Contacts of the strand formed by residues 334 - 340 (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 ALA 334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A ASN 2.9 10.3 + - - +
213A ILE* 4.3 5.6 - - + -
214A ARG* 2.8 28.4 + - - +
305A VAL 3.9 4.0 - - - +
306A ARG* 3.3 15.7 - - - +
327A ALA* 3.8 11.0 - - + -
328A GLY* 3.6 33.7 - - - +
332A LEU 3.2 0.6 + - - +
333A PRO* 1.3 75.3 - - - +
335A GLU* 1.3 61.6 + - - +
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Residues in contact with GLU 335 (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* 5.0 1.6 - - - -
214A ARG* 3.5 26.8 + - + +
216A MET* 3.3 24.5 - - + +
230A TYR* 2.8 38.9 + - + +
234A GLN* 4.3 7.8 + - - +
306A ARG 2.9 9.8 + - - +
307A PHE* 3.2 7.0 - - + +
308A VAL* 3.0 23.2 + - - +
327A ALA* 4.6 3.4 - - - +
334A ALA* 1.3 78.2 - - - +
336A ALA* 1.3 68.4 + - - +
337A MET* 4.7 2.9 - - + -
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Residues in contact with ALA 336 (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* 4.2 7.3 - - + +
214A ARG 2.8 11.4 + - - +
215A TYR* 4.1 15.0 - - + -
216A MET* 2.9 30.8 + - - +
308A VAL* 3.3 7.4 - - + +
320A TYR* 4.3 3.4 - - + +
324A THR* 3.6 39.0 - - + +
327A ALA* 6.0 0.2 - - + -
335A GLU* 1.3 73.3 - - - +
337A MET* 1.3 60.0 + - - +
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Residues in contact with MET 337 (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* 3.5 34.3 - - + -
217A LEU 4.0 1.3 - - - +
218A MET* 3.5 49.1 - - + -
230A TYR* 3.7 38.6 - - + +
308A VAL 2.9 10.9 + - - +
309A VAL* 3.3 11.9 - - + +
310A HIS* 2.9 25.8 + - - -
320A TYR* 6.1 0.6 - - - -
324A THR* 5.7 0.2 - - - +
335A GLU* 4.1 3.1 - - + +
336A ALA* 1.3 73.3 - - - +
338A LEU* 1.3 63.2 + - - +
339A PHE* 3.5 22.9 - - + -
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Residues in contact with LEU 338 (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 3.0 14.0 + - - +
217A LEU* 3.2 26.3 - - + +
218A MET 2.7 33.1 + - - +
310A HIS* 3.6 24.7 - - + +
313A ILE* 3.8 32.5 - - + -
314A PRO* 4.5 2.2 - - + -
320A TYR* 4.5 13.9 - - + +
337A MET* 1.3 74.2 - - - +
339A PHE* 1.3 68.4 + - - +
340A TYR* 3.6 1.9 + - + +
371A MET* 4.2 24.5 - - + -
374A PHE* 4.3 12.1 - - + -
375A ALA* 4.6 0.7 - - + -
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Residues in contact with PHE 339 (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 MET* 3.3 22.2 - - + -
220A LYS* 4.0 19.7 + - + +
223A PRO 4.7 0.7 - - - -
226A GLN* 3.7 33.4 - - + -
227A LEU* 3.7 24.0 - - + -
230A TYR* 4.0 16.8 - - + -
309A VAL* 3.5 34.8 - - + -
310A HIS 2.9 15.2 + - - +
311A PHE* 3.5 36.2 - + + +
313A ILE 4.5 4.2 + - - -
337A MET* 3.5 20.6 - - + -
338A LEU* 1.3 77.9 - - - +
340A TYR* 1.3 61.0 + - - +
341A ASP 3.8 2.1 + - - -
344A ASP* 4.8 0.2 - - - +
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Residues in contact with TYR 340 (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* 4.0 27.1 - - + -
218A MET 2.8 11.4 + - - +
219A GLU* 3.6 13.3 - - + +
220A LYS* 2.8 24.4 + - - -
313A ILE* 3.7 28.5 - - + -
338A LEU* 3.6 5.1 + - + -
339A PHE* 1.3 71.2 - - - +
341A ASP* 1.3 73.0 + - - +
342A PRO* 3.7 25.3 - - + +
345A MET* 3.9 17.6 - - + +
372A GLY* 4.5 2.1 + - - -
375A ALA* 3.7 29.4 - - + -
376A GLU* 2.4 40.3 + - - +
474A ARG* 4.4 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