Contacts of the helix formed by residues 93 - 108 (chain B) in PDB entry 2B4J
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 93 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ILE* 4.8 0.2 - - - +
91B ALA* 2.9 26.3 + - + +
92B GLU* 1.3 79.8 - - - +
94B GLY* 1.3 63.2 + - - +
95B GLN* 3.7 8.4 + - - +
96B GLU* 3.3 26.0 + - - +
97B THR* 2.8 25.7 + - - -
120B ASN* 3.5 6.7 - - - +
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Residues in contact with GLY 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B THR* 1.3 73.3 - - - +
95B GLN* 1.3 57.1 + - - +
98B ALA* 2.7 33.1 + - - +
120B ASN* 3.5 22.2 - - - +
123B SER* 3.4 24.3 + - - -
125B THR* 4.0 7.0 - - - -
126B VAL* 3.5 3.4 - - - +
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Residues in contact with GLN 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A HIS* 6.0 2.9 - - + -
173A LYS* 5.2 10.3 - - - +
174A THR* 4.8 5.1 + - - -
93B THR* 3.2 8.5 + - - +
94B GLY* 1.3 76.3 - - - +
96B GLU* 1.3 67.5 + - + +
98B ALA* 4.6 3.9 - - - +
99B TYR* 3.1 30.6 + - - +
102B LEU* 6.4 0.2 - - - +
125B THR* 3.7 19.9 + - + +
366C ASP* 3.3 42.1 - - - +
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Residues in contact with GLU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A LYS* 4.4 14.9 + - - -
74B LEU* 4.4 2.5 - - - +
89B ILE* 4.1 18.5 - - + +
90B PRO* 3.5 37.3 - - + +
91B ALA* 3.5 29.4 - - + +
93B THR* 3.3 12.9 + - - +
95B GLN* 1.3 83.0 - - + +
97B THR* 1.3 62.1 + - - +
99B TYR* 3.5 14.8 + - - +
100B PHE* 3.2 23.4 + - - +
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Residues in contact with THR 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 4.8 1.8 - - + -
74B LEU* 3.9 18.8 - - + +
89B ILE* 4.8 4.2 - - - +
93B THR 2.8 22.0 + - - -
94B GLY 3.7 3.6 - - - -
96B GLU* 1.3 74.7 - - - +
98B ALA* 1.3 64.4 + - - +
100B PHE* 3.3 4.0 + - - +
101B LEU* 3.0 32.0 + - + +
120B ASN* 3.0 20.0 + - - +
121B PHE* 3.6 35.4 - - + -
126B VAL* 3.8 14.1 - - + -
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLY 2.7 20.5 + - - +
95B GLN* 3.8 7.9 - - - +
97B THR* 1.3 73.3 - - - +
99B TYR* 1.3 57.3 + - - +
101B LEU* 3.3 5.0 + - - +
102B LEU* 2.9 36.0 + - + +
125B THR* 3.4 33.4 - - - +
126B VAL* 3.8 6.4 - - - +
129B ALA* 4.0 13.4 - - + +
365C ILE 5.9 0.2 - - - +
366C ASP* 6.5 0.4 - - - -
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Residues in contact with TYR 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLU* 3.3 30.1 + - - +
88A VAL 4.5 2.6 + - - -
173A LYS* 3.7 67.2 - - + +
174A THR* 4.9 7.9 - - - -
177A GLN* 3.8 15.1 + - + -
95B GLN* 3.1 27.3 + - - +
96B GLU* 3.8 14.6 - - - +
97B THR 3.3 0.2 - - - -
98B ALA* 1.3 75.1 - - - +
100B PHE* 1.3 64.7 + - + +
102B LEU* 3.3 11.1 + - + +
103B LYS* 3.1 58.0 + - + +
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Residues in contact with PHE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LEU* 4.3 12.6 - - + -
74B LEU* 3.5 53.8 - - + -
76B ALA* 3.7 33.0 - - + -
85B GLU* 4.1 22.2 - - + -
86B ALA 4.3 3.1 - - - -
87B GLU* 4.0 34.5 - - + +
89B ILE* 5.3 3.6 - - + -
96B GLU 3.2 9.3 + - - +
97B THR 3.6 0.7 - - - +
99B TYR* 1.3 80.6 - - - +
101B LEU* 1.3 59.4 + - - +
103B LYS* 3.3 15.0 + - - +
104B LEU* 3.0 31.2 + - + +
107B ARG* 5.0 3.8 + - - -
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 3.9 25.4 - - + -
97B THR* 3.0 17.4 + - + +
98B ALA* 3.6 9.4 - - - +
100B PHE* 1.3 74.2 - - - +
102B LEU* 1.3 62.9 + - - +
104B LEU* 3.2 15.5 + - + +
105B ALA* 2.8 32.7 + - - +
113B VAL* 3.7 32.3 - - + -
