Contacts of the helix formed by residues 92 - 102 (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 HIS 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ALA 3.2 18.7 + - - +
56A ARG 2.9 24.8 + - - -
57A VAL 3.6 6.3 + - - -
58A GLY* 3.5 24.5 - - - -
87A ALA* 2.9 10.8 + - - +
90A ARG* 3.4 27.6 + - + +
91A GLY* 1.3 76.3 - - - +
93A LEU* 1.3 58.9 + - - +
94A GLU* 3.3 4.9 - - - -
95A ILE* 3.2 21.1 + - + +
96A VAL* 3.0 28.8 + - - +
128A ILE* 4.0 2.5 - - - -
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Residues in contact with LEU 93 (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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91A GLY 3.1 9.5 + - - +
92A HIS* 1.3 71.1 - - - +
94A GLU* 1.3 76.3 + - - +
96A VAL* 3.2 4.0 + - + +
97A GLU* 2.9 50.3 + - + +
127A GLU* 3.8 40.4 - - + +
128A ILE* 3.6 30.3 - - + +
131A VAL* 4.1 20.0 - - + -
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Residues in contact with GLU 94 (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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60A LEU* 3.8 28.3 - - + +
92A HIS* 3.3 1.9 - - - -
93A LEU* 1.3 97.3 + - - +
95A ILE* 1.3 61.5 + - + +
97A GLU* 3.4 17.8 + - - +
98A VAL* 3.1 23.0 + - - +
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Residues in contact with ILE 95 (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 ALA 4.0 7.4 - - - +
55A ALA* 3.9 12.8 - - + +
58A GLY* 3.4 42.2 - - - +
59A HIS 3.9 2.2 - - - +
60A LEU* 3.8 27.8 - - + +
63A VAL* 4.0 11.4 - - + -
87A ALA* 3.6 21.3 - - + -
92A HIS* 3.2 19.6 + - + +
94A GLU* 1.3 73.2 - - + +
96A VAL* 1.3 66.4 + - - +
98A VAL* 3.1 8.6 + - - +
99A LEU* 2.9 40.1 + - + +
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Residues in contact with VAL 96 (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* 4.0 18.4 - - + -
87A ALA* 3.8 6.1 - - + +
88A ALA* 3.7 33.4 - - - +
92A HIS 3.0 18.0 + - - +
93A LEU* 3.4 10.5 - - + +
95A ILE* 1.3 75.3 - - - +
97A GLU* 1.3 64.3 + - - +
99A LEU* 3.4 2.4 + - - +
100A LEU* 3.1 43.5 + - + +
128A ILE* 4.2 24.5 - - + -
131A VAL* 4.8 8.7 - - + -
132A LEU* 4.4 5.8 - - + -
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Residues in contact with GLU 97 (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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93A LEU* 2.9 40.1 + - + +
94A GLU* 3.5 26.0 - - - +
96A VAL* 1.3 77.1 - - - +
98A VAL* 1.3 57.1 + - - +
100A LEU* 3.5 7.8 + - - +
101A LYS* 3.0 27.0 + - - +
131A VAL* 4.2 22.9 - - + +
135A TYR* 4.9 3.8 + - - -
142B GLN* 5.9 0.9 + - - -
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Residues in contact with VAL 98 (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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60A LEU* 3.8 15.0 - - + -
63A VAL* 3.7 26.2 - - + -
64A GLU* 4.3 20.0 - - + +
67A LEU* 4.1 6.3 - - + -
68A LYS* 5.4 0.7 - - - +
94A GLU 3.1 15.6 + - - +
95A ILE* 3.1 9.8 + - - +
97A GLU* 1.3 73.8 - - - +
99A LEU* 1.3 70.5 + - - +
101A LYS* 3.1 13.2 + - + +
102A TYR* 3.0 43.9 + - + -
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Residues in contact with LEU 99 (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 LEU* 4.0 26.9 - - + -
55A ALA* 4.4 0.9 - - + -
63A VAL* 4.2 7.4 - - + -
67A LEU* 4.2 4.5 - - + -
73A VAL* 3.6 21.1 - - + +
83A PRO* 3.7 17.5 - - + +
84A LEU* 3.7 35.0 - - + +
87A ALA* 4.1 4.0 - - + -
95A ILE* 2.9 39.0 + - + +
96A VAL 3.8 2.5 - - - +
98A VAL* 1.3 79.5 - - + +
100A LEU* 1.3 60.0 + - - +
102A TYR 3.2 4.5 + - - -
103A GLY 3.2 5.5 + - - -
104A ALA* 2.9 35.1 + - + +
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Residues in contact with LEU 100 (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* 3.9 25.8 - - + -
96A VAL* 3.1 39.5 + - + +
97A GLU* 3.7 4.3 - - - +
99A LEU* 1.3 75.4 - - - +
101A LYS* 1.3 64.7 + - - +
103A GLY* 3.0 12.8 + - - -
104A ALA 3.9 17.3 - - - +
106A VAL* 4.1 9.4 - - + -
131A VAL* 3.9 21.8 - - + +
132A LEU* 4.2 10.3 - - + -
135A TYR* 3.8 48.4 - - + -
138B ASP* 5.5 0.3 - - - -
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Residues in contact with LYS 101 (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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68A LYS* 5.6 2.4 - - - +
97A GLU 3.0 15.3 + - - +
98A VAL* 3.1 16.3 + - + +
100A LEU* 1.3 76.0 - - - +
102A TYR* 1.3 83.5 + - + +
103A GLY* 3.3 2.9 + - - -
135A TYR* 4.6 1.9 - - - +
105B ASP* 5.1 9.0 + - - -
107B ASN* 4.1 46.1 + - + +
108B ALA* 5.9 0.4 - - - +
109B ASP* 5.9 2.2 - - - -
138B ASP* 4.2 22.6 - - + +
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Residues in contact with TYR 102 (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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67A LEU* 3.7 49.8 - - + -
68A LYS* 3.1 39.1 + - - +
73A VAL* 3.5 19.1 - - + +
98A VAL* 3.0 33.6 + - + +
99A LEU 3.4 6.3 - - - +
100A LEU 3.1 0.4 - - - -
101A LYS* 1.3 103.9 + - + +
103A GLY* 1.3 58.9 + - - +
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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