Contacts of the helix formed by residues 321 - 335 (chain B) in PDB entry 5M7T
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 ASN 321 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B TRP* 3.6 11.3 - - - -
84B ARG* 5.3 2.5 - - - -
314B PRO* 3.4 19.2 - - + +
315B ASN* 2.8 62.2 + - - +
317B GLU 3.6 3.6 + - - -
318B PHE* 3.5 17.7 + - + +
319B GLU 3.2 2.6 - - - -
320B ALA* 1.3 78.0 - - - +
322B TYR* 1.3 65.0 + - - +
323B VAL 3.4 1.6 - - - -
324B ALA* 3.9 7.1 - - + +
325B ILE* 3.1 44.2 + - + +
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Residues in contact with TYR 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ARG* 3.6 29.7 - - - +
87B LYS* 4.4 4.9 + - - -
88B TRP* 3.5 29.2 - + - -
319B GLU 3.8 4.2 + - - +
320B ALA 3.3 2.6 - - - -
321B ASN* 1.3 76.9 - - - +
323B VAL* 1.3 58.4 + - + +
326B HIS* 2.9 40.0 + + + +
383B ALA 3.7 9.6 - - - -
386B GLU* 2.7 38.4 + - + +
387B TRP* 3.3 69.5 - + + +
390B GLU* 4.3 17.7 + - + +
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Residues in contact with VAL 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B LEU* 3.2 32.8 - - + +
294B GLY 3.4 14.6 - - - +
320B ALA 4.6 3.1 + - - +
321B ASN* 3.4 0.4 - - - +
322B TYR* 1.3 76.3 - - + +
324B ALA* 1.3 64.5 + - - +
327B THR* 2.8 44.3 + - + -
380B LEU* 3.9 12.1 - - + -
383B ALA* 4.2 16.6 - - + -
384B LEU* 3.5 31.4 - - + +
387B TRP* 4.4 13.4 - - + -
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Residues in contact with ALA 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B HIS* 3.4 52.6 + - + +
292B PHE 5.0 1.5 + - - +
296B TYR* 4.8 1.6 - - - +
312B THR* 5.0 5.6 + - - +
314B PRO* 4.5 8.7 - - + -
315B ASN* 5.0 1.6 - - - +
320B ALA 4.9 0.8 + - - -
321B ASN* 3.5 20.7 + - - +
322B TYR 3.4 0.6 - - - -
323B VAL* 1.3 78.9 - - - +
325B ILE* 1.3 61.8 + - + +
327B THR* 3.4 2.6 + - - -
328B LEU* 3.4 20.1 + - - +
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Residues in contact with ILE 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B VAL* 3.7 17.5 - - + -
73B TRP* 5.8 1.8 - - + -
81B LEU* 3.7 26.2 - - + -
84B ARG* 6.0 3.6 - - - +
85B LEU* 3.9 12.1 - - + -
88B TRP* 3.7 20.9 - - + -
90B LEU* 3.5 24.6 - - + +
312B THR* 4.7 6.5 - - + -
314B PRO* 5.0 4.9 - - + -
318B PHE* 6.1 1.6 - - + -
321B ASN* 3.1 35.3 + - + +
324B ALA* 1.3 76.7 - - + +
326B HIS* 1.3 65.9 + - - +
327B THR 3.3 0.2 - - - -
328B LEU* 3.3 8.0 + - + +
329B ALA* 3.0 22.2 + - - +
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Residues in contact with HIS 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B TRP* 3.6 44.5 + + + -
322B TYR* 2.9 27.6 + + + +
323B VAL 3.8 2.5 - - - +
325B ILE* 1.3 76.1 - - - +
327B THR* 1.3 57.7 + - - +
329B ALA* 3.3 5.6 + - - +
330B THR* 3.1 35.5 + - - -
333B LYS* 5.4 0.3 + - - -
379B ALA 4.5 2.2 + - - -
382B LEU* 4.0 18.2 - - + -
383B ALA* 3.4 37.7 - - + +
386B GLU* 3.1 27.8 + - - +
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Residues in contact with THR 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B PRO* 3.8 9.1 - - + +
296B TYR* 2.9 29.0 + - - +
323B VAL* 2.8 45.4 + - + +
324B ALA* 3.4 5.2 + - - -
326B HIS* 1.3 70.5 - - - +
328B LEU* 1.3 62.5 + - - +
330B THR* 3.3 8.9 + - - +
331B TRP* 2.9 28.2 + - - +
374B TYR* 3.7 10.6 + - - -
379B ALA* 3.8 31.4 - - + +
383B ALA* 4.1 3.8 - - + -
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Residues in contact with LEU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B CYS* 4.1 22.0 - - - -
