Contacts of the helix formed by residues 67 - 77 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A LEU* 5.1 4.7 - - - +
64A LEU* 2.9 15.1 - - + +
66A MSE 1.3 79.4 + - - +
68A ALA* 1.3 60.7 + - - +
69A VAL* 3.3 14.6 + - - +
70A ALA* 2.9 32.4 + - + +
71A ARG* 3.0 29.4 - - - +
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Residues in contact with ALA 68 (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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66A MSE 3.7 3.4 + - - -
67A ASP* 1.3 74.4 + - - +
69A VAL* 1.3 60.1 + - + +
71A ARG* 3.3 31.0 + - - +
72A LEU* 3.0 26.7 + - - +
87A GLU* 4.6 6.5 - - - +
90A PRO* 3.9 25.2 - - + +
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Residues in contact with VAL 69 (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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8A LEU* 4.8 7.4 - - + -
42A LEU* 3.9 14.8 - - + -
67A ASP* 3.3 12.6 + - - +
68A ALA* 1.3 75.2 - - + +
70A ALA* 1.3 64.6 + - - +
72A LEU* 3.3 3.6 + - + +
73A VAL* 2.9 29.3 + - + +
90A PRO* 4.2 9.6 - - + -
91A ASP 3.9 22.2 - - - +
92A VAL* 4.2 20.2 - - + -
95A ALA* 3.9 33.7 - - + -
96A VAL* 6.4 0.2 - - + -
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Residues in contact with ALA 70 (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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42A LEU* 4.1 21.5 - - + +
61A LEU* 3.7 11.8 - - + +
64A LEU* 3.5 37.7 - - + +
67A ASP* 2.9 24.2 + - + +
69A VAL* 1.3 76.5 - - - +
71A ARG* 1.3 57.9 + - - +
73A VAL* 3.5 2.8 + - - +
74A ALA* 2.9 27.0 + - - +
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Residues in contact with ARG 71 (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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65A LYS* 2.7 54.5 + - + +
66A MSE 3.0 24.5 + - - +
67A ASP 3.0 8.6 - - - +
68A ALA* 3.4 28.9 - - - +
69A VAL 3.1 0.2 - - - -
70A ALA* 1.3 75.2 - - - +
72A LEU* 1.3 63.7 + - - +
74A ALA* 3.2 6.8 + - - +
75A ARG* 3.1 53.0 + - - +
87A GLU* 2.9 38.9 + - - +
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Residues in contact with LEU 72 (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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8A LEU* 4.4 15.9 - - + -
68A ALA 3.0 13.3 + - - +
69A VAL 3.5 9.2 - - - +
71A ARG* 1.3 75.5 - - - +
73A VAL* 1.3 57.0 + - - +
75A ARG* 3.4 10.0 + - - +
76A GLN* 2.9 65.0 + - + +
77A TRP* 4.2 4.4 - - + -
89A PRO* 4.4 13.7 - - + -
90A PRO* 3.7 24.5 - - + -
92A VAL* 4.0 27.1 - - + -
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Residues in contact with VAL 73 (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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8A LEU* 4.1 32.1 - - + -
12A PHE* 4.5 1.6 - - + -
42A LEU* 4.1 20.4 - - + -
45A ALA* 5.7 0.2 - - + -
46A MSE 4.5 10.8 - - + -
49A LEU* 4.1 16.4 - - + -
61A LEU* 3.9 21.3 - - + -
69A VAL* 2.9 22.1 + - + +
70A ALA 3.7 4.0 - - - +
71A ARG 3.3 0.2 - - - -
72A LEU* 1.3 74.4 - - - +
74A ALA* 1.3 64.7 + - - +
77A TRP* 3.0 31.6 + - + -
78A ALA* 3.1 6.4 + - - +
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Residues in contact with ALA 74 (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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61A LEU* 3.8 21.3 - - + +
70A ALA 2.9 14.8 + - - +
71A ARG* 3.2 11.9 + - - +
73A VAL* 1.3 76.2 - - - +
75A ARG* 1.3 59.9 + - + +
78A ALA* 3.0 13.7 - - - +
79A GLY 2.9 24.8 + - - -
80A VAL* 2.9 25.2 + - + +
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Residues in contact with ARG 75 (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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71A ARG* 3.1 42.9 + - - +
72A LEU* 3.9 7.8 - - - +
74A ALA* 1.3 79.3 - - + +
76A GLN* 1.3 69.0 + - + +
79A GLY* 3.5 18.0 + - - -
80A VAL* 3.2 22.5 + - + +
82A SER* 3.4 39.4 + - - +
83A THR* 6.3 0.2 - - - +
84A GLU* 5.2 8.5 - - - +
87A GLU* 3.0 42.0 + - - +
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Residues in contact with GLN 76 (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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72A LEU* 2.9 47.9 + - + +
75A ARG* 1.3 84.9 - - + +
77A TRP* 1.3 80.8 + - + +
79A GLY* 4.8 0.7 - - - -
89A PRO* 5.8 4.2 - - - +
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Residues in contact with TRP 77 (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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8A LEU* 3.7 30.3 - - + -
9A PRO* 4.2 32.2 - - + +
12A PHE* 3.3 52.0 - + + +
49A LEU* 4.0 16.4 - - + +
54A GLU* 5.0 5.0 - - - +
72A LEU* 4.5 9.4 - - + -
73A VAL* 3.0 22.0 + - + +
76A GLN* 1.3 104.0 - - + +
78A ALA* 1.3 61.9 + - - +
79A GLY 3.6 0.7 - - - -
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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