Contacts of the helix formed by residues 336 - 349 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334B GLN 4.2 2.9 - - - -
335B LEU* 1.3 79.7 - - - +
337B GLU* 1.3 66.4 + - - +
338B GLU* 3.5 15.0 - - - +
339B GLU* 2.8 26.1 + - + +
340B TYR* 3.1 14.6 + - - -
376B TYR* 2.8 27.1 + + - +
380B ASN* 4.8 7.4 - - + -
381B ARG* 3.0 44.0 + - - -
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Residues in contact with GLU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B MET* 3.4 25.4 - - + +
158B GLN* 5.1 13.8 + - + +
162B PHE* 5.9 2.6 - - - -
290B THR* 5.0 15.2 - - - +
336B HIS* 1.3 72.2 - - - +
338B GLU* 1.3 60.3 + - - +
340B TYR* 3.2 11.1 + - - +
341B VAL* 2.9 29.8 + - - +
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Residues in contact with GLU 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ILE* 3.7 26.9 - - + -
155B MET* 3.8 28.4 - - + +
336B HIS* 3.5 9.5 - - - +
337B GLU* 1.3 76.8 + - - +
339B GLU* 1.3 56.3 + - - +
341B VAL* 3.1 6.4 - - - +
342B LEU* 3.0 33.1 + - + +
376B TYR* 3.4 43.3 + - + -
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Residues in contact with GLU 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B LEU* 3.3 22.1 - - + +
336B HIS* 2.8 31.9 + - - +
338B GLU* 1.3 74.0 - - - +
340B TYR* 1.3 59.8 + - - +
342B LEU* 3.3 2.3 + - - +
343B MET* 3.0 33.9 + - - +
373B LEU* 4.1 21.1 - - + +
376B TYR* 3.6 28.4 - - + -
377B ILE* 3.5 20.5 - - - +
381B ARG* 2.9 34.7 + - - -
389B LEU* 4.0 1.9 - - - +
393B ILE* 4.7 2.5 - - + -
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Residues in contact with TYR 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B GLN* 5.0 4.5 - - - +
286B LEU* 3.8 18.1 - - + +
289B ASN* 2.6 33.3 + - - -
290B THR* 3.7 36.1 - - + -
330B LEU* 3.9 24.1 + - + +
331B LYS* 4.5 8.5 + - - +
334B GLN* 6.0 0.2 - - - -
335B LEU* 3.7 38.6 + - + +
336B HIS 3.1 24.4 + - - -
337B GLU* 3.6 12.8 - - - +
339B GLU* 1.3 75.9 - - - +
341B VAL* 1.3 56.9 + - - +
343B MET* 3.2 12.8 + - - +
344B GLN* 3.0 37.0 + - - +
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Residues in contact with VAL 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ILE* 4.9 2.2 - - + +
154B LEU* 3.4 48.4 - - + +
155B MET* 3.9 23.3 - - + -
158B GLN* 4.0 13.9 - - + +
257B PHE* 3.7 20.7 - - + -
337B GLU 2.9 10.4 + - - +
338B GLU* 3.1 15.3 - - - +
340B TYR* 1.3 76.9 - - - +
342B LEU* 1.3 62.6 + - + +
344B GLN* 3.3 10.7 + - - +
345B ALA* 3.0 26.9 + - - +
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Residues in contact with LEU 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B MET* 5.1 1.1 - - - -
151B ILE* 4.3 18.4 - - + -
154B LEU* 3.5 24.7 - - + -
338B GLU 3.0 24.0 + - - +
339B GLU* 3.8 4.3 - - - +
340B TYR 3.2 0.2 - - - -
341B VAL* 1.3 75.1 - - + +
343B MET* 1.3 59.6 + - - +
345B ALA* 3.2 2.6 + - - +
346B ILE* 2.9 36.5 + - - +
369B PHE* 4.0 24.0 - - + +
372B THR* 4.0 21.3 - - + +
373B LEU* 3.7 40.4 - - + +
376B TYR* 4.5 5.8 - - + -
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Residues in contact with MET 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU* 3.5 34.8 - - + +
326B PHE* 5.1 1.3 - - + -
330B LEU* 4.0 16.2 - - + -
335B LEU* 3.6 29.8 - - - -
