Contacts of the strand formed by residues 197 - 210 (chain A) in PDB entry 1O9T
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 ILE 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A TYR* 3.7 3.2 - - - -
190A VAL* 3.1 38.1 + - + +
191A GLN 5.0 0.7 - - - +
192A ASP* 3.5 40.6 - - + +
195A ALA 4.3 1.8 - - - +
196A VAL* 1.3 79.5 - - - +
198A PRO* 1.3 76.1 - - + +
199A VAL* 3.6 5.7 + - + +
235A LYS* 6.1 0.9 - - - +
313A ARG* 4.1 23.3 - - - +
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Residues in contact with PRO 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLU* 3.6 33.9 - - + +
153A LEU* 3.5 28.9 - - + -
187A VAL* 4.0 4.7 - - + -
188A GLN 4.0 1.3 - - - +
189A TYR* 3.6 24.0 - - + -
197A ILE* 1.3 94.7 - - + +
199A VAL* 1.3 60.3 + - - +
235A LYS* 4.2 7.4 + - - -
236A TYR* 3.9 26.6 - - + +
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Residues in contact with VAL 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A VAL* 4.3 0.2 - - - +
188A GLN* 2.8 23.9 + - + +
189A TYR 4.0 3.4 - - - +
190A VAL* 4.0 24.5 - - + -
197A ILE* 3.9 11.7 - - + +
198A PRO* 1.3 77.0 - - - +
200A ARG* 1.3 71.4 + - + +
235A LYS* 4.1 15.0 + - - +
236A TYR* 3.8 11.6 - - - -
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Residues in contact with ARG 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A VAL* 3.1 7.9 - - - +
188A GLN* 2.6 58.0 + - + +
198A PRO 4.0 0.2 - - - -
199A VAL* 1.3 89.9 - - + +
201A VAL* 1.3 59.1 + - - +
202A HIS* 3.6 36.1 + - - +
235A LYS 5.1 1.1 - - - +
236A TYR* 3.6 19.9 - - - +
238A ASP* 3.1 44.3 + - - +
240A ASP* 3.7 15.9 + - - +
241A THR* 3.3 18.8 + - - +
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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
----------------------------------------------------------
157A LEU* 4.0 15.9 - - + -
185A VAL* 4.4 6.5 - - + -
186A THR 3.9 5.8 - - - +
187A VAL* 4.0 9.0 - - + -
200A ARG* 1.3 72.9 + - - +
202A HIS* 1.3 62.3 + - - +
203A THR 4.0 9.0 - - - +
204A ILE* 3.4 37.2 - - + -
232A VAL* 3.9 17.9 - - + -
236A TYR* 3.0 33.0 + - + +
237A LEU* 4.6 2.0 - - + -
241A THR* 2.9 33.0 + - + +
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Residues in contact with HIS 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A MET* 3.7 21.3 - - + +
186A THR* 2.9 23.5 + - - +
188A GLN* 3.5 38.4 - - + -
200A ARG* 3.3 24.4 + - - +
201A VAL* 1.3 72.9 - - - +
203A THR* 1.3 69.4 + - + +
241A THR* 3.5 2.9 - - - -
242A ILE* 2.8 44.2 + - + +
329B LEU* 3.9 29.2 - - + +
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Residues in contact with THR 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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185A VAL* 3.9 0.2 - - - -
186A THR* 3.1 54.9 + - + +
201A VAL* 3.5 1.4 - - - +
202A HIS* 1.3 99.9 - - + +
204A ILE* 1.3 73.1 + - - +
205A VAL* 4.3 0.4 - - - +
242A ILE* 3.0 26.5 + - + +
244A HIS* 3.7 20.3 - - - -
136B GLN* 3.7 18.6 - - - +
329B LEU* 4.9 4.3 - - + -
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Residues in contact with ILE 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 3.8 27.6 - - + -
184A GLN 3.6 6.5 - - - +
185A VAL* 4.7 9.4 - - + -
201A VAL* 3.4 30.7 - - + -
203A THR* 1.3 73.9 + - - +
205A VAL* 1.3 65.1 + - - +
206A ILE* 4.1 6.7 + - + -
228A ILE* 3.6 41.5 - - + -
