Contacts of the strand formed by residues 213 - 219 (chain A) in PDB entry 4TMU
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 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A ARG* 3.1 40.2 + - + +
212A ASN* 1.3 87.9 - - - +
214A ARG* 1.3 66.0 + - - +
215A TYR* 3.6 32.8 + - + +
324A THR 3.6 23.6 - - - +
325A GLY* 4.1 3.6 - - - -
327A ALA* 3.6 24.7 - - + +
334A ALA* 3.5 8.5 - - + +
335A GLU 5.0 0.4 - - - -
336A ALA* 4.2 12.8 - - + +
382A ARG* 2.8 26.5 + - - -
399A ASN* 3.8 1.6 + - - -
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Residues in contact with ARG 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 ASN 3.7 0.8 + - - +
213A ILE* 1.3 71.8 - - - +
215A TYR* 1.3 59.2 + - - +
216A MET* 3.6 24.8 + - - +
334A ALA 2.8 16.2 + - - +
335A GLU* 3.5 24.9 + - + +
336A ALA 2.8 29.4 + - - +
399A ASN* 3.0 42.2 + - - +
404A LEU* 3.4 28.4 - - - +
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Residues in contact with TYR 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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208A PHE 5.1 0.2 + - - -
210A ARG* 4.1 16.6 + - + +
213A ILE* 3.6 27.3 - - + +
214A ARG* 1.3 70.7 - - - +
216A MET* 1.3 60.1 + - - +
320A TYR* 3.3 26.0 - + - +
321A TYR* 4.2 14.7 - - - -
324A THR* 3.8 21.1 + - - -
325A GLY* 5.8 0.3 + - - -
336A ALA* 3.9 8.7 - - + -
374A PHE* 4.9 0.9 - - + -
381A ARG* 4.2 19.2 - - + +
382A ARG* 3.6 44.0 - - + -
385A LEU* 3.7 29.4 - - + +
399A ASN 3.7 4.0 + - - -
400A CYS* 3.2 6.6 - - + +
401A ASP* 3.1 26.1 + - - +
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Residues in contact with MET 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 ARG* 3.7 28.3 - - + +
215A TYR* 1.3 76.3 - - - +
217A LEU* 1.3 62.4 + - - +
320A TYR* 4.7 4.5 + - - -
335A GLU* 3.3 26.5 - - - +
336A ALA* 2.9 18.6 + - - +
337A MET* 3.5 23.1 - - + -
338A LEU* 3.0 24.1 + - - +
374A PHE* 6.2 0.2 - - - -
381A ARG* 5.3 0.7 - - - -
400A CYS 4.0 0.9 - - - -
401A ASP* 3.5 39.7 - - + -
404A LEU* 4.4 7.9 - - + -
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Residues in contact with LEU 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 MET* 1.3 77.9 - - - +
218A MET* 1.3 75.3 + - - +
219A GLU* 4.2 4.0 - - + +
337A MET* 4.0 3.9 - - - +
338A LEU* 3.2 30.7 - - + +
340A TYR* 4.0 16.6 - - + -
374A PHE* 5.3 2.9 - - + -
375A ALA* 3.3 42.4 - - + +
381A ARG* 3.5 30.3 - - - +
401A ASP* 3.4 8.4 + - - +
514A ARG* 3.5 29.2 - - + +
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Residues in contact with MET 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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217A LEU* 1.3 79.2 - - - +
219A GLU* 1.3 66.3 + - - +
226A GLN* 3.9 26.9 - - - +
230A TYR* 4.6 14.1 - - + -
233A GLU* 6.1 0.4 - - - +
337A MET* 3.5 35.0 - - + -
338A LEU 2.7 10.5 + - - +
339A PHE* 3.3 22.7 - - + -
340A TYR 2.8 24.1 + - - -
514A ARG 3.8 16.6 - - - +
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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 LEU* 4.2 8.3 - - + +
218A MET* 1.3 71.0 - - - +
220A LYS* 1.3 60.8 + - - +
221A PHE* 3.2 33.9 + - + -
226A GLN* 2.9 23.0 + - - -
340A TYR* 3.6 12.3 - - + +
342A PRO* 4.8 2.3 - - + +
471A SER* 4.0 9.5 + - - -
474A ARG* 3.1 47.2 - - - +
513A PRO* 3.7 16.8 - - - +
514A ARG* 3.2 22.0 + - + +
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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