121B PHE* 6.0 1.1 - - + -
126B VAL* 4.0 27.6 - - + +
129B ALA* 5.1 6.3 - - + -
130B CYS* 4.1 14.8 - - - -
135B ILE* 4.2 15.3 - - + -
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Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A THR* 3.7 36.8 - - + +
177A GLN* 4.2 21.9 - - + +
178A MET* 5.0 3.8 - - + +
181A PHE* 5.0 3.7 - - + +
98B ALA* 2.9 21.0 + - + +
99B TYR* 3.3 15.2 + - + +
101B LEU* 1.3 77.4 - - - +
103B LYS* 1.3 62.9 + - - +
105B ALA* 3.4 5.4 + - + +
106B GLY* 3.3 18.4 + - - -
129B ALA* 4.1 19.7 - - + +
132B TRP* 4.2 21.8 - - + -
133B ALA* 4.7 5.6 - - + -
365C ILE* 4.0 21.3 - - + -
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Residues in contact with LYS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ALA 5.5 0.2 - - - +
87A GLU* 2.9 33.2 + - + +
103A LYS* 4.6 2.2 - - - +
177A GLN* 3.5 41.1 - - + +
180A VAL* 6.0 1.0 - - - +
87B GLU* 3.9 23.1 + - - -
99B TYR* 3.1 38.3 + - + +
100B PHE* 3.5 14.6 - - + +
102B LEU* 1.3 77.9 - - - +
104B LEU* 1.3 61.7 + - - +
106B GLY* 3.3 10.3 + - - -
107B ARG* 3.5 36.8 + - - +
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B TRP* 3.8 33.2 - - + -
63B LEU* 4.4 12.3 - - + -
76B ALA* 4.0 23.6 - - + -
85B GLU* 3.7 29.8 - - + +
100B PHE* 3.0 22.8 + - + +
101B LEU* 3.6 17.0 - - + +
103B LYS* 1.3 77.5 - - - +
105B ALA* 1.3 60.4 + - - +
107B ARG* 3.2 11.9 + - - +
108B TRP* 3.1 32.1 + - + +
110B VAL* 3.9 15.6 - - + +
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Residues in contact with ALA 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A PHE* 3.5 9.4 - - + -
185A LYS* 2.9 29.3 + - - -
101B LEU 2.8 20.0 + - - +
102B LEU* 3.9 4.7 - - - +
103B LYS 3.3 0.2 - - - -
104B LEU* 1.3 73.9 - - - +
106B GLY* 1.3 57.2 + - - +
108B TRP 2.9 2.8 - - - +
110B VAL* 3.8 13.5 + - + +
133B ALA* 4.0 17.5 - - + +
135B ILE* 3.8 25.4 - - + -
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Residues in contact with GLY 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A TYR* 4.1 0.9 - - - -
177A GLN 5.5 0.7 - - - -
180A VAL* 4.9 6.1 - - - -
181A PHE* 3.7 28.5 - - - -
184A ASN* 3.1 33.9 + - - +
185A LYS* 4.1 5.6 + - - -
197A GLY* 5.9 0.2 - - - -
102B LEU 3.3 9.1 + - - -
103B LYS 3.3 7.6 + - - -
104B LEU 3.2 0.8 - - - -
105B ALA* 1.3 77.5 - - - +
107B ARG* 1.3 58.7 + - - +
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Residues in contact with ARG 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A TYR* 3.1 27.7 - - - +
85A GLU* 3.1 34.0 + - - +
107A ARG* 3.0 40.8 - - - +
108A TRP* 3.9 10.3 - - + +
185A LYS* 4.6 1.8 - - - -
197A GLY* 5.5 5.2 - - - +
201A VAL* 5.7 1.0 - - - +
85B GLU* 2.5 28.0 + - - -
100B PHE* 5.0 4.4 + - - -
103B LYS* 3.5 26.9 + - - +
104B LEU* 3.2 26.1 + - - +
106B GLY* 1.3 80.0 - - - +
108B TRP* 1.3 83.3 + - + +
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Residues in contact with TRP 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ARG* 3.9 11.4 - - + -
108A TRP* 3.6 34.8 - + - -
185A LYS* 3.0 6.4 + - - -
201A VAL* 4.2 14.4 - - + -
61B TRP* 3.5 29.4 - + + -
83B TYR* 3.5 28.6 + + - -
85B GLU* 2.8 25.9 + - - -
104B LEU* 3.1 15.4 + - + +
105B ALA 2.9 19.9 - - - +
107B ARG* 1.3 100.4 - - + +
109B PRO* 1.4 75.9 - - + +
110B VAL* 3.0 12.3 + - + +
200B ILE* 3.7 37.7 - - + -
201B VAL* 4.1 7.0 - - + -
204B ILE* 4.6 5.4 - - + -
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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
------------------------------------------------------------
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