - + +
250D GLU* 3.9 6.2 - - + +
251D SER* 3.7 24.0 - - - +
301D VAL* 3.8 22.4 - - + -
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Residues in contact with ALA 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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60D THR 3.0 12.9 + - - +
61D PHE* 3.1 13.4 + - + +
63D MET* 1.3 75.3 - - - +
65D LYS* 1.3 62.7 + - - +
67D LEU* 4.1 0.4 - - - +
68D CYS* 3.0 32.4 + - - -
74D THR* 3.4 22.8 + - + +
76D VAL* 5.4 0.7 - - + -
88D PHE* 4.3 9.2 - - + -
95D CYS* 5.0 0.4 - - - -
99D LEU* 3.7 26.2 - - + -
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Residues in contact with LYS 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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61D PHE* 3.1 21.6 + - - +
62D GLU* 3.9 22.6 + - - +
63D MET 3.3 0.4 - - - -
64D ALA* 1.3 76.7 - - - +
66D VAL* 1.3 63.4 + - + +
68D CYS* 3.9 0.2 - - - +
69D LYS* 3.3 28.4 - - - +
88D PHE* 4.1 11.7 - - + -
92D ASN* 3.5 36.7 + - - +
95D CYS* 4.1 11.9 - - - -
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Residues in contact with VAL 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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62D GLU 3.6 11.2 + - - +
63D MET 3.2 4.7 + - - +
65D LYS* 1.3 78.5 - - + +
67D LEU* 1.3 70.4 + - + +
69D LYS* 3.0 23.3 + - + +
70D PHE* 3.4 24.3 - - + -
250D GLU* 3.8 24.7 - - + +
301D VAL* 3.7 23.8 - - + -
302D GLU* 4.1 14.6 - - + +
305D ILE* 5.2 0.4 - - + -
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Residues in contact with LEU 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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51D ILE 5.3 0.2 - - - -
52D ALA* 3.8 23.1 - - + +
63D MET* 3.0 39.6 + - + +
64D ALA 4.1 0.4 - - - +
66D VAL* 1.3 79.0 - - - +
68D CYS* 1.3 55.9 + - - +
70D PHE* 2.9 18.8 + - - +
72D LEU* 2.9 55.3 + - + +
73D PHE 3.7 20.4 - - - +
74D THR* 3.9 11.4 - - - +
245D LEU* 4.5 7.9 - - + -
301D VAL* 4.3 5.8 - - + -
305D ILE* 3.9 22.9 - - + -
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Residues in contact with CYS 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 ALA* 3.0 26.1 + - - +
65D LYS 3.9 1.8 - - - +
67D LEU* 1.3 75.2 - - - +
69D LYS* 1.3 77.2 + - - +
71D SER* 3.0 19.2 + - - +
72D LEU 4.0 10.6 + - - -
94D ASP 4.6 3.4 - - - +
95D CYS* 3.5 42.2 - - - -
97D GLU* 6.5 0.7 - - - -
98D HIS* 5.6 8.3 - - - -
99D LEU* 5.3 2.2 - - - -
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Residues in contact with LYS 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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65D LYS 3.3 25.4 - - - +
66D VAL* 3.0 12.9 + - + +
68D CYS* 1.3 87.8 + - - +
70D PHE* 1.3 68.7 + - + +
71D SER* 3.4 1.8 + - - -
94D ASP* 5.0 13.1 + - - +
95D CYS* 4.7 11.5 - - - -
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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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48D VAL* 3.6 10.2 - - - +
66D VAL* 3.4 34.8 - - + -
67D LEU* 2.9 8.9 + - - +
69D LYS* 1.3 84.6 - - + +
71D SER* 1.3 72.2 + - - +
72D LEU* 3.5 13.1 + - + +
302D GLU* 3.9 39.7 - - + -
305D ILE* 3.6 30.3 - - + -
306D ARG* 3.7 37.5 - - + -
309D LEU* 4.3 14.5 - - + +
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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