Contacts of the strand formed by residues 72 - 79 (chain A) in PDB entry 2B33
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 VAL 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A LEU* 5.3 0.2 - - + -
62A LEU* 3.7 39.7 - - + -
68A SER 4.0 0.7 - - - +
69A LEU 3.2 18.1 + - - +
70A LYS 4.2 5.2 - - - +
71A ASP* 1.3 77.0 - - - +
73A VAL* 1.3 62.2 + - - +
74A LYS 3.9 2.5 - - - +
75A VAL* 3.4 33.2 - - + -
96A PHE* 3.8 14.4 - - + -
99A HIS* 5.6 2.3 - - - +
101A PRO* 3.4 18.7 - - + +
121A ALA* 4.1 9.6 - - + -
122A ILE 3.7 12.1 - - - +
123A ALA* 3.8 2.7 - - + -
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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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71A ASP 3.3 13.9 + - - +
72A VAL* 1.3 73.5 - - - +
74A LYS* 1.3 70.6 + - + +
101A PRO* 3.7 7.7 - - - +
102A ALA* 2.9 27.0 + - - +
122A ILE* 3.0 22.8 + - + +
124A VAL* 4.0 35.2 - - + +
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Residues in contact with LYS 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 VAL 3.8 0.2 - - - -
73A VAL* 1.3 89.8 - - + +
75A VAL* 1.3 76.3 + - - +
76A THR* 2.8 30.0 + - - +
102A ALA* 3.4 24.9 - - + +
103A ARG 4.5 2.5 - - - +
104A SER* 3.9 22.2 + - - +
121A ALA* 3.3 5.0 - - - +
122A ILE* 2.8 45.9 + - + +
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Residues in contact with VAL 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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58A LEU* 5.4 0.4 - - + -
72A VAL* 3.4 30.7 - - + -
74A LYS* 1.3 88.6 + - - +
76A THR* 1.3 67.7 + - - +
77A VAL* 4.4 3.4 - - + -
92A TYR* 3.3 36.3 - - + +
96A PHE* 4.5 7.9 - - + -
101A PRO* 3.8 8.1 - - + -
102A ALA 2.9 8.2 + - - +
103A ARG* 3.3 5.3 - - + -
104A SER 3.2 12.8 + - - -
119A ILE* 3.4 29.6 - - + -
120A GLU 3.5 5.6 - - - +
121A ALA* 4.2 4.9 - - + +
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Residues in contact with THR 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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74A LYS* 2.8 25.1 + - - +
75A VAL* 1.3 72.5 - - - +
77A VAL* 1.3 66.3 + - - +
78A PHE* 3.5 32.7 + - + -
104A SER* 3.4 16.3 - - - +
106A VAL* 5.0 4.5 - - + -
118A GLU 3.9 0.9 - - - +
119A ILE* 3.5 3.5 - - - -
120A GLU* 3.1 53.3 + - - +
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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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75A VAL* 4.4 2.5 - - + -
76A THR* 1.3 74.9 - - - +
78A PHE* 1.3 64.9 + - - +
79A THR* 3.9 2.0 - - + -
88A VAL* 4.5 1.3 - - + -
92A TYR* 4.4 11.4 - - + -
103A ARG* 4.2 17.9 - - - -
104A SER 2.9 7.5 + - - +
105A PHE* 3.5 45.0 - - + -
106A VAL* 3.0 31.4 + - - +
117A ILE* 3.4 30.3 - - + -
118A GLU 3.7 3.1 - - - -
119A ILE* 4.1 19.1 - - + -
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Residues in contact with PHE 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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76A THR* 3.5 29.8 - - + -
77A VAL* 1.3 74.3 - - - +
79A THR* 1.3 66.9 + - - +
106A VAL* 3.4 22.9 - - + +
108A VAL* 3.9 18.2 - - + -
111A LEU* 3.8 22.4 - - + -
117A ILE* 3.5 1.4 - - - +
118A GLU* 2.7 58.0 + - + +
119A ILE 5.0 0.4 - - - -
120A GLU* 4.0 29.6 - - + -
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Residues in contact with THR 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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77A VAL* 3.9 0.7 - - + -
78A PHE* 1.3 79.9 - - - +
80A THR* 1.3 60.4 + - - +
81A SER 3.3 22.9 + - - +
82A MET* 4.6 0.2 - - - -
84A TYR* 4.5 6.7 - - + -
88A VAL* 4.9 2.9 - - + -
105A PHE* 3.7 28.1 - - + -
106A VAL 3.0 12.3 + - - -
107A ALA* 3.2 7.3 - - - +
108A VAL* 2.7 33.5 + - - +
111A LEU* 4.2 3.6 - - - -
116A GLU 3.2 13.0 - - - +
117A ILE* 3.4 22.7 - - + -
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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