Contacts of the helix formed by residues 351 - 364 (chain B) in PDB entry 3H8E
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 GLU 351 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B VAL* 3.5 28.0 - - + +
267B LYS* 4.2 11.9 + - - -
269B ILE* 4.2 19.9 - - + +
322B ASN* 3.2 28.1 + - + +
348B THR 3.5 11.9 - - - +
349B ASP* 2.4 46.4 + - - +
350B ALA* 1.3 72.0 - - - +
352B GLY* 1.3 69.4 + - - +
353B ARG 3.2 2.0 - - - -
354B LEU* 3.0 21.9 + - + +
355B VAL* 3.2 12.7 + - - +
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Residues in contact with GLY 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LYS* 3.5 38.3 - - - +
269B ILE* 4.5 0.9 - - - -
350B ALA 3.7 0.2 - - - -
351B GLU* 1.3 82.8 - - - +
353B ARG* 1.3 61.9 + - - +
354B LEU 3.2 0.2 + - - -
355B VAL* 3.4 6.0 + - - +
356B LEU* 3.0 33.3 + - - +
377B LEU* 4.6 4.0 - - - +
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Residues in contact with ARG 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B ALA* 3.5 33.0 + - - +
352B GLY* 1.3 74.8 - - - +
354B LEU* 1.4 61.2 + - + +
356B LEU* 3.8 2.7 - - - -
357B CYS* 2.9 31.2 + - - +
377B LEU* 4.0 32.1 + - + +
378B THR* 4.0 9.5 - - - +
427B LEU* 5.2 0.8 - - - +
436B ASN* 2.9 31.4 + - - -
437B ILE* 4.3 8.1 - - - +
438B GLY 5.0 0.8 - - - +
443B GLY 5.0 1.4 + - - -
446B THR* 4.7 5.5 + - - -
447B ALA* 3.7 37.1 - - - +
450B PHE* 3.5 35.9 - - + +
451B LEU* 3.7 16.4 - - + +
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Residues in contact with LEU 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ALA* 3.5 28.2 - - + +
234B PHE 3.6 4.6 + - - -
237B VAL* 3.6 22.7 - - + -
343B VAL* 3.9 28.0 - - + -
345B ILE* 3.9 29.2 - - + -
347B ASN 5.2 0.2 - - - +
348B THR* 5.7 1.8 - - - +
350B ALA 3.4 19.7 - - - +
351B GLU* 3.0 9.5 + - + +
353B ARG* 1.4 76.9 - - - +
355B VAL* 1.3 66.4 + - - +
357B CYS* 3.4 18.0 + - - -
358B ASP 3.7 1.9 + - - -
436B ASN* 4.0 15.3 - - + +
450B PHE* 4.0 13.9 - - + -
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Residues in contact with VAL 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B PHE* 3.3 37.9 - - + +
237B VAL* 3.8 33.9 - - + -
267B LYS* 4.8 4.0 - - + -
269B ILE* 4.0 17.7 - - + -
318B ALA* 3.7 24.7 - - + +
320B ALA* 4.4 4.3 - - + -
351B GLU 3.2 5.5 + - - +
352B GLY* 3.5 12.3 - - - +
354B LEU* 1.3 78.2 - - - +
356B LEU* 1.3 67.9 + - + +
358B ASP* 3.6 1.2 + - - +
359B THR* 2.9 27.8 + - - -
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Residues in contact with LEU 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B VAL* 3.6 28.0 - - + +
266B GLY 4.3 1.3 - - - +
267B LYS* 4.0 25.6 - - + +
318B ALA* 4.8 3.1 - - + -
352B GLY 3.0 30.5 + - - +
355B VAL* 1.3 79.6 - - + +
357B CYS* 1.3 57.7 + - - +
359B THR* 3.1 4.4 + - - -
360B LEU* 2.8 33.3 + - + +
373B ASP* 4.3 13.7 - - + +
374B ILE 5.0 0.4 - - - +
375B ALA* 3.7 26.2 - - + -
377B LEU* 4.1 13.0 - - + -
451B LEU* 3.6 23.1 - - + -
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Residues in contact with CYS 357 (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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233B ALA* 3.8 17.7 - - - -
337B THR* 4.0 6.5 - - - -
353B ARG 2.9 18.6 + - - +
354B LEU* 3.4 17.9 - - - -
355B VAL 3.4 0.4 - - - -
356B LEU* 1.3 74.8 - - - +
358B ASP* 1.3 67.2 + - - +
360B LEU* 3.3 6.3 + - - +
361B THR* 3.1 23.2 + - - -
450B PHE* 3.9 9.2 - - + -
451B LEU* 4.4 6.3 - - + -
454B PHE* 3.5 55.7 - - + -
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Residues in contact with ASP 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B MET* 3.0 36.2 - - + +
