Contacts of the helix formed by residues 207 - 215 (chain A) in PDB entry 2JB3
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 ALA 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A TYR* 3.7 4.5 - - - -
206A PHE* 1.3 74.2 - - - +
208A MET* 1.3 67.8 + - - +
209A GLN* 4.7 3.1 - - + +
210A GLU* 2.9 28.7 + - + +
211A VAL* 3.0 19.2 + - - +
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Residues in contact with MET 208 (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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139A TYR* 3.4 48.5 + - + -
142A GLU* 5.2 7.0 - - - +
143A LEU* 3.7 29.4 - - + -
207A ALA* 1.3 74.3 - - - +
209A GLN* 1.3 67.6 + - + +
211A VAL* 3.1 2.8 + - - +
212A ILE* 3.0 31.0 + - + +
156B VAL* 3.4 36.8 - - + +
157B LEU* 3.8 13.2 - - + -
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Residues in contact with GLN 209 (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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207A ALA* 3.5 2.3 - - + +
208A MET* 1.3 83.2 - - + +
210A GLU* 1.3 58.5 + - - +
212A ILE* 3.4 6.2 + - - +
213A ARG* 2.9 43.7 + - + +
158B SER* 4.1 6.5 + - - -
161B ASP* 2.8 42.1 + - - +
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Residues in contact with GLU 210 (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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120A THR* 3.9 21.6 - - - +
121A SER* 3.0 24.8 + - - -
122A LEU* 4.5 7.4 - - + +
206A PHE* 3.5 20.8 - - + +
207A ALA* 2.9 51.0 + - + +
209A GLN* 1.3 75.5 - - - +
211A VAL* 1.3 59.4 + - - +
214A SER* 2.8 37.0 + - - -
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Residues in contact with VAL 211 (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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122A LEU* 4.6 2.2 - - + -
135A ASP* 3.9 20.9 - - + +
136A THR* 3.8 39.5 - - + +
139A TYR* 4.1 12.6 - - + -
206A PHE* 3.6 27.6 - - + -
207A ALA 3.0 17.0 + - - +
208A MET 3.6 7.0 - - - +
210A GLU* 1.3 76.0 - - - +
212A ILE* 1.3 65.8 + - + +
214A SER* 2.7 22.6 + - - -
215A GLY* 3.7 2.9 + - - -
216A ILE* 4.1 11.2 + - + +
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Residues in contact with ILE 212 (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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139A TYR* 5.5 3.6 - - + -
143A LEU* 4.1 13.2 - - + -
208A MET* 3.0 33.8 + - + +
209A GLN* 3.9 4.9 - - - +
211A VAL* 1.3 83.7 - - + +
213A ARG* 1.3 62.2 + - + +
214A SER 3.4 0.2 + - - -
215A GLY* 3.5 9.7 + - - -
157B LEU* 3.6 30.3 - - + -
161B ASP* 3.6 29.2 - - + +
164B ALA* 3.9 17.1 - - + +
165B LEU* 3.9 23.1 - - + +
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Residues in contact with ARG 213 (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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118A SER* 3.7 10.7 - - - -
119A ASP* 4.9 16.0 + - + +
120A THR* 3.5 19.9 - - + +
209A GLN* 2.9 38.7 + - + +
212A ILE* 1.3 75.8 - - + +
214A SER* 1.3 62.8 + - - +
215A GLY* 3.2 0.7 + - - -
158B SER* 3.8 3.0 + - - -
160B GLU* 3.4 36.8 + - - +
161B ASP* 2.8 48.6 + - - +
164B ALA* 4.3 9.5 - - - +
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Residues in contact with SER 214 (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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116A TYR* 4.4 6.1 - - - +
118A SER* 3.5 19.0 + - - -
120A THR* 3.7 13.2 - - - +
122A LEU* 3.7 20.3 - - - +
210A GLU 2.8 14.8 + - - -
211A VAL 2.7 20.6 + - - -
213A ARG* 1.3 77.8 - - - +
215A GLY* 1.3 61.6 + - - +
216A ILE* 3.3 25.0 + - - +
218A ARG* 3.2 14.4 + - - -
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Residues in contact with GLY 215 (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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116A TYR* 3.6 1.5 - - - -
211A VAL 3.7 0.8 + - - -
212A ILE 3.5 10.6 + - - -
213A ARG 3.2 4.0 + - - -
214A SER* 1.3 78.6 + - - +
216A ILE* 1.3 57.1 + - - +
217A GLY 3.1 7.4 - - - -
218A ARG* 2.9 49.3 + - - +
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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