339B GLU 3.0 16.0 + - - +
340B TYR* 3.3 13.0 - - - +
342B LEU* 1.3 76.6 - - - +
344B GLN* 1.4 61.6 + - - +
346B ILE* 3.3 3.5 + - - +
347B SER* 3.0 25.3 + - - -
373B LEU* 4.8 1.3 - - + -
393B ILE* 3.4 34.3 - - + +
396B MET* 4.9 6.5 - - + -
397B LEU* 3.7 28.7 - - + +
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Residues in contact with GLN 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B GLN* 2.8 43.6 + - - +
257B PHE* 3.4 26.8 - - + -
283B LEU* 3.4 26.4 - - + +
286B LEU* 3.9 24.7 - - + +
287B ARG* 3.5 27.7 + - - +
290B THR* 6.0 0.3 - - - +
340B TYR* 3.0 20.9 + - - +
341B VAL* 3.3 8.1 + - - +
343B MET* 1.4 77.0 - - - +
345B ALA* 1.3 51.7 + - - +
347B SER 3.4 0.3 + - - -
348B LEU* 2.8 35.2 + - - +
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Residues in contact with ALA 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B LEU* 3.9 15.5 - - + -
257B PHE* 4.8 4.9 - - + -
261B ILE* 5.5 0.4 - - + -
341B VAL 3.0 13.4 + - - +
342B LEU 3.2 7.8 + - - +
344B GLN* 1.3 72.9 - - - +
346B ILE* 1.4 59.2 + - - +
348B LEU* 3.2 6.0 + - - -
349B PHE* 2.9 40.2 + - + +
369B PHE* 3.8 37.2 - - + -
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Residues in contact with ILE 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B LEU 2.9 22.9 + - - +
343B MET 3.3 4.5 + - - +
345B ALA* 1.4 74.0 - - - +
347B SER* 1.3 62.0 + - - +
349B PHE 3.7 4.9 - - - -
350B SER* 3.5 0.5 + - - -
366B GLN* 2.9 50.8 + - + +
369B PHE* 3.9 21.1 - - + +
370B ALA* 3.9 20.9 - - + +
373B LEU* 3.8 28.3 - - + -
394B MET* 4.0 23.3 - - + -
397B LEU* 3.8 20.2 - - + -
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Residues in contact with SER 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ALA* 3.7 1.0 - - - +
282B GLU* 2.8 31.2 + - - +
283B LEU* 3.3 18.4 - - - +
286B LEU* 4.7 2.2 - - - -
343B MET 3.0 17.3 + - - -
344B GLN* 3.7 3.6 - - - -
346B ILE* 1.3 75.8 - - - +
348B LEU* 1.3 64.7 + - - +
350B SER* 2.9 21.9 + - - -
353B ARG* 3.0 16.8 + - - +
397B LEU* 4.5 13.4 - - - +
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Residues in contact with LEU 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B ILE* 5.9 0.4 - - + -
257B PHE* 4.6 8.1 - - + -
258B ALA* 3.8 26.0 - - + -
261B ILE* 4.3 10.1 - - + -
264B PHE* 4.0 25.8 - - + -
275B LEU* 3.5 35.9 - - + +
276B LEU* 4.3 16.8 - - + -
279B ALA* 4.0 11.7 - - + -
283B LEU* 4.0 10.0 - - + +
344B GLN 2.8 21.4 + - - +
345B ALA* 3.2 5.4 + - - +
347B SER* 1.3 74.3 + - - +
349B PHE* 1.3 80.0 + - + +
350B SER* 3.0 6.6 + - - -
353B ARG* 5.0 0.7 + - - -
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Residues in contact with PHE 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B ILE* 4.3 10.8 - - + -
263B TYR* 3.9 18.6 - - + -
264B PHE* 3.7 34.5 - + + -
267B LEU* 4.0 14.1 - - + -
275B LEU* 4.5 4.0 - - + -
345B ALA* 2.9 31.9 + - - +
346B ILE 3.7 4.7 - - - -
348B LEU* 1.3 86.9 - - + +
350B SER* 1.3 58.9 + - - +
351B PRO* 3.4 3.6 - - - +
362B VAL* 3.5 19.6 - - + +
365B LEU* 3.6 31.4 - - + -
366B GLN* 3.1 34.4 - - - +
369B PHE* 3.4 24.7 - + - -
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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