Contacts of the helix formed by residues 73 - 84 (chain A) in PDB entry 5BS8
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 SER 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A ALA 3.3 5.1 + - - -
72A LYS* 1.3 70.6 - - - +
74A ALA* 1.3 60.2 + - - +
76A SER* 3.1 10.1 + - - +
77A VAL* 3.0 25.1 + - - +
93A TYR* 3.4 17.6 - - - -
96A LEU* 4.4 7.1 - - - +
116A PHE* 5.6 0.4 - - - -
127A MET* 3.1 15.3 + - - +
130A THR* 2.7 38.5 + - - -
132A ALA* 4.2 19.7 - - - -
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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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72A LYS* 3.1 7.6 - - + +
73A SER* 1.3 82.6 + - - +
75A ARG* 1.3 57.9 + - + +
77A VAL* 3.4 1.8 + - - +
78A ALA* 2.8 31.5 + - - +
127A MET* 3.6 40.1 + - + +
128A ARG* 5.6 2.5 - - - +
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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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64A PHE* 3.8 33.8 - - + -
68A ARG* 5.8 3.4 - - - +
71A ALA* 4.5 9.7 - - - +
72A LYS* 2.9 32.7 + - + +
74A ALA* 1.3 78.3 - - + +
76A SER* 1.3 58.5 + - - +
78A ALA* 4.0 4.1 - - - +
79A GLU* 3.1 34.8 + - + +
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Residues in contact with SER 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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58A ALA* 4.5 0.3 - - - +
59A MET* 3.4 23.9 - - - +
64A PHE* 3.1 27.8 - - - -
72A LYS 3.7 3.2 + - - -
73A SER* 3.1 12.0 + - - -
75A ARG* 1.3 77.4 - - - +
77A VAL* 1.3 60.3 + - - +
79A GLU* 3.4 3.4 + - - +
80A THR* 2.7 34.8 + - - -
96A LEU* 3.7 23.7 - - - +
132A ALA* 4.5 3.8 + - - +
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Residues in contact with VAL 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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73A SER 3.0 13.9 + - - +
74A ALA 3.7 6.7 - - - +
76A SER* 1.3 75.4 - - - +
78A ALA* 1.3 58.8 + - - +
80A THR* 3.2 3.7 + - - -
81A MET* 2.8 39.0 + - + +
89A ASP* 3.6 37.5 - - + +
92A ILE* 4.0 16.7 - - + +
93A TYR* 4.0 28.9 - - + +
96A LEU* 4.9 6.7 - - + -
127A MET* 3.8 19.3 - - - -
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Residues in contact with ALA 78 (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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74A ALA 2.8 22.8 + - - +
75A ARG* 4.0 5.2 - - - +
77A VAL* 1.3 73.6 - - - +
79A GLU* 1.3 58.3 + - + +
81A MET* 3.7 14.6 - - + +
82A GLY* 2.8 28.6 + - - -
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Residues in contact with GLU 79 (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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58A ALA* 4.2 11.0 - - + +
61A ASP* 5.4 3.8 - - - +
62A SER* 3.4 27.7 + - - +
64A PHE* 5.4 1.6 - - + -
75A ARG* 3.1 21.7 + - + +
76A SER* 3.9 4.5 - - - +
78A ALA* 1.3 76.9 - - + +
80A THR* 1.3 62.8 + - - +
83A ASN* 3.2 53.2 + - - +
84A TYR* 3.9 7.3 + - - -
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Residues in contact with THR 80 (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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51A VAL 4.8 0.2 - - - +
54A ARG* 3.8 8.7 - - + +
55A VAL* 3.5 44.4 + - + +
58A ALA* 3.2 18.5 - - - +
76A SER 2.7 23.1 + - - -
77A VAL 3.5 4.0 - - - -
79A GLU* 1.3 76.9 - - - +
81A MET* 1.3 54.2 + - - +
84A TYR* 3.0 12.5 + - - -
85A HIS* 2.7 48.9 + - + -
92A ILE* 4.4 8.5 - - + -
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Residues in contact with MET 81 (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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77A VAL* 2.8 24.3 + - + +
78A ALA* 3.7 12.6 - - + +
80A THR* 1.3 77.9 - - - +
82A GLY* 1.3 61.0 + - - +
83A ASN 3.7 0.3 + - - -
85A HIS 3.2 21.5 - - - +
86A PRO* 4.5 1.9 - - - +
87A HIS 3.1 28.0 - - - +
88A GLY* 5.0 0.4 - - - -
89A ASP* 3.4 37.2 - - + +
92A ILE* 4.1 9.6 - - + +
156A TYR* 3.8 9.5 + - - -
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Residues in contact with GLY 82 (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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78A ALA 2.8 17.3 + - - -
79A GLU* 4.1 0.4 - - - -
81A MET* 1.3 77.9 - - - +
83A ASN* 1.3 61.8 + - - +
156A TYR* 2.9 18.8 + - - -
159A ARG* 3.8 13.2 + - - -
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Residues in contact with ASN 83 (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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79A GLU* 3.2 40.3 + - - +
82A GLY* 1.3 83.2 - - - +
84A TYR* 1.3 83.8 + - + +
155A ASN* 2.8 33.6 + - - +
156A TYR* 3.6 5.9 - - - -
159A ARG* 3.4 29.9 - - - +
160A VAL* 3.9 16.4 - - + +
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Residues in contact with TYR 84 (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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54A ARG* 3.4 46.9 + - + -
57A TYR* 3.5 26.2 - + - -
58A ALA* 3.9 30.7 - - + -
61A ASP* 3.8 15.9 + - - +
79A GLU* 3.9 12.1 + - - -
80A THR 3.0 4.9 + - - +
83A ASN* 1.3 103.7 + - + +
85A HIS* 1.3 61.2 + - - +
86A PRO* 3.3 11.6 - - - +
155A ASN* 4.7 2.7 - - + -
156A TYR* 3.6 12.4 + - - +
160A VAL* 4.0 15.5 - - + +
161A GLN 3.8 20.6 + - - -
162A GLU* 3.7 25.3 - - + +
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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