Contacts of the strand formed by residues 195 - 202 (chain A) in PDB entry 2G27
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 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A LEU* 3.5 8.3 - - - +
189A ILE* 3.2 31.3 + - + +
190A LYS* 5.0 6.6 + - - +
193A VAL* 2.7 31.4 + - + +
194A TRP* 1.3 74.3 - - - +
196A ILE* 1.3 63.5 + - - +
215A LEU* 3.9 18.3 - - + +
216A ALA 3.4 24.0 - - - +
217A LEU* 4.1 5.6 - - + +
301A PRO 5.7 0.2 + - - -
302A THR* 2.6 37.0 + - - +
305A THR* 3.1 21.0 - - - +
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Residues in contact with ILE 196 (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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186A ILE* 3.6 35.9 - - + +
187A ASN 4.0 3.8 - - - +
188A LEU* 4.0 16.6 - - + -
189A ILE* 3.5 10.0 - - - +
195A GLN* 1.3 78.2 - - - +
197A GLN* 1.3 58.9 + - - +
198A MET 3.2 1.6 + - - -
215A LEU 3.8 0.2 - - - -
216A ALA* 2.8 44.6 + - + +
218A VAL* 4.4 5.4 - - + -
265A LEU* 3.3 44.0 - - + -
308A LEU* 5.2 1.6 - - + -
327A ILE* 4.1 15.5 - - + -
329A PHE* 4.4 13.7 - - + -
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Residues in contact with GLN 197 (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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186A ILE* 4.6 5.6 - - + +
187A ASN 4.6 5.0 + - - +
189A ILE* 3.4 23.0 - - + +
196A ILE* 1.3 72.6 - - - +
198A MET* 1.3 66.8 + - - +
199A LYS* 3.3 36.2 + - - +
213A GLY* 3.5 16.0 + - - +
214A CYS 2.7 29.9 - - - +
215A LEU* 3.7 8.5 - - - +
265A LEU* 4.7 0.3 - - - +
266A GLY* 4.4 10.9 + - - -
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Residues in contact with MET 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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196A ILE 3.2 5.9 + - - -
197A GLN* 1.3 79.9 - - - +
199A LYS* 1.3 63.6 - - - +
200A GLY 3.7 11.9 - - - +
201A VAL* 3.3 28.3 - - + -
210A CYS* 4.0 0.2 - - - -
214A CYS* 2.7 40.9 + - - +
216A ALA* 3.9 14.4 - - + -
263A PHE* 3.6 39.3 - - + -
264A HIS 3.6 7.0 - - - +
265A LEU* 3.6 21.1 - - + -
306A TRP* 3.5 37.7 - - + -
308A LEU* 5.2 1.6 - - + -
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Residues in contact with LYS 199 (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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197A GLN* 3.3 40.3 + - - +
198A MET* 1.3 76.6 - - - +
200A GLY* 1.3 58.4 + - - +
210A CYS* 4.4 1.6 - - - -
212A ASP 3.5 25.4 - - - +
213A GLY* 4.1 4.9 - - - -
264A HIS* 2.8 52.6 + - + +
266A GLY* 5.1 7.5 - - - +
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Residues in contact with GLY 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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198A MET* 4.2 2.0 - - - +
199A LYS* 1.3 73.1 - - - +
201A VAL* 1.3 65.0 + - - -
202A SER* 4.1 0.9 + - - -
207A THR* 5.5 5.6 - - - -
209A LEU 3.5 5.2 - - - -
210A CYS* 2.9 35.6 + - - -
211A GLU* 4.3 3.1 - - - -
263A PHE* 4.1 0.3 - - - -
264A HIS* 3.1 27.7 + - - +
269A GLU* 4.7 0.5 - - - +
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Residues in contact with VAL 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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198A MET* 3.3 33.9 - - + -
200A GLY* 1.3 74.8 - - - -
202A SER* 1.3 65.9 + - - +
207A THR* 4.0 7.5 - - - +
209A LEU* 3.0 45.9 + - + +
210A CYS* 3.8 4.3 - - + -
235A LEU* 4.7 2.0 - - + -
261A ILE* 4.1 19.3 - - + -
262A SER 3.4 12.1 - - - +
263A PHE* 4.2 9.2 - - + +
306A TRP* 3.4 33.0 - - + -
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Residues in contact with SER 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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200A GLY 5.3 1.1 - - - -
201A VAL* 1.3 79.1 - - - +
203A VAL* 1.3 64.7 + - - +
204A GLY* 3.2 18.5 + - - -
207A THR* 3.2 34.5 + - - +
261A ILE* 3.3 8.0 - - - +
262A SER* 2.8 51.4 + - - -
269A GLU* 4.5 7.4 - - - -
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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
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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