233B ALA* 2.9 34.1 + - - -
234B PHE* 2.9 22.1 + - + -
337B THR* 3.3 9.0 - - - -
338B MET* 2.7 28.8 + - - +
339B SER 4.6 0.2 + - - -
354B LEU 3.7 0.6 + - - +
355B VAL 3.6 1.7 + - - +
356B LEU 3.3 0.4 - - - -
357B CYS* 1.3 79.6 - - - +
359B THR* 1.3 58.4 + - - +
361B THR* 3.2 7.5 + - - -
362B TYR* 3.0 25.5 + - - +
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Residues in contact with THR 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B MET* 4.8 2.3 - - - +
234B PHE* 4.6 4.5 - - - -
247B LEU* 4.0 20.8 - - + +
265B VAL* 3.7 20.0 - - + -
316B LEU* 3.6 32.5 - - + +
318B ALA* 3.4 16.4 - - + +
355B VAL 2.9 17.4 + - - -
356B LEU 3.1 4.4 + - - -
358B ASP* 1.3 75.9 - - - +
360B LEU* 1.3 59.9 + - - +
362B TYR* 3.2 6.9 + - + +
363B ALA* 3.0 27.4 + - - +
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Residues in contact with LEU 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B VAL* 4.3 11.7 - - + -
356B LEU* 2.8 19.4 + - + +
357B CYS 3.5 7.2 - - - +
359B THR* 1.3 73.0 - - - +
361B THR* 1.3 65.9 + - - +
363B ALA* 3.2 11.8 + - - +
364B GLU* 3.6 3.5 + - - +
371B VAL* 3.8 21.3 - - + -
373B ASP* 4.1 10.8 - - + +
451B LEU* 3.8 45.3 - - + +
454B PHE* 3.9 14.3 - - + +
455B ALA* 4.8 1.6 - - + -
458B TYR* 2.7 34.3 + - + +
460B TRP* 3.9 21.8 - - + +
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Residues in contact with THR 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B MET* 3.9 28.1 - - + +
339B SER* 3.6 33.8 + - - +
357B CYS 3.1 14.9 + - - -
358B ASP* 3.2 8.9 + - - -
360B LEU* 1.3 76.2 - - - +
362B TYR* 1.3 64.8 + - - +
364B GLU* 3.1 39.5 + - - +
365B ARG* 4.6 1.0 + - - -
454B PHE* 4.0 10.8 + - - +
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Residues in contact with TYR 362 (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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219B GLU* 4.5 9.9 + - - -
221B LEU* 3.8 28.7 - - + +
225B LYS* 6.0 1.2 - - - -
229B LEU* 3.9 9.6 - - + -
231B MET* 3.6 31.0 - - + -
247B LEU* 4.1 8.3 - - + -
249B VAL* 4.0 23.2 - - + +
316B LEU* 4.1 11.4 - - + -
338B MET* 3.9 6.5 - - + -
358B ASP 3.0 6.6 + - - +
359B THR* 3.2 11.0 + - - +
361B THR* 1.3 76.0 - - - +
363B ALA* 1.3 61.8 + - - +
364B GLU 3.1 1.4 + - - -
365B ARG* 2.9 76.5 + - - +
366B PHE* 3.9 18.0 - + - -
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Residues in contact with ALA 363 (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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263B VAL* 4.1 15.2 - - + +
265B VAL* 4.9 0.7 - - + -
316B LEU* 3.7 16.8 - - + -
359B THR 3.0 12.6 + - - +
360B LEU* 3.5 12.8 - - - +
361B THR 3.1 1.0 - - - -
362B TYR* 1.3 74.5 - - - +
364B GLU* 1.3 64.5 + - - +
365B ARG 3.1 1.1 + - - -
366B PHE* 3.2 27.3 + - - +
368B PRO* 3.8 8.8 - - - +
371B VAL* 4.6 6.1 - - + -
458B TYR* 4.1 13.9 - - + +
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Residues in contact with GLU 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B SER* 6.1 0.3 - - - -
360B LEU 3.6 2.4 + - - +
361B THR* 3.1 29.8 + - - +
363B ALA* 1.3 77.7 - - - +
365B ARG* 1.3 62.6 + - - +
367B LYS* 3.1 25.3 + - - +
368B PRO* 4.0 1.0 - - - +
454B PHE 4.3 12.5 - - - +
456B LYS 5.7 0.2 + - - -
457B ALA* 3.7 25.4 + - + +
458B TYR* 3.8 23.8 - - + -
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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
------------------------------------------------------------
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