Contacts of the helix formed by residues 116 - 121 (chain B) in PDB entry 2BEW
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 LYS 116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111B VAL* 2.7 38.6 + - - +
112B ASN* 3.5 32.5 - - - +
113B GLU 3.1 1.6 + - - -
115B ALA* 1.3 79.6 - - + +
117B TYR* 1.3 66.6 + - - +
118B ARG 3.4 2.0 - - - -
119B TYR* 3.4 12.3 + - + -
120B ARG* 3.0 36.2 + - + +
157B CYS* 4.1 10.7 - - - +
158B PRO* 5.0 7.2 + - - +
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Residues in contact with TYR 117 (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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110A PHE* 3.7 4.7 - - - -
158A VAL* 3.6 23.7 - - + +
159A THR* 5.8 2.5 - - - -
170A GLN* 2.8 27.0 + - - -
84B ILE* 3.5 16.6 - - + -
88B VAL* 3.5 26.5 - - + +
113B GLU* 3.0 27.5 + - - +
114B ALA 3.5 9.6 + - - +
115B ALA 3.5 2.0 - - - -
116B LYS* 1.3 79.5 - - - +
118B ARG* 1.3 58.7 + - - +
120B ARG* 3.2 34.3 + - - +
121B SER* 3.1 25.9 + - - -
125B PHE* 3.5 17.0 - - + +
126B ASN* 4.0 18.4 - - - -
127B CYS* 3.9 15.0 - - - +
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Residues in contact with ARG 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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366A ASP* 3.5 23.5 - - + +
367A VAL 5.0 3.1 - - - +
368A TYR* 4.1 0.6 - - - +
369A GLN* 3.6 54.1 - - - +
114B ALA 5.0 0.6 + - - -
115B ALA 5.1 1.0 + - - +
116B LYS 3.4 0.4 - - - -
117B TYR* 1.3 76.8 - - - +
119B TYR* 1.3 69.6 + - - +
121B SER* 3.3 3.3 + - - -
123B ASP* 2.7 75.2 + - - +
125B PHE 3.5 8.3 - - - -
126B ASN* 3.6 41.3 + - + +
128B GLY* 4.2 2.8 - - - -
182B LYS* 2.8 29.1 + - - +
183B ASN* 4.6 1.8 + - - +
184B PRO* 6.0 0.2 - - - +
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Residues in contact with TYR 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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144A ARG* 3.0 63.8 + - + +
363A LEU* 2.8 41.4 + - - +
365A SER 3.2 25.1 - - - -
366A ASP* 3.2 13.5 + - - +
367A VAL* 3.7 25.5 + - + +
115B ALA 5.3 0.9 + - - +
116B LYS* 3.4 17.3 + - + +
118B ARG* 1.3 80.8 - - - +
120B ARG* 1.3 69.5 + - + +
122B GLY 3.1 4.2 + - - -
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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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141A GLY* 4.5 8.9 - - - +
144A ARG* 4.8 3.1 - - - -
145A GLN* 3.4 53.2 + - + +
159A THR* 4.0 19.0 + - + +
161A SER* 3.2 22.2 + - - -
163A PRO* 5.3 0.4 - - - +
170A GLN* 4.7 0.6 + - - -
112B ASN 3.3 15.0 + - - -
113B GLU* 2.7 46.3 + - - +
116B LYS* 3.0 24.1 + - + +
117B TYR* 3.2 41.5 + - - +
119B TYR* 1.3 86.4 - - + +
121B SER* 1.4 60.4 + - - +
122B GLY 3.4 0.6 + - - -
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Residues in contact with SER 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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140A LEU 3.8 2.9 - - - +
141A GLY* 4.0 7.1 - - - -
159A THR* 3.4 30.5 - - - -
117B TYR* 3.1 10.8 + - - -
118B ARG 3.3 4.0 + - - -
119B TYR 3.1 0.4 - - - -
120B ARG* 1.4 79.2 - - - +
122B GLY* 1.3 59.8 + - - +
124B LEU* 3.1 25.9 + - - +
125B PHE* 2.9 41.9 + - - -
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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