Contacts of the strand formed by residues 210 - 220 (chain A) in PDB entry 1W57
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 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A PHE 3.6 16.5 + - - +
209A GLU* 1.3 77.4 - - - +
211A PHE* 1.3 67.1 + - - +
212A THR* 4.3 0.4 + - - -
301A ILE* 3.6 29.4 - - + -
362A ASN* 3.6 38.8 - - + +
363A LEU 3.4 6.1 - - - +
364A LYS* 4.3 5.8 - - + -
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Residues in contact with PHE 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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209A GLU* 4.1 24.7 - - + -
210A ILE* 1.3 79.9 - - - +
212A THR* 1.3 61.6 + - - +
260A ALA* 3.7 25.5 - - - +
298A PHE* 3.8 24.2 - + + -
362A ASN* 3.2 7.4 - - - -
363A LEU* 2.7 49.3 + - + +
364A LYS* 5.8 0.2 - - - -
365A TYR* 3.4 36.6 - + - -
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Residues in contact with THR 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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210A ILE* 4.3 0.8 + - - -
211A PHE* 1.3 76.1 - - - +
213A GLY* 1.3 64.0 + - - +
214A ASN* 5.3 4.5 - - + +
259A GLY 4.5 1.4 - - - +
260A ALA* 3.4 14.9 - - - +
360A SER* 5.1 3.8 + - - -
361A VAL 3.2 7.4 + - - -
362A ASN* 2.9 18.0 + - - -
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Residues in contact with GLY 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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212A THR* 1.3 80.3 + - - +
214A ASN* 1.3 62.1 + - - +
256A ALA* 3.7 22.7 - - - +
259A GLY 4.6 1.6 - - - -
260A ALA* 3.7 10.1 - - - +
360A SER* 3.4 6.9 + - - -
361A VAL 3.0 33.3 + - - +
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Residues in contact with ASN 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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212A THR* 5.9 4.0 - - - +
213A GLY* 1.3 74.8 - - - +
215A GLY* 1.3 59.4 + - - +
216A PHE* 5.3 0.5 + - - +
255A ASP* 4.0 4.5 - - - +
256A ALA* 3.3 14.1 + - - -
259A GLY* 5.2 3.7 - - - -
358A LEU* 5.3 8.3 - - + -
359A SER 3.3 8.5 - - - +
360A SER* 5.4 1.1 - - - +
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Residues in contact with GLY 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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214A ASN* 1.3 78.0 + - - +
216A PHE* 1.3 60.4 + - - +
252A SER* 2.9 37.4 + - - -
255A ASP* 4.0 5.8 - - - -
256A ALA* 3.7 4.7 - - - +
358A LEU* 3.4 7.9 - - - +
359A SER 2.9 25.4 + - - -
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Residues in contact with PHE 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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214A ASN* 5.3 1.2 + - - +
215A GLY* 1.3 73.7 - - - -
217A ASP* 1.3 66.7 + - - +
218A VAL* 3.6 23.3 - - + -
252A SER* 4.5 1.1 + - - -
255A ASP* 4.1 13.4 + - - +
308A MET* 4.2 11.9 - - + -
348A PHE* 6.0 0.4 - + - -
349A ILE* 5.7 0.4 - - + -
356A ALA* 3.6 27.1 - - + -
357A VAL 3.5 11.4 - - - -
358A LEU* 4.2 13.9 - - + -
1374A GPP 3.7 63.3 - - + -
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Residues in contact with ASP 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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216A PHE* 1.3 78.2 - - - +
218A VAL* 1.3 70.6 + - - +
219A HIS* 3.4 8.7 + - - -
248A VAL* 3.7 9.6 - - + +
251A HIS* 3.8 9.5 + - - +
252A SER* 4.2 22.0 - - - +
255A ASP* 5.0 5.0 - - - +
266A ILE* 5.4 4.4 - - - +
356A ALA* 3.2 5.2 - - - +
357A VAL 3.0 31.7 + - - -
1371A ZN 2.0 37.7 - - - -
1372A C5P 3.7 17.0 + - - -
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Residues in contact with VAL 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 PHE* 3.6 28.9 - - + -
217A ASP* 1.3 84.6 + - - +
219A HIS* 1.3 86.5 + - - +
248A VAL* 4.0 0.4 - - - -
348A PHE* 3.7 35.4 - - + -
354A GLY* 5.6 0.2 - - - -
355A MET 3.5 9.6 - - - +
356A ALA* 4.3 2.0 - - + -
1372A C5P 5.6 1.2 + - - -
1374A GPP 5.8 1.1 - - + -
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Residues in contact with HIS 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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218A VAL* 1.3 83.9 + - - +
220A GLU* 1.3 60.4 + - - +
240A LEU* 3.9 19.5 - - + +
241A LYS 4.7 2.8 + - - +
242A ALA* 4.0 17.0 - - + +
243A HIS* 3.3 23.4 + + - -
246A GLY 3.6 19.5 - - - -
248A VAL* 3.2 29.8 - - + -
251A HIS* 3.5 7.7 + - - -
354A GLY* 3.0 3.3 - - - -
355A MET 2.8 33.0 + - - +
1371A ZN 2.4 32.3 - - - -
1372A C5P 5.5 2.2 - - - -
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Residues in contact with GLU 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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219A HIS* 1.3 74.7 + - - +
221A PHE* 1.3 71.0 + - - +
240A LEU* 3.4 6.8 - - - +
241A LYS* 2.8 66.1 + - + +
353A GLU* 3.7 12.8 - - + +
354A GLY* 4.0 1.1 - - - -
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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