Contacts of the helix formed by residues 75 - 86 (chain A) in PDB entry 1WBB
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 ALA 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A PRO* 2.8 17.8 + - + +
74A HIS* 1.3 78.9 - - - +
76A VAL* 1.3 64.5 + - - +
77A GLU 3.4 2.0 - - - -
78A ASN* 3.4 22.6 + - + +
79A TYR* 3.2 27.7 + - + -
24F G 3.8 32.1 - - - +
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Residues in contact with VAL 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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30A PHE* 3.9 28.0 - - + -
37A TYR* 3.8 29.4 - - + +
71A ILE* 4.0 8.7 - - + -
72A PRO 3.7 1.4 + - - -
73A TYR 3.2 19.2 + - - +
74A HIS 3.3 1.9 - - - -
75A ALA* 1.3 77.5 - - - +
77A GLU* 1.3 82.2 + - + +
79A TYR* 2.9 15.2 + - - +
80A LEU* 2.9 24.3 + - + -
92A ILE* 5.0 3.4 - - + -
112A ARG* 5.6 3.6 - - - +
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Residues in contact with GLU 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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74A HIS 5.2 1.4 + - - +
75A ALA 3.4 1.0 + - - -
76A VAL* 1.3 89.1 - - + +
78A ASN* 1.3 64.0 + - - +
80A LEU* 3.3 29.9 + - - +
81A ALA* 3.2 21.5 + - - +
112A ARG* 3.6 14.6 + - - -
121A ASP* 3.8 26.0 - - - +
123A ALA* 5.3 3.8 - - - +
124A LEU* 4.5 12.8 - - - +
361A ARG* 4.3 21.7 + - - +
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Residues in contact with ASN 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 HIS 5.2 1.8 + - - -
75A ALA* 3.8 20.9 + - + +
76A VAL 3.2 1.0 - - - -
77A GLU* 1.3 80.5 - - - +
79A TYR* 1.3 67.2 + - + +
81A ALA* 3.4 8.7 + - - +
82A LYS* 3.3 25.6 + - - +
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Residues in contact with TYR 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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30A PHE* 4.7 4.3 - - + -
51A LEU* 3.8 32.6 + - + +
53A ILE* 3.9 24.2 - - + +
71A ILE* 3.4 43.1 - - + -
75A ALA* 3.2 29.6 - - + -
76A VAL 2.9 6.3 + - - +
78A ASN* 1.3 77.2 - - + +
80A LEU* 1.3 63.9 + - - +
81A ALA 3.1 1.6 - - - -
82A LYS* 3.3 28.5 + - - +
83A LEU* 3.2 29.4 + - - +
23F T 3.4 8.6 + - - -
24F G 2.6 29.8 + - - -
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Residues in contact with LEU 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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30A PHE* 4.2 8.3 - - + -
76A VAL* 2.9 25.4 + - + +
77A GLU* 3.3 37.2 - - - +
79A TYR* 1.3 74.6 - - - +
81A ALA* 1.3 56.5 + - - +
83A LEU* 3.4 5.0 + - - +
84A VAL* 3.0 31.9 + - - +
90A VAL* 4.0 18.1 - - + +
92A ILE* 4.0 20.0 - - + -
112A ARG* 4.1 14.6 - - - +
114A VAL* 3.9 30.6 - - + +
121A ASP* 5.9 1.1 - - - +
124A LEU* 4.4 13.9 - - + +
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Residues in contact with ALA 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 GLU 3.2 10.8 + - - +
78A ASN* 3.5 12.1 - - - +
79A TYR 3.1 0.6 - - - -
80A LEU* 1.3 78.2 - - - +
82A LYS* 1.3 64.8 + - - +
84A VAL* 3.5 1.5 + - - +
85A ASN* 2.7 38.9 + - - +
123A ALA* 5.2 5.2 - - + +
124A LEU* 3.7 20.4 - - + +
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Residues in contact with LYS 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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50A LEU 4.5 13.2 - - - +
51A LEU* 3.4 33.3 + - + +
52A ASP* 5.4 1.9 - - - +
78A ASN* 3.3 11.9 + - - +
79A TYR* 3.3 29.4 + - - +
81A ALA* 1.3 79.4 - - + +
83A LEU* 1.3 57.3 + - - +
85A ASN* 3.9 4.1 + - - +
86A GLN* 2.7 39.2 + - - +
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Residues in contact with LEU 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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28A LEU* 4.2 14.6 - - + -
30A PHE* 3.8 25.4 - - + -
47A ALA* 6.0 0.2 - - - -
50A LEU* 4.0 28.9 - - + -
51A LEU* 3.4 26.5 - - + -
79A TYR 3.2 17.6 + - - +
80A LEU* 3.7 6.5 - - - +
81A ALA 3.1 0.6 - - - -
82A LYS* 1.3 75.9 - - - +
84A VAL* 1.3 60.8 + - - +
86A GLN* 2.9 20.5 + - - +
87A GLY 3.2 0.2 + - - -
88A GLU* 3.1 29.7 + - + +
90A VAL* 3.4 31.4 - - + -
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Residues in contact with VAL 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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80A LEU 3.0 20.1 + - - +
81A ALA* 3.6 11.9 - - - +
83A LEU* 1.3 77.1 - - - +
85A ASN* 1.3 68.1 + - - +
87A GLY* 3.1 15.9 + - - -
88A GLU 3.9 10.1 - - - +
114A VAL* 4.6 7.4 - - + -
115A THR 4.3 1.8 - - - -
116A PRO* 3.7 35.1 - - + +
119A ILE* 3.8 22.4 - - + -
124A LEU* 4.3 24.0 - - + +
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Residues in contact with ASN 85 (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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81A ALA* 2.7 32.5 + - - +
82A LYS* 4.2 5.6 - - - +
83A LEU 3.2 0.6 - - - -
84A VAL* 1.3 88.7 - - - +
86A GLN* 1.3 59.4 + - + +
87A GLY 3.3 0.8 + - - -
124A LEU* 5.3 7.0 + - - +
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Residues in contact with GLN 86 (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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50A LEU* 3.3 52.3 + - - +
82A LYS* 2.7 31.3 + - - +
83A LEU* 2.9 9.1 + - - +
85A ASN* 1.3 77.2 - - + +
87A GLY* 1.3 61.1 + - - +
88A GLU* 3.4 13.4 + - + +
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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