Contacts of the helix formed by residues 336 - 349 (chain A) in PDB entry 5A86
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 HIS 336 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334A GLN 4.1 3.8 - - - -
335A LEU* 1.3 77.8 - - - +
337A GLU* 1.3 65.6 + - - +
338A GLU* 3.1 15.3 - - - +
339A GLU* 2.8 25.6 + - + +
340A TYR* 3.1 14.6 + - - -
376A TYR* 2.8 28.8 + + - +
380A ASN* 4.9 9.6 - - + -
381A ARG* 3.6 36.1 + - + -
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Residues in contact with GLU 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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155A MET* 3.5 25.0 - - + +
158A GLN* 5.2 13.3 + - + +
162A PHE* 6.1 2.1 - - - -
290A THR* 4.9 14.5 - - - +
336A HIS* 1.3 72.5 - - - +
338A GLU* 1.3 61.5 + - - +
340A TYR* 3.2 9.9 + - - +
341A VAL* 3.0 30.3 + - - +
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Residues in contact with GLU 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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151A ILE* 3.8 27.4 - - + -
155A MET* 3.8 27.0 - - + +
336A HIS* 3.6 9.4 - - - +
337A GLU* 1.3 78.8 + - - +
339A GLU* 1.3 57.2 + - - +
341A VAL* 3.2 6.6 - - - +
342A LEU* 3.0 33.6 + - + +
376A TYR* 3.5 42.4 + - + -
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Residues in contact with GLU 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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335A LEU* 3.3 22.2 - - + +
336A HIS* 2.8 31.9 + - + +
338A GLU* 1.3 72.6 - - - +
340A TYR* 1.4 61.1 + - - +
342A LEU* 3.3 2.3 + - - +
343A MET* 2.9 34.3 + - - +
373A LEU* 4.1 21.5 - - + +
376A TYR* 3.6 27.4 - - + -
377A ILE* 3.5 15.1 - - + +
381A ARG* 2.7 43.5 + - - -
389A LEU* 4.0 1.2 - - - +
393A ILE* 4.7 1.8 - - + -
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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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158A GLN* 5.0 4.0 - - - +
286A LEU* 3.8 18.8 - - + +
289A ASN* 2.5 36.4 + - - -
290A THR* 3.7 33.0 - - + -
330A LEU* 3.9 21.2 + - + +
331A LYS* 4.5 8.2 + - - +
334A GLN* 6.0 0.2 - - - -
335A LEU* 3.7 37.8 + - + +
336A HIS 3.1 25.0 + - - -
337A GLU* 3.2 13.0 + - - +
339A GLU* 1.4 77.0 - - - +
341A VAL* 1.3 56.8 + - - +
343A MET* 3.2 11.6 + - - +
344A GLN* 3.0 38.1 + - - +
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Residues in contact with VAL 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ILE* 4.9 2.2 - - + +
154A LEU* 3.4 50.0 - - + +
155A MET* 3.9 18.2 - - + -
158A GLN* 4.0 14.8 - - + +
257A PHE* 3.7 19.6 - - + -
337A GLU 3.0 14.7 + - - +
338A GLU* 3.2 15.9 - - - +
340A TYR* 1.3 77.3 - - - +
342A LEU* 1.3 62.5 + - + +
344A GLN* 3.3 10.5 + - - +
345A ALA* 3.0 26.2 + - - +
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Residues in contact with LEU 342 (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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150A MET* 5.1 0.7 - - - -
151A ILE* 4.3 18.6 - - + -
154A LEU* 3.5 24.7 - - + -
338A GLU 3.0 25.2 + - - +
339A GLU 3.8 3.8 - - - +
341A VAL* 1.3 76.2 - - + +
343A MET* 1.3 60.1 + - - +
345A ALA* 3.2 2.6 + - - +
346A ILE* 2.9 35.2 + - - +
369A PHE* 4.0 20.6 - - + +
372A THR* 3.9 26.0 - - + +
373A LEU* 3.8 40.6 - - + +
376A TYR* 4.6 6.3 - - + -
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Residues in contact with MET 343 (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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286A LEU* 3.5 33.0 - - + -
326A PHE* 5.1 1.6 - - + -
330A LEU* 4.0 17.3 - - + -
335A LEU* 3.6 30.3 - - - -