232A VAL* 4.4 12.8 - - + -
237A LEU* 4.6 4.3 - - + -
241A THR* 4.8 1.6 - - + -
242A ILE 2.7 11.0 + - - +
243A TYR* 3.5 12.8 - - + +
244A HIS 2.8 27.5 + - - +
245A LEU* 4.6 0.7 - - - +
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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
----------------------------------------------------------
182A LYS 4.1 0.7 - - - +
183A THR* 3.5 2.9 - - - +
184A GLN* 2.8 51.6 + - + +
203A THR* 4.3 1.8 - - - +
204A ILE* 1.3 73.6 - - - +
206A ILE* 1.3 65.9 + - - +
207A SER* 4.8 0.7 - - - +
244A HIS* 3.3 31.4 - - + +
247A PRO* 4.1 13.5 - - + -
1398A PO4 3.4 30.1 - - - +
136B GLN* 3.3 32.8 - - + -
323B ILE* 4.9 2.0 - - + -
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Residues in contact with ILE 206 (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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161A LEU* 4.7 10.1 - - + -
165A MET* 3.3 42.6 - - + -
181A SER* 6.1 0.2 - - - -
182A LYS 3.5 7.9 - - - +
183A THR* 4.4 7.4 - - - +
204A ILE* 4.1 13.0 - - + -
205A VAL* 1.3 78.2 - - - +
207A SER* 1.3 67.8 + - - +
223A LEU* 3.7 17.9 - - + +
227A VAL* 4.1 13.5 - - + -
228A ILE* 4.2 4.0 - - + -
244A HIS 3.0 4.7 + - - +
245A LEU* 3.3 34.8 - - + -
246A GLN* 2.9 25.8 + - - +
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Residues in contact with SER 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A SER* 3.1 4.8 - - - -
182A LYS* 2.8 47.8 + - - +
206A ILE* 1.3 75.6 - - - +
208A VAL* 1.3 60.7 + - - +
246A GLN* 2.9 8.3 - - - -
247A PRO* 3.5 19.7 - - - +
248A SER* 5.6 0.3 + - - -
251A PHE* 4.5 15.0 - - - -
1397A MET* 5.7 6.5 - - - -
1398A PO4 3.6 18.6 + - - -
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Residues in contact with VAL 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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165A MET* 3.5 29.8 - - + -
176A TRP* 4.5 1.1 - - + -
177A LEU* 3.5 27.8 - - + -
178A ARG 3.6 14.1 - - - +
180A ASP 3.6 7.0 - - - +
181A SER* 3.9 9.6 - - - -
207A SER* 1.3 76.5 - - - +
209A GLN* 1.3 76.2 + - - +
210A HIS* 3.5 3.3 + - - -
219A MET* 4.3 4.7 - - + -
223A LEU* 4.5 5.6 - - + -
246A GLN* 2.7 45.3 + - - +
251A PHE* 3.8 9.6 - - - +
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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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93A TYR* 3.5 9.3 + - - -
98A LYS 2.8 23.2 - - - +
177A LEU* 4.0 1.0 - - - -
178A ARG* 3.1 43.6 + - + +
179A PRO 4.0 1.4 - - - -
180A ASP* 2.7 45.0 + - - +
208A VAL* 1.3 85.0 - - - +
210A HIS* 1.3 60.0 + - - +
251A PHE* 3.1 25.4 - - + +
252A VAL 3.2 26.4 - - - +
255A GLY* 3.1 19.5 + - - -
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Residues in contact with HIS 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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176A TRP* 3.2 15.9 - - + +
178A ARG* 3.1 25.6 + - - +
208A VAL 3.5 6.5 + - - -
209A GLN* 1.3 76.9 - - - +
211A ASN* 1.3 80.1 + - - +
214A ILE* 4.5 0.4 - - + -
216A LEU* 5.3 0.2 - - + -
219A MET* 3.2 42.7 - - + +
246A GLN* 3.6 4.0 + - - -
249A GLY 4.5 1.8 - - - -
250A ARG* 3.5 26.2 + - - -
251A PHE* 2.9 42.4 + - + -
252A VAL* 3.2 37.1 - - + +
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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