Contacts of the helix formed by residues 82 - 90 (chain A) in PDB entry 2BKG
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 THR 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A HIS* 3.8 2.9 - - - -
73A VAL 4.7 0.9 - - - -
74A ASN* 3.9 22.3 + - + +
75A ALA 3.3 4.9 - - - +
76A LEU* 3.7 23.6 - - + -
81A SER* 1.3 74.2 - - - +
83A PRO* 1.3 76.7 - - - +
84A LEU* 3.5 9.9 + - - +
85A HIS* 2.9 41.0 + - + +
86A LEU* 3.4 6.6 + - - +
105A ASP 5.1 0.5 + - - -
108A ALA* 3.9 24.2 - - + +
116A PRO* 5.1 0.2 - - - +
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Residues in contact with PRO 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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49A THR* 5.1 0.7 - - - +
51A LEU* 3.8 29.2 - - + +
52A HIS* 3.6 24.9 - - + +
55A ALA* 3.7 13.4 - - + +
72A ASP 4.6 2.0 - - - +
73A VAL 3.5 14.1 - - - +
75A ALA 3.4 13.7 - - - +
82A THR* 1.3 88.5 - - - +
84A LEU* 1.3 55.4 + - - +
86A LEU* 3.1 6.2 + - + +
87A ALA* 3.0 28.4 + - - +
99A LEU* 3.7 24.7 - - + -
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Residues in contact with LEU 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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73A VAL 5.1 0.8 + - - +
74A ASN* 5.9 0.2 - - - +
82A THR* 3.1 10.2 + - - +
83A PRO* 1.3 76.2 - - - +
85A HIS* 1.3 67.7 + - - +
88A ALA* 2.9 24.5 + - + +
96A VAL* 4.0 43.5 - - + +
99A LEU* 3.7 12.2 - - + +
100A LEU* 3.9 24.9 - - + -
104A ALA* 4.1 15.7 - - + +
105A ASP 3.7 22.2 - - - +
106A VAL* 4.0 4.9 - - - -
116A PRO* 3.8 19.5 - - + -
132A LEU* 4.1 8.1 - - + -
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Residues in contact with HIS 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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80A GLY 4.1 7.2 - - - -
81A SER* 3.8 12.7 - - - +
82A THR* 2.9 38.0 + - - +
84A LEU* 1.3 78.5 - - - +
86A LEU* 1.3 59.9 + - + +
88A ALA* 3.8 0.7 - - - +
89A LYS* 3.0 31.0 + - - +
108A ALA* 3.1 39.5 + - + -
110A ASP* 3.7 16.8 + - + -
114A SER 3.0 27.1 + - - -
115A THR 3.9 0.2 - - - -
116A PRO* 3.7 18.5 - - + +
119A LEU* 3.5 28.2 - - + +
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Residues in contact with LEU 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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48A ASP* 4.1 7.6 - - - +
52A HIS* 3.6 46.4 - - + +
55A ALA 4.4 1.3 - - - -
56A ARG* 4.0 39.5 - - + +
77A ASP* 4.6 2.0 - - - +
81A SER* 3.9 22.7 - - - +
82A THR 3.6 9.4 - - - +
83A PRO 3.1 6.1 + - - +
85A HIS* 1.3 83.2 - - + +
87A ALA* 1.3 56.5 + - - +
89A LYS* 3.5 9.7 + - + +
90A ARG* 3.0 37.6 + - - +
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Residues in contact with ALA 87 (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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55A ALA 3.5 13.6 + - - +
83A PRO 3.0 15.1 + - - +
84A LEU 4.0 2.5 - - - +
86A LEU* 1.3 76.6 - - - +
88A ALA* 1.3 61.6 + - - +
90A ARG 3.4 0.7 + - - -
91A GLY 3.2 3.3 + - - -
92A HIS* 2.9 30.7 + - - +
95A ILE* 3.6 33.9 - - + -
96A VAL* 3.8 15.3 - - + +
99A LEU* 4.1 4.0 - - + -
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Residues in contact with ALA 88 (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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84A LEU* 2.9 21.4 + - + +
85A HIS 3.8 3.6 - - - +
87A ALA* 1.3 74.1 - - - +
89A LYS* 1.3 65.4 + - - +
91A GLY* 3.3 9.7 + - - -
96A VAL* 3.7 11.3 - - + +
116A PRO* 3.9 29.8 - - + +
119A LEU* 4.9 0.2 - - + -
120A ALA* 3.8 12.2 - - + +
125A HIS* 3.8 10.0 + - - -
128A ILE* 4.1 19.2 - - + +
132A LEU* 4.6 1.6 - - + -
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Residues in contact with LYS 89 (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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85A HIS 3.0 18.6 + - - +
86A LEU* 3.8 11.9 - - + +
88A ALA* 1.3 75.4 - - - +
90A ARG* 1.3 84.8 + - + +
119A LEU* 4.0 42.7 - - + +
122A ASP* 5.9 1.0 + - - -
123A THR* 3.3 34.7 + - + +
125A HIS* 3.8 1.2 - - - -
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Residues in contact with ARG 90 (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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56A ARG* 3.3 37.4 - - + +
86A LEU* 3.0 20.7 + - - +
88A ALA 3.2 0.4 - - - -
89A LYS* 1.3 107.7 + - + +
91A GLY* 1.3 60.8 + - - +
92A HIS* 3.4 30.7 + - + +
125A HIS* 4.0 4.9 + - - -
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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