Contacts of the strand formed by residues 197 - 205 (chain A) in PDB entry 2G1O
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
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Residue Dist Surf HB Arom Phob DC
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190A LEU* 3.5 7.2 - - - +
191A ILE* 3.0 32.2 + - + +
192A LYS 4.6 0.5 + - - -
195A VAL* 2.8 31.5 + - + +
196A TRP* 1.3 73.9 - - - +
198A ILE* 1.3 63.5 + - - +
217A LEU* 3.1 25.6 - - + +
218A ALA 3.3 22.9 - - - +
219A LEU* 3.6 4.0 - - + -
303A PRO 5.2 1.4 + - - -
304A THR* 2.8 35.1 + - - +
307A THR* 3.0 23.1 + - - +
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Residues in contact with ILE 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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188A ILE* 3.4 44.6 - - + +
189A ASN 3.8 15.7 - - - +
190A LEU* 4.1 6.3 - - + -
191A ILE* 3.7 12.0 - - - +
197A GLN* 1.3 78.8 - - - +
199A GLN* 1.3 64.4 + - - +
218A ALA* 2.8 47.1 + - + +
220A VAL* 4.3 11.0 - - + -
267A LEU* 4.0 19.5 - - + -
329A ILE* 3.7 24.5 - - + -
331A PHE* 4.1 9.6 - - + -
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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
----------------------------------------------------------
188A ILE* 4.4 6.7 - - + +
189A ASN 4.5 4.8 + - - +
191A ILE* 3.7 26.8 - - + +
198A ILE* 1.3 75.8 - - - +
200A MET* 1.3 62.6 + - - +
201A LYS* 3.0 29.3 + - + +
214A ASP 5.3 0.3 - - - +
215A GLY* 4.2 7.4 - - - -
216A CYS* 3.4 28.4 + - - +
217A LEU* 4.4 6.3 - - - +
267A LEU* 4.3 6.1 - - - +
268A GLY 4.3 2.9 + - - -
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Residues in contact with MET 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 ILE 3.5 0.6 + - - -
199A GLN* 1.3 73.4 - - - +
201A LYS* 1.3 62.3 + - - +
202A GLY 3.3 10.7 + - - +
203A VAL* 3.5 19.5 - - + -
212A CYS* 3.4 1.2 - - - -
215A GLY* 3.8 0.3 - - - -
216A CYS* 3.1 39.5 + - - +
217A LEU 4.2 1.3 - - - +
218A ALA* 3.7 15.3 - - + -
265A PHE* 3.8 26.9 - - + -
266A HIS 3.6 9.2 - - - +
267A LEU* 3.4 26.5 - - + -
308A TRP* 3.3 47.1 - - + -
310A LEU* 5.2 2.9 - - - -
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Residues in contact with LYS 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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188A ILE* 5.3 1.4 - - - +
199A GLN* 3.0 40.8 + - + +
200A MET* 1.3 71.2 - - - +
202A GLY* 1.3 54.5 + - - +
212A CYS* 3.3 11.0 - - - +
213A GLU* 4.8 1.9 - - - -
214A ASP 4.9 0.9 + - - -
215A GLY* 3.9 13.0 + - - -
266A HIS* 2.8 39.0 + - + +
267A LEU 3.7 2.7 - - - -
268A GLY* 3.0 36.2 - - - +
269A GLY* 3.5 7.0 - - - +
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Residues in contact with GLY 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 MET* 3.3 5.0 - - - +
201A LYS* 1.3 80.1 - - - +
203A VAL* 1.3 65.0 + - - +
209A THR* 4.7 8.1 - - - -
211A LEU 4.2 0.7 - - - -
212A CYS* 3.3 17.0 - - - -
264A SER 4.0 0.2 - - - +
265A PHE 3.6 0.2 - - - -
266A HIS* 2.7 40.2 + - - +
271A GLU* 5.4 0.2 - - - +
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Residues in contact with VAL 203 (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 MET* 3.5 32.8 - - + -
202A GLY* 1.3 77.9 - - - +
204A SER* 1.3 64.8 + - - +
205A VAL* 5.4 0.7 - - + -
209A THR* 3.3 10.1 - - - +
211A LEU* 3.1 44.6 + - + +
212A CYS* 3.6 13.0 - - + -
237A LEU* 5.1 1.3 - - + -
263A ILE* 4.4 11.7 - - + -
264A SER 3.3 11.4 - - - +
265A PHE* 3.9 18.8 - - + -
308A TRP* 3.8 20.6 - - + -
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Residues in contact with SER 204 (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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203A VAL* 1.3 77.0 - - - +
205A VAL* 1.3 64.4 + - - +
206A GLY 3.8 14.2 + - - -
208A SER 5.0 0.4 - - - -
209A THR* 3.8 28.0 - - - +
210A LEU 4.8 0.2 - - - +
262A ASP 3.8 0.3 - - - +
263A ILE* 3.2 7.4 - - - +
264A SER* 2.8 60.5 + - - +
271A GLU* 3.8 6.6 + - - -
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Residues in contact with VAL 205 (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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203A VAL* 5.4 0.9 - - + -
204A SER* 1.3 76.5 - - - +
206A GLY* 1.3 61.2 + - - +
207A SER 3.9 0.2 + - - -
208A SER* 3.5 21.5 + - - -
210A LEU* 3.9 18.5 - - + +
211A LEU* 4.4 14.1 - - + -
237A LEU* 3.9 28.0 - - + -
240A ALA* 4.3 15.5 - - + +
241A LEU* 3.9 28.9 - - + -
261A PRO* 4.1 10.6 - - + +
262A ASP 3.6 4.9 - - - +
263A ILE* 4.7 7.9 - - + -
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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