63B GLY 3.6 25.8 - - - +
90B LEU* 4.6 9.2 - - + -
296B TYR* 3.9 38.9 - - + +
310B VAL* 4.1 9.2 - - + +
312B THR* 3.7 24.0 - - + +
324B ALA 3.4 12.1 + - - +
325B ILE* 3.3 9.3 + - + +
327B THR* 1.3 81.1 + - - +
329B ALA* 1.3 57.5 + - - +
331B TRP* 3.3 17.1 + - + +
332B TYR* 2.9 27.0 + - - +
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Residues in contact with ALA 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B TRP* 3.5 39.7 - - + +
90B LEU* 3.9 19.5 - - + +
325B ILE 3.0 13.8 + - - +
326B HIS 3.5 9.2 - - - +
328B LEU* 1.3 75.8 - - - +
330B THR* 1.3 57.5 + - - +
332B TYR* 3.3 1.8 + - - +
333B LYS* 2.9 41.1 + - - +
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Residues in contact with THR 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B HIS* 3.1 30.2 + - - -
327B THR* 3.3 10.4 + - - -
329B ALA* 1.3 74.3 - - - +
331B TRP* 1.3 63.1 + - - +
333B LYS* 3.6 13.7 + - - +
334B SER* 3.1 25.5 + - - -
374B TYR* 4.0 16.8 - - + -
379B ALA* 4.3 14.1 - - + +
382B LEU* 4.3 15.3 - - + +
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Residues in contact with TRP 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B PHE* 4.9 4.0 - + - -
62B CYS* 5.1 0.2 - - - -
296B TYR* 3.7 22.4 - + + -
299B ARG* 3.0 30.9 + - + -
300B SER 3.5 17.5 - - - -
301B THR* 3.7 15.2 - - + +
303B LEU* 4.6 3.4 - - + -
304B ILE* 3.4 37.9 - - + +
307B LEU* 4.9 6.3 - - + -
310B VAL* 3.9 29.4 - - + -
327B THR 2.9 14.4 + - - +
328B LEU* 3.4 26.2 - - + +
330B THR* 1.3 75.0 - - - +
332B TYR* 1.3 80.0 - - + +
334B SER* 2.8 21.3 + - - -
335B ASN 4.0 0.9 + - - -
372B VAL* 5.8 0.2 - - + -
374B TYR* 3.6 41.1 - + + -
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Residues in contact with TYR 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B PHE* 3.2 55.4 + + + +
62B CYS* 3.9 29.4 - - + -
89B GLU 4.1 20.9 - - - -
90B LEU* 4.3 4.9 - - + -
91B ASN* 4.1 10.3 + - - -
304B ILE* 4.1 11.1 - - + +
328B LEU 2.9 19.4 + - - +
329B ALA* 3.7 3.6 - - - +
331B TRP* 1.3 80.7 - - + +
333B LYS* 1.3 68.1 + - + +
334B SER 3.2 1.2 + - - -
335B ASN 3.5 9.9 + - - +
336B MET* 3.6 49.9 + - + +
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Residues in contact with LYS 333 (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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88B TRP* 3.0 34.3 + - - +
89B GLU* 3.5 32.5 - - + +
329B ALA* 2.9 35.2 + - - +
330B THR* 4.0 11.9 + - - +
332B TYR* 1.3 80.2 - - + +
334B SER* 1.3 60.3 + - - +
335B ASN 3.4 0.7 + - - -
336B MET* 4.4 20.5 + - + +
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Residues in contact with SER 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B THR* 3.3 20.3 - - - +
330B THR* 3.1 18.0 + - - -
331B TRP 2.8 17.5 + - - -
332B TYR 3.2 0.4 - - - -
333B LYS* 1.3 76.5 - - - +
335B ASN* 1.3 59.5 + - - +
336B MET 4.0 0.2 - - - -
373B LEU* 3.7 38.9 + - - +
374B TYR* 3.9 6.2 - - - +
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Residues in contact with ASN 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B THR* 3.2 46.9 + - + +
302B GLU* 4.5 5.9 + - - +
304B ILE* 3.6 17.4 - - + +
305B PRO* 4.3 12.1 - - - +
331B TRP 4.0 0.6 + - - -
332B TYR 3.5 4.7 + - - -
334B SER* 1.3 80.8 + - - +
336B MET* 1.3 62.5 + - - +
337B ASN* 3.4 2.1 + - - -
338B GLY* 3.7 20.9 + - - -
373B LEU* 5.3 9.9 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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