339A GLU 2.9 15.7 + - - +
340A TYR* 3.3 14.1 - - - +
342A LEU* 1.3 76.6 - - - +
344A GLN* 1.4 61.4 + - - +
346A ILE* 3.4 4.5 + - - +
347A SER* 3.0 24.8 + - - -
373A LEU* 4.9 1.5 - - + +
393A ILE* 3.4 31.4 - - + +
396A MET* 4.9 6.3 - - + -
397A LEU* 3.7 30.6 - - + +
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Residues in contact with GLN 344 (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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158A GLN* 2.8 43.8 + - - +
257A PHE* 3.4 26.2 - - + -
283A LEU* 3.4 28.1 - - + +
286A LEU* 3.9 22.7 - - + +
287A ARG* 3.5 27.1 + - - +
290A THR* 6.0 0.3 - - - +
340A TYR* 3.0 22.1 + - - +
341A VAL* 3.4 8.9 - - - +
342A LEU 3.3 0.2 - - - -
343A MET* 1.4 74.3 - - - +
345A ALA* 1.3 56.2 + - - +
347A SER 3.4 0.7 + - - -
348A LEU* 2.8 31.1 + - - +
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Residues in contact with ALA 345 (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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154A LEU* 3.9 15.5 - - + -
257A PHE* 4.8 4.6 - - + -
341A VAL 3.0 13.2 + - - +
342A LEU 3.2 8.3 + - - +
344A GLN* 1.3 73.0 - - - +
346A ILE* 1.3 59.1 + - - +
348A LEU* 3.2 5.6 + - - -
349A PHE* 2.8 40.0 + - + +
369A PHE* 3.8 36.6 - - + -
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Residues in contact with ILE 346 (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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342A LEU 2.9 22.7 + - - +
343A MET* 3.4 4.2 + - - +
345A ALA* 1.3 74.7 - - - +
347A SER* 1.3 62.9 + - - +
349A PHE 3.7 4.9 - - - -
350A SER* 3.6 0.7 + - - -
366A GLN* 2.9 49.5 + - + +
369A PHE* 3.9 19.5 - - + +
370A ALA* 3.9 21.8 - - + +
373A LEU* 3.7 28.5 - - + -
394A MET* 4.0 24.2 - - + -
397A LEU* 3.8 19.7 - - + -
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Residues in contact with SER 347 (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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279A ALA* 3.7 0.3 - - - +
282A GLU* 2.8 30.3 + - - +
283A LEU* 3.2 22.9 - - - +
286A LEU* 4.6 2.2 - - - -
343A MET 3.0 17.0 + - - -
344A GLN* 4.6 0.2 - - - -
346A ILE* 1.3 75.8 - - - +
348A LEU* 1.3 63.9 + - - +
350A SER* 2.9 21.5 + - - -
353A ARG* 2.9 17.6 + - - +
397A LEU* 4.4 14.8 - - - -
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Residues in contact with LEU 348 (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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254A ILE* 5.9 0.7 - - + -
257A PHE* 4.5 15.0 - - + -
258A ALA* 3.8 26.5 - - + -
261A ILE* 5.4 2.0 - - + -
264A PHE* 4.0 25.4 - - + -
275A LEU* 3.4 36.3 - - + +
276A LEU* 4.3 16.8 - - + -
279A ALA* 4.0 10.8 - - + -
283A LEU* 4.1 9.6 - - + +
344A GLN 2.8 21.7 + - - +
345A ALA* 3.6 4.9 - - - +
347A SER* 1.3 74.7 + - - +
349A PHE* 1.3 76.4 + - + +
350A SER* 3.1 6.8 + - - -
353A ARG* 5.0 0.5 + - - -
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Residues in contact with PHE 349 (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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154A LEU* 6.0 0.7 - - + -
261A ILE* 4.3 7.6 - - + -
263A TYR* 3.9 17.3 - - + -
264A PHE* 3.7 31.2 - + + -
267A LEU* 3.9 18.4 - - + -
275A LEU* 4.5 4.5 - - + -
345A ALA* 2.8 34.1 + - + +
346A ILE 3.7 4.5 - - - -
347A SER 3.4 0.2 - - - -
348A LEU* 1.3 88.0 - - + +
350A SER* 1.3 57.4 + - - +
351A PRO* 3.4 3.6 - - - +
362A VAL* 3.5 13.7 - - + +
365A LEU* 3.7 32.1 - - + -
366A GLN* 3.1 39.1 - - - +
369A PHE* 3.5 25.1 - + + -
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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