Contacts of the strand formed by residues 210 - 224 (chain A) in PDB entry 3OTC
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 THR 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A LEU* 5.3 3.1 + - - +
55A THR* 3.8 16.6 + - + +
71A ALA 3.9 0.4 - - - +
72A TYR* 2.9 18.6 - - - -
73A GLY 3.2 23.1 + - - -
78A TYR* 3.5 22.6 + - - +
205A MET* 4.1 9.9 - - + +
209A GLY* 1.3 72.7 - - - -
211A VAL* 1.3 74.2 + - - +
212A LEU* 4.7 0.4 - - + -
247A PRO* 3.9 18.6 - - + -
249A HIS* 3.4 28.9 + - + +
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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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70A ILE* 3.9 29.6 - - + -
71A ALA 3.6 4.7 - - - +
72A TYR* 3.7 21.8 - - + -
209A GLY 4.9 0.9 - - - +
210A THR* 1.3 77.9 - - - +
212A LEU* 1.3 66.1 + - - +
213A ILE* 4.2 3.6 - - + -
246A VAL 3.5 1.2 - - - +
247A PRO* 3.4 6.2 - - - +
248A LEU* 2.9 47.9 + - + +
250A CYS* 4.4 10.3 - - - +
252A ILE* 3.8 22.4 - - + -
257A PHE* 4.1 17.3 - - + -
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Residues in contact with LEU 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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55A THR* 3.8 16.2 - - + -
58A ALA* 3.7 30.1 - - + -
59A GLN* 3.9 21.5 - - + +
62A MET* 3.8 26.8 - - - +
70A ILE* 3.4 4.9 - - - +
71A ALA* 2.9 35.0 + - + +
78A TYR* 3.9 18.4 - - + +
211A VAL* 1.3 76.6 - - - +
213A ILE* 1.3 66.0 + - - +
245A PRO* 4.2 3.8 - - + +
246A VAL 3.7 2.9 - - - -
247A PRO* 3.7 32.1 - - + -
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Residues in contact with ILE 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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62A MET* 4.9 0.9 - - - -
69A VAL 4.2 6.3 - - - +
70A ILE* 4.2 9.4 - - + -
211A VAL* 4.4 2.5 - - + +
212A LEU* 1.3 80.2 - - - +
214A TRP* 1.3 69.4 + - - +
215A GLN* 3.8 9.1 + - - +
245A PRO* 3.1 5.2 - - - +
246A VAL* 2.9 34.3 + - + +
248A LEU* 3.4 34.1 - - + -
257A PHE* 4.0 20.9 - - + -
261A HIS* 3.4 32.3 - - + +
263A GLU* 5.7 1.3 - - - +
264A ILE* 4.0 19.7 - - + -
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Residues in contact with TRP 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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62A MET* 3.4 50.1 - - + +
63A GLU* 4.4 7.0 - - + -
68A ILE* 2.6 29.2 + - + -
69A VAL* 3.8 17.4 + - + -
213A ILE* 1.3 82.5 - - - +
215A GLN* 1.3 62.6 + - - +
243A THR* 3.5 35.9 - - + -
244A LYS 3.5 18.8 - - - -
245A PRO* 3.3 26.9 - - + -
263A GLU* 5.3 5.0 - - - +
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Residues in contact with GLN 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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213A ILE* 4.4 13.5 - - - +
214A TRP* 1.3 77.5 - - - +
216A LYS* 1.3 71.8 + - - +
217A VAL* 3.3 7.3 + - + +
243A THR* 3.4 6.2 - - - -
244A LYS 2.9 31.5 + - - +
246A VAL* 3.5 40.1 - - + +
248A LEU* 4.8 7.3 - - - +
261A HIS* 5.1 6.1 - - - -
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Residues in contact with LYS 216 (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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215A GLN* 1.3 79.8 - - - +
217A VAL* 1.3 61.5 + - - +
218A ASP* 4.1 4.8 + - + +
241A THR* 4.3 16.4 - - - +
243A THR* 3.2 30.3 - - + +
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Residues in contact with VAL 217 (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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215A GLN* 3.3 17.0 + - + +
216A LYS* 1.3 77.9 - - - +
218A ASP* 1.3 68.4 + - - +
219A GLU* 6.3 0.7 - - + -
241A THR* 4.2 2.0 + - - -
242A ARG* 3.0 39.4 + - + +
244A LYS* 4.4 30.5 - - + -
246A VAL* 4.4 15.0 - - + -
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Residues in contact with ASP 218 (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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216A LYS 4.1 4.0 - - - +
217A VAL* 1.3 83.2 - - - +
219A GLU* 1.3 61.5 + - - +
220A VAL* 4.2 6.0 + - - +
239A THR* 4.5 23.0 - - - +
241A THR* 3.9 21.1 - - - +
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Residues in contact with GLU 219 (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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217A VAL* 4.2 0.6 + - + -
218A ASP* 1.3 74.7 - - - +
220A VAL* 1.3 66.8 + - - +
221A MET* 4.3 22.0 - - + +
238A VAL 3.7 1.6 - - - +
239A THR* 4.4 0.2 - - - -
240A ARG* 2.8 45.1 + - + +
242A ARG* 3.1 27.4 + - + +
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Residues in contact with VAL 220 (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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218A ASP* 4.3 7.4 + - - +
219A GLU* 1.3 82.0 - - - +
221A MET* 1.3 65.9 + - - +
237A ALA* 4.1 25.1 - - + -
238A VAL 3.7 9.4 - - - +
239A THR* 3.4 28.9 - - + -
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Residues in contact with MET 221 (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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219A GLU* 4.3 32.1 - - + +
220A VAL* 1.3 78.7 - - - +
222A THR* 1.3 65.6 + - - +
223A LYS* 5.0 9.6 - - + -
237A ALA* 4.9 1.1 - - - -
238A VAL* 2.8 46.3 + - + +
240A ARG* 4.5 26.9 - - + +
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Residues in contact with THR 222 (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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221A MET* 1.3 78.7 - - - +
223A LYS* 1.3 64.9 + - - +
235A LYS* 3.5 50.8 + - + -
236A MET 3.9 8.7 - - - +
237A ALA* 4.7 4.5 - - - +
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Residues in contact with LYS 223 (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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221A MET* 3.6 13.6 + - + -
222A THR* 1.3 77.1 - - - +
224A GLU* 1.3 66.6 + - - +
235A LYS* 3.7 6.5 - - - -
236A MET* 3.0 35.6 + - + +
238A VAL* 3.0 48.1 - - + +
240A ARG* 5.7 9.6 - - - +
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Residues in contact with GLU 224 (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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222A THR 4.4 0.4 + - - -
223A LYS* 1.3 81.1 - - - +
225A ILE* 1.3 72.8 + - - +
226A LYS* 4.2 13.9 + - + +
233A GLY 4.0 14.7 - - - +
234A LYS 4.2 2.5 - - - -
235A LYS* 3.5 29.2 + - - +
236A MET* 5.8 0.2 - - - +
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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