Contacts of the helix formed by residues 197 - 202 (chain A) in PDB entry 2EE4
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 GLN 197 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LYS* 3.6 16.7 + - - +
120A LEU* 3.4 26.5 - - + -
193A THR* 2.7 47.4 + - - +
196A GLN* 1.3 82.6 + - - +
198A CYS* 1.3 66.1 + - - +
199A GLN* 2.7 6.3 + - - -
200A PHE* 2.9 21.4 + - + +
201A PHE* 2.9 26.1 + - + -
206A GLU 5.2 2.5 - - - -
207A ILE* 3.9 11.7 - - + -
208A VAL* 2.8 46.7 + - - +
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Residues in contact with CYS 198 (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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142A ILE* 3.3 33.7 - - + -
143A THR* 3.5 24.7 - - - -
146A ASN* 3.8 12.8 - - + -
194A PHE 2.8 17.2 + - - +
195A ILE 2.8 19.1 + - - +
196A GLN 3.2 0.4 - - - -
197A GLN* 1.3 75.9 - - - +
199A GLN* 1.3 63.7 + - - +
201A PHE* 3.3 7.2 - - - +
202A PHE* 3.1 27.4 + - - +
203A TYR* 4.1 6.3 + - - -
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Residues in contact with GLN 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A THR* 5.5 4.0 + - - +
146A ASN* 3.2 31.4 + - - +
147A ARG* 5.9 3.0 - - - +
150A GLN* 4.8 7.0 - - - +
196A GLN 5.2 2.9 - - - +
197A GLN* 2.7 6.1 + - - -
198A CYS* 1.3 70.9 - - - +
200A PHE* 1.3 50.7 + - - +
201A PHE 2.6 12.5 + - - -
202A PHE 2.7 0.2 + - - -
203A TYR* 2.5 52.1 + - - +
204A ASN 2.5 24.7 + - - -
205A GLY* 3.2 22.9 - - - +
206A GLU 4.6 5.2 - - - +
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Residues in contact with PHE 200 (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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117A THR* 5.9 0.2 - - + -
120A LEU* 3.7 30.5 - - + -
121A HIS* 3.6 35.9 - + - -
124A LYS* 3.3 34.6 - - + +
197A GLN* 2.9 18.6 + - + +
199A GLN* 1.3 74.1 - - - +
201A PHE* 1.3 64.9 + + - +
204A ASN* 3.5 18.6 + - - -
205A GLY* 3.1 30.4 - - - +
206A GLU 4.5 8.5 + - - +
207A ILE* 4.1 22.9 - - + +
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Residues in contact with PHE 201 (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 LEU* 3.9 14.8 - - + -
123A LEU* 3.6 34.5 - - + -
124A LYS* 3.4 38.5 - - + +
127A VAL* 5.3 3.1 - - + -
193A THR 3.7 2.2 - - - -
194A PHE* 3.3 55.9 - + - -
197A GLN* 2.9 41.6 + - + -
198A CYS* 3.3 10.5 - - - +
199A GLN 2.6 5.5 + - - -
200A PHE* 1.3 79.1 - + - +
202A PHE* 1.3 79.1 + + + +
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Residues in contact with PHE 202 (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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127A VAL* 4.4 23.8 - - + -
135A TYR* 3.8 15.0 - - - -
138A PHE* 4.6 9.0 - + - -
139A ARG* 3.3 83.8 + - + +
142A ILE* 4.3 7.9 - - + -
143A THR* 4.6 2.7 - - - -
194A PHE* 5.4 1.3 - + - -
198A CYS* 3.1 35.5 + - - -
199A GLN 2.7 7.1 + - - -
201A PHE* 1.3 92.1 - + + +
203A TYR* 1.3 64.3 + + + +
204A ASN* 2.9 11.8 + - - +
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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