Contacts of the helix formed by residues 113 - 124 (chain B) in PDB entry 2EBJ
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 PRO 113 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B PHE* 1.3 92.6 - - + +
114B VAL* 1.3 65.2 + - - +
116B PRO* 3.5 24.5 - - + -
117B VAL* 3.0 28.3 + - + +
155B PRO* 5.8 0.9 - - + -
191B HIS* 3.7 35.2 - - + +
192B LEU* 4.3 9.0 - - + -
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Residues in contact with VAL 114 (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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75B LEU* 3.9 21.2 - - + +
76B GLU 4.2 18.4 - - - +
77B ARG* 4.5 16.4 - - + +
110B ALA* 4.8 5.8 - - + -
112B PHE* 2.8 34.2 + - + +
113B PRO* 1.3 71.2 - - - +
115B LYS* 1.3 73.1 + - + +
116B PRO* 3.9 0.2 - - - +
117B VAL* 3.9 1.7 - - - +
118B LEU* 3.0 45.7 + - + +
130B PRO* 4.2 14.6 - - + -
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Residues in contact with LYS 115 (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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84A ASP* 3.1 24.8 + - - -
96A GLU* 4.2 15.0 + - - +
97A ASP* 3.0 29.0 + - - +
77B ARG* 3.6 23.1 - - - +
114B VAL* 1.3 90.9 - - + +
116B PRO* 1.3 72.7 - - + +
118B LEU* 3.2 12.0 + - + +
119B ALA* 2.9 23.4 + - - +
130B PRO* 4.9 11.0 - - - -
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Residues in contact with PRO 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PRO* 3.4 30.5 - - + +
115B LYS* 1.3 96.3 - - + +
117B VAL* 1.3 56.7 + - - +
119B ALA* 3.3 7.2 + - + +
120B ARG* 2.9 28.2 + - - +
191B HIS* 3.9 14.7 + - + +
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Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 3.7 15.0 - - + -
112B PHE* 3.6 17.5 - - + -
113B PRO* 3.0 23.4 + - + +
114B VAL 3.9 2.5 - - - +
116B PRO* 1.3 71.8 - - - +
118B LEU* 1.3 61.1 + - - +
120B ARG* 3.2 3.6 + - + +
121B TRP* 2.9 59.2 + - + +
187B LEU 5.0 1.1 - - - -
188B ALA* 3.9 14.6 - - + -
191B HIS* 3.5 37.2 - - + +
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Residues in contact with LEU 118 (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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75B LEU* 4.1 8.1 - - + -
114B VAL* 3.0 35.3 + - + +
115B LYS* 3.6 13.2 - - + +
117B VAL* 1.3 76.3 - - - +
119B ALA* 1.3 57.3 + - - +
121B TRP* 3.3 30.5 + - + +
122B ARG* 3.0 26.5 + - - +
126B ILE 5.1 0.3 - - - +
128B GLY* 3.9 4.9 - - - +
129B ARG* 3.7 27.8 - - - +
130B PRO* 3.7 30.7 - - + -
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Residues in contact with ALA 119 (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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115B LYS 2.9 13.2 + - - +
116B PRO* 3.5 11.4 - - + +
117B VAL 3.2 0.2 - - - -
118B LEU* 1.3 74.7 - - - +
120B ARG* 1.3 65.2 + - - +
122B ARG* 3.3 10.9 + - - +
123B GLU* 3.1 27.4 + - + +
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Residues in contact with ARG 120 (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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116B PRO 2.9 16.9 + - - +
117B VAL* 3.2 5.4 + - - +
119B ALA* 1.3 76.5 - - - +
121B TRP* 1.3 63.5 + - + +
123B GLU* 3.2 38.4 + - - +
124B ALA* 3.2 16.7 + - - +
183B ARG* 5.4 3.8 - - - +
187B LEU* 3.8 37.0 - - + +
190B GLU* 4.9 6.8 + - - +
191B HIS* 3.8 26.9 - - + +
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Residues in contact with TRP 121 (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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73B LEU* 3.7 35.4 - - + -
75B LEU* 3.8 15.0 - - + -
117B VAL* 2.9 34.7 + - + +
118B LEU* 3.5 35.2 - - + +
120B ARG* 1.3 77.9 - - + +
122B ARG* 1.3 61.3 + - - +
124B ALA* 2.9 12.9 + - - +
125B GLY 3.0 0.2 + - - -
126B ILE* 2.8 42.5 + - + +
127B PRO 4.4 2.9 - - - -
128B GLY* 4.4 8.1 - - - -
159B LEU* 3.5 35.4 - - + -
184B ALA* 2.9 37.9 + - + -
187B LEU* 3.9 23.4 - - + +
188B ALA* 4.5 0.2 - - + -
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Residues in contact with ARG 122 (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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118B LEU 3.0 14.3 + - - +
119B ALA* 3.5 13.5 - - - +
120B ARG 3.3 0.2 - - - -
121B TRP* 1.3 75.3 - - - +
123B GLU* 1.3 60.4 + - + +
125B GLY* 2.9 18.5 + - - -
126B ILE 3.7 9.1 + - - +
127B PRO* 5.9 0.4 - - - +
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Residues in contact with GLU 123 (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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119B ALA* 3.1 14.4 + - - +
120B ARG* 3.2 42.2 + - - +
122B ARG* 1.3 77.7 - - + +
124B ALA* 1.3 58.9 + - - +
125B GLY 3.2 1.1 + - - -
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Residues in contact with ALA 124 (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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120B ARG* 3.2 11.5 + - - +
121B TRP 2.9 9.0 + - - +
123B GLU* 1.3 76.5 - - - +
125B GLY* 1.3 61.6 + - - +
126B ILE* 3.9 4.4 - - + +
183B ARG* 2.9 48.2 + - - +
187B LEU* 3.8 24.2 - - + -
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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