Contacts of the helix formed by residues 67 - 78 (chain D) in PDB entry 4BSX
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 ASP 67 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D LEU* 5.2 4.2 - - - +
64D LEU* 2.9 15.3 - - + +
66D MSE 1.3 78.5 + - - +
68D ALA* 1.3 66.0 + - - +
69D VAL* 3.1 16.2 + - - +
70D ALA* 2.9 33.6 + - + +
71D ARG* 3.0 24.7 - - - +
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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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66D MSE 3.7 3.4 + - - -
67D ASP* 1.3 74.4 + - - +
69D VAL* 1.3 58.6 + - + +
71D ARG* 3.2 31.0 + - - +
72D LEU* 3.0 26.9 + - - +
87D GLU* 4.5 6.4 - - - +
90D PRO* 3.8 25.4 - - + +
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Residues in contact with VAL 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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8D LEU* 4.8 7.4 - - + -
42D LEU* 4.0 14.6 - - + -
67D ASP* 3.1 12.6 + - - +
68D ALA* 1.3 75.1 - - + +
70D ALA* 1.3 61.3 + - - +
72D LEU* 3.2 3.3 + - + +
73D VAL* 2.9 35.1 + - + +
90D PRO* 4.2 9.0 - - + -
91D ASP 3.8 22.2 - - - +
92D VAL* 4.2 20.9 - - + -
95D ALA* 3.9 31.9 - - + -
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Residues in contact with ALA 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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42D LEU* 4.1 16.5 - - + +
61D LEU* 3.8 10.8 - - + +
64D LEU* 3.4 44.9 - - + +
67D ASP* 2.9 23.1 + - + +
69D VAL* 1.3 75.8 - - - +
71D ARG* 1.3 57.7 + - - +
73D VAL* 3.5 2.5 + - - +
74D ALA* 2.9 27.7 + - - +
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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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65D LYS* 2.7 55.6 + - + +
66D MSE 3.1 24.2 + - - +
67D ASP 3.0 8.1 - - - +
68D ALA* 3.4 27.6 - - - +
69D VAL 3.1 0.2 - - - -
70D ALA* 1.3 75.4 - - - +
72D LEU* 1.3 63.7 + - - +
74D ALA* 3.2 8.1 + - - +
75D ARG* 3.0 52.1 + - - +
87D GLU* 2.8 39.3 + - - +
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Residues in contact with LEU 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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8D LEU* 4.4 15.7 - - + -
68D ALA 3.0 13.7 + - - +
69D VAL 3.5 7.9 - - - +
71D ARG* 1.3 75.5 - - - +
73D VAL* 1.3 56.6 + - - +
75D ARG* 3.3 10.1 + - + +
76D GLN* 2.8 66.2 + - + +
77D TRP* 4.3 4.9 - - + -
89D PRO* 4.3 13.9 - - + -
90D PRO* 3.6 25.1 - - + +
92D VAL* 4.0 27.4 - - + -
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Residues in contact with VAL 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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8D LEU* 4.1 32.3 - - + -
12D PHE* 4.5 1.1 - - + -
42D LEU* 4.1 16.4 - - + -
46D MSE 4.4 15.0 - - + +
49D LEU* 4.1 16.2 - - + -
61D LEU* 4.0 21.3 - - + -
69D VAL* 2.9 22.1 + - + +
70D ALA 3.8 3.8 - - - +
72D LEU* 1.3 73.9 - - - +
74D ALA* 1.3 64.9 + - - +
77D TRP* 3.0 32.9 + - + -
78D ALA 3.1 5.4 + - - -
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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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61D LEU* 3.8 21.1 - - + +
70D ALA 2.9 15.6 + - - +
71D ARG* 3.2 11.9 + - - +
73D VAL* 1.3 75.2 - - - +
75D ARG* 1.3 59.7 + - + +
78D ALA* 3.1 14.0 - - - +
79D GLY 2.9 25.5 + - - -
80D VAL* 3.0 24.3 + - + +
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Residues in contact with ARG 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* 3.0 42.3 + - - +
72D LEU* 3.8 7.6 - - + +
74D ALA* 1.3 79.2 - - + +
76D GLN* 1.3 69.4 + - + +
79D GLY* 3.5 18.5 + - - -
80D VAL* 3.2 23.0 + - + +
82D SER* 3.4 40.0 + - - +
83D THR* 6.2 0.6 - - - +
84D GLU* 5.2 8.9 - - - +
87D GLU* 3.0 42.0 + - - +
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Residues in contact with GLN 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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72D LEU* 2.8 48.8 + - + +
75D ARG* 1.3 82.4 - - + +
77D TRP* 1.3 81.1 + - + +
79D GLY* 4.8 0.9 - - - -
89D PRO* 5.7 4.8 - - - +
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Residues in contact with TRP 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 LEU* 3.8 29.6 - - + -
9D PRO* 4.1 32.4 - - + +
12D PHE* 3.3 51.7 - + + +
49D LEU* 3.9 16.9 - - + +
54D GLU* 5.0 4.7 - - - +
72D LEU* 4.6 9.2 - - + -
73D VAL* 3.0 22.9 + - + +
76D GLN* 1.3 103.6 - - + +
78D ALA* 1.3 61.0 + - - +
79D GLY 3.6 0.7 - - - -
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Residues in contact with ALA 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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49D LEU* 4.0 17.0 - - + -
54D GLU* 3.7 5.6 - - - +
58D ARG* 2.8 45.4 + - + -
61D LEU* 3.8 17.9 - - + -
73D VAL 3.1 3.6 + - - +
74D ALA* 3.1 22.4 - - - +
77D TRP* 1.3 76.4 - - - +
79D GLY* 1.3 59.0 + - - +
80D VAL* 3.3 1.5 + - + -
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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