Contacts of the helix formed by residues 332 - 350 (chain B) in PDB entry 6T8O
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 SER 332 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B SER* 3.2 12.1 + - - +
331B TYR* 1.3 79.2 - - - +
333B PRO* 1.3 73.9 - - - +
334B GLU* 3.3 17.8 + - - +
335B SER* 2.8 34.2 + - - -
336B LEU* 3.1 21.9 + - - +
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Residues in contact with PRO 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B TYR 4.4 1.6 - - - +
332B SER* 1.3 87.2 - - - +
334B GLU* 1.3 56.2 + - - +
336B LEU* 3.9 8.0 - - + +
337B GLU* 2.9 30.2 + - - +
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Residues in contact with GLU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B SER* 3.3 20.6 + - - +
333B PRO* 1.3 76.5 - - + +
335B SER* 1.3 62.3 + - - +
337B GLU* 3.7 9.9 - - - +
338B ALA* 2.9 28.1 + - - +
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Residues in contact with SER 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B SER 4.5 7.7 + - - -
331B TYR* 5.0 1.6 - - - -
332B SER* 2.8 31.7 + - - -
334B GLU* 1.3 77.3 - - - +
336B LEU* 1.3 62.5 + - - +
338B ALA* 3.3 8.1 + - - +
339B MET* 2.9 26.9 + - - +
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Residues in contact with LEU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B TYR* 3.9 23.6 - - + +
332B SER 3.1 16.6 + - - +
333B PRO* 4.2 6.3 - - + +
335B SER* 1.3 75.7 - - - +
337B GLU* 1.3 61.2 + - - +
339B MET* 3.3 8.9 + - + +
340B SER* 2.9 33.4 + - - -
359B VAL* 4.0 22.7 - - + -
361B PRO* 3.9 29.2 - - + -
366B THR* 4.6 21.5 - - + +
368B PHE* 4.5 7.9 - - + -
415B ASN* 5.7 7.4 - - - +
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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
----------------------------------------------------------
333B PRO 2.9 21.0 + - - +
334B GLU* 3.7 9.4 - - - +
335B SER 3.3 0.2 - - - -
336B LEU* 1.3 75.0 - - - +
338B ALA* 1.3 64.1 + - - +
340B SER* 3.3 6.0 + - - +
341B ARG* 2.9 66.4 + - + +
359B VAL* 6.0 0.9 - - - -
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Residues in contact with ALA 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B GLU 2.9 18.0 + - - +
335B SER* 3.3 8.0 + - - +
337B GLU* 1.3 81.9 + - - +
339B MET* 1.3 55.9 + - - +
341B ARG* 3.5 5.5 + - - +
342B LEU* 2.9 30.1 + - - +
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Residues in contact with MET 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B SER 2.9 13.8 + - - +
336B LEU* 3.5 16.6 - - + +
338B ALA* 1.3 77.0 - - - +
340B SER* 1.3 57.2 + - - +
342B LEU* 3.3 23.6 + - + +
343B LEU* 2.9 27.3 + - - +
368B PHE* 3.6 26.5 - - + -
392B LEU* 5.1 17.5 - - - +
394B VAL* 5.4 9.9 - - + -
413B ILE* 5.2 10.8 - - + -
415B ASN* 5.9 2.2 - - - +
416B GLU* 4.9 15.9 - - + +
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Residues in contact with SER 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B LEU 2.9 19.1 + - - -
337B GLU* 3.8 7.4 - - - -
339B MET* 1.3 74.8 - - - +
341B ARG* 1.3 68.5 + - - +
343B LEU* 3.2 7.7 + - - +
344B GLU* 2.9 31.8 + - - +
356B VAL* 3.8 24.0 - - - +
359B VAL* 3.4 23.2 - - - +
368B PHE* 3.8 12.3 - - - -
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Residues in contact with ARG 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B GLU* 2.9 49.5 + - - +
338B ALA* 4.0 4.9 - - - +
340B SER* 1.3 83.9 - - - +
342B LEU* 1.3 59.9 + - - +
344B GLU* 3.3 33.9 + - - +
345B ILE* 3.0 37.8 + - + +
356B VAL* 4.9 6.7 + - - +
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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
----------------------------------------------------------
338B ALA 2.9 19.8 + - - +
339B MET* 3.4 20.4 - - + +
340B SER 3.3 0.2 - - - -
341B ARG* 1.3 76.6 - - - +
343B LEU* 1.3 56.6 + - - +
345B ILE* 3.4 6.9 + - + -
346B LYS* 2.9 58.8 + - + +
391B SER 5.3 1.1 - - - +
392B LEU* 3.8 28.5 - - + +
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Residues in contact with LEU 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B MET* 2.9 14.0 + - + +
340B SER* 3.2 9.2 + - - +
342B LEU* 1.3 73.8 - - - +
344B GLU* 1.3 60.6 + - - +
346B LYS* 3.9 1.6 - - - +
347B LEU* 3.0 53.4 + - + +
354B VAL* 4.5 2.2 - - + -
356B VAL* 4.0 8.5 - - + -
368B PHE* 3.6 27.6 - - + -
370B ILE* 3.8 25.1 - - + -
388B LEU* 5.0 3.8 - - + -
392B LEU* 4.2 19.9 - - + +
411B ILE* 4.2 15.5 - - + -
413B ILE* 3.8 17.7 - - + -
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Residues in contact with GLU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B SER 2.9 14.4 + - - +
341B ARG* 3.3 40.9 + - - +
343B LEU* 1.3 76.6 - - - +
345B ILE* 1.3 60.9 + - + +
347B LEU* 3.5 1.4 + - - +
348B LYS* 2.9 31.1 + - - +
354B VAL* 3.8 23.0 - - + +
355B SER* 3.4 10.0 - - - -
356B VAL* 2.8 40.6 + - + +
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Residues in contact with ILE 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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341B ARG* 3.0 24.1 + - + +
342B LEU* 3.9 8.3 - - + +
344B GLU* 1.3 80.5 - - + +
346B LYS* 1.3 62.0 + - + +
348B LYS* 3.1 10.1 + - + +
349B GLU* 2.9 46.0 + - + +
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Residues in contact with LYS 346 (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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371A GLN* 6.0 1.8 - - - +
342B LEU* 2.9 39.8 + - + +
343B LEU 4.2 2.0 - - - +
344B GLU 3.4 0.2 - - - -
345B ILE* 1.3 79.7 - - + +
347B LEU* 1.3 60.1 + - - +
349B GLU* 3.8 32.8 + - - +
350B PHE* 3.2 27.6 - - + -
388B LEU* 4.2 11.2 - - + -
391B SER* 3.6 40.1 + - - +
392B LEU* 3.9 15.0 - - + -
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Residues in contact with LEU 347 (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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343B LEU* 3.0 34.4 + - + +
346B LYS* 1.3 76.0 - - - +
348B LYS* 1.3 62.9 + - - +
349B GLU 3.2 0.2 - - - -
350B PHE* 3.4 10.9 + - + +
352B VAL* 2.9 41.7 - - + +
354B VAL* 3.7 38.1 - - + -
381B ILE* 4.9 11.4 - - + -
384B LEU* 4.3 20.6 - - + -
388B LEU* 3.8 35.0 - - + -
411B ILE* 4.5 8.1 - - + -
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Residues in contact with LYS 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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344B GLU 2.9 19.3 + - - +
345B ILE* 3.1 12.5 + - + +
347B LEU* 1.3 74.3 - - - +
349B GLU* 1.3 60.6 + - - +
350B PHE 2.9 13.0 - - - +
352B VAL 3.6 11.7 - - - +
353B GLU* 4.2 32.3 - - + +
354B VAL* 5.3 1.5 - - - +
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Residues in contact with GLU 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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374A ALA* 3.6 33.2 - - + +
375A GLY* 3.3 26.1 + - - +
345B ILE* 2.9 32.5 + - + +
346B LYS* 3.9 39.7 + - - +
347B LEU 3.2 0.6 - - - -
348B LYS* 1.3 77.8 - - - +
350B PHE* 1.3 63.1 + - + +
391B SER* 5.9 0.5 - - - -
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Residues in contact with PHE 350 (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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375A GLY* 3.7 27.6 - - - -
376A VAL 3.5 27.4 - - - -
377A LYS* 4.2 17.7 - - + -
346B LYS* 3.2 27.1 - - + -
347B LEU* 3.4 11.7 + - + +
348B LYS 2.9 17.8 - - - +
349B GLU* 1.3 80.7 - - + +
351B GLY* 1.3 66.3 + - - +
352B VAL* 3.3 3.2 + - + +
384B LEU* 3.6 34.1 - - + -
387B ASP* 4.1 24.5 - - + -
388B LEU* 5.1 3.4 - - - -
390B ARG* 5.0 4.9 - - - -
391B SER* 4.8 12.8 - - - -
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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
------------------------------------------